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A

a - Variable in class ambit2.db.simiparity.space.QMapSpace
 
A_ATTR_charge - Static variable in class ambit2.sln.SLNConst
 
A_ATTR_fcharge - Static variable in class ambit2.sln.SLNConst
 
A_ATTR_I - Static variable in class ambit2.sln.SLNConst
 
A_ATTR_s - Static variable in class ambit2.sln.SLNConst
 
A_ATTR_spin - Static variable in class ambit2.sln.SLNConst
 
A_ATTR_USER_DEFINED - Static variable in class ambit2.sln.SLNConst
 
A_spin_d - Static variable in class ambit2.sln.SLNConst
 
A_spin_s - Static variable in class ambit2.sln.SLNConst
 
A_spin_t - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_D - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_D_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_DE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_DM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_E - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_I - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_I_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_IE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_IM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_L - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_L_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_LE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_LM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_M - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_N - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_N_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_NE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_NM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_R - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_R_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_RE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_Rel - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_RM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_S - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_S_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_SE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_SM - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_U - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_U_ - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_UE - Static variable in class ambit2.sln.SLNConst
 
A_STEREO_UM - Static variable in class ambit2.sln.SLNConst
 
absolute(int) - Method in class ambit2.db.results.AmbitRows
 
ABSOLUTE_CIS - Static variable in class ambit2.smarts.SmartsConst
 
ABSOLUTE_TRANS - Static variable in class ambit2.smarts.SmartsConst
 
AbstractAmbitAction - Class in ambit2.ui
 
AbstractAmbitAction(String) - Constructor for class ambit2.ui.AbstractAmbitAction
 
AbstractAmbitAction(String, Icon) - Constructor for class ambit2.ui.AbstractAmbitAction
 
AbstractAmbitAction(String, String, String) - Constructor for class ambit2.ui.AbstractAmbitAction
 
AbstractAmbitAction(String, Icon, String) - Constructor for class ambit2.ui.AbstractAmbitAction
 
AbstractAnnotator<U,V> - Class in ambit2.base.ro
 
AbstractAnnotator(File) - Constructor for class ambit2.base.ro.AbstractAnnotator
 
AbstractAnnotator(File, String[]) - Constructor for class ambit2.base.ro.AbstractAnnotator
 
AbstractAnnotator(File, String[], boolean) - Constructor for class ambit2.base.ro.AbstractAnnotator
 
AbstractAnnotator._dictionaries - Enum in ambit2.base.ro
 
AbstractAtomCountDescriptor - Class in ambit2.descriptors.constitutional
 
AbstractAtomCountDescriptor(String[]) - Constructor for class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
AbstractAttributeSelection<T> - Class in ambit2.featureselection
 
AbstractAttributeSelection() - Constructor for class ambit2.featureselection.AbstractAttributeSelection
 
AbstractComponent - Class in ambit2.structure2name.components
 
AbstractComponent() - Constructor for class ambit2.structure2name.components.AbstractComponent
 
AbstractDataset - Class in ambit2.base.data
 
AbstractDataset() - Constructor for class ambit2.base.data.AbstractDataset
 
AbstractDataset._props - Enum in ambit2.base.data
 
AbstractDescriptorCalculationProcessor<ITEM,DESCRIPTOR extends org.openscience.cdk.qsar.IDescriptor> - Class in ambit2.descriptors.processors
 
AbstractDescriptorCalculationProcessor() - Constructor for class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
AbstractDescriptorCalculationProcessor(DESCRIPTOR) - Constructor for class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
AbstractDescriptorCalculator<INTERNAL> - Class in ambit2.db.processors
 
AbstractDescriptorCalculator() - Constructor for class ambit2.db.processors.AbstractDescriptorCalculator
 
AbstractDescriptorFactory<Result> - Class in ambit2.descriptors.processors
 
AbstractDescriptorFactory() - Constructor for class ambit2.descriptors.processors.AbstractDescriptorFactory
 
AbstractDescriptorResultType<T> - Class in ambit2.core.data
 
AbstractDescriptorResultType() - Constructor for class ambit2.core.data.AbstractDescriptorResultType
 
AbstractDescriptorResultType(T) - Constructor for class ambit2.core.data.AbstractDescriptorResultType
 
AbstractDescriptorShell - Class in ambit2.dragon
 
AbstractDescriptorShell() - Constructor for class ambit2.dragon.AbstractDescriptorShell
 
AbstractDescriptorSolver - Class in ambit2.rules.conditions
 
AbstractDescriptorSolver() - Constructor for class ambit2.rules.conditions.AbstractDescriptorSolver
 
AbstractFacet<T> - Class in ambit2.base.facet
 
AbstractFacet() - Constructor for class ambit2.base.facet.AbstractFacet
 
AbstractFacet(String) - Constructor for class ambit2.base.facet.AbstractFacet
 
AbstractFinder<REQUEST,RESULT> - Class in ambit2.base.processors.search
 
AbstractFinder(Template, REQUEST, AbstractFinder.MODE) - Constructor for class ambit2.base.processors.search.AbstractFinder
 
AbstractFinder.MODE - Enum in ambit2.base.processors.search
 
AbstractFinder.SITE - Enum in ambit2.base.processors.search
 
AbstractGroup - Class in ambit2.core.groups
 
AbstractGroup() - Constructor for class ambit2.core.groups.AbstractGroup
 
AbstractGroup(String) - Constructor for class ambit2.core.groups.AbstractGroup
 
AbstractGroup(String, int) - Constructor for class ambit2.core.groups.AbstractGroup
 
AbstractGroup.EmptyIterator<T> - Class in ambit2.core.groups
 
AbstractGroup.SelfIterable<T> - Class in ambit2.core.groups
 
AbstractImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,OUTPUT> - Class in ambit2.db.reporters
 
AbstractImageReporter(String, String) - Constructor for class ambit2.db.reporters.AbstractImageReporter
 
AbstractImageReporter(String, String, Dimension) - Constructor for class ambit2.db.reporters.AbstractImageReporter
 
AbstractKekulizationVerifier - Class in ambit2.descriptors
 
AbstractKekulizationVerifier() - Constructor for class ambit2.descriptors.AbstractKekulizationVerifier
 
AbstractKekulizationVerifier.names_index - Enum in ambit2.descriptors
 
AbstractLabel<LABEL extends Enum> - Class in ambit2.base.data
 
AbstractLabel() - Constructor for class ambit2.base.data.AbstractLabel
 
AbstractLabel(LABEL) - Constructor for class ambit2.base.data.AbstractLabel
 
AbstractModel<ID,Features,ResultType extends Comparable<?>> - Class in ambit2.model
 
AbstractModel() - Constructor for class ambit2.model.AbstractModel
 
AbstractModelBuilder<DATA,A extends Algorithm,Model extends ModelQueryResults> - Class in ambit2.model.builder
Abstract class for model building
AbstractModelBuilder() - Constructor for class ambit2.model.builder.AbstractModelBuilder
 
AbstractModelBuilder(String[], String[]) - Constructor for class ambit2.model.builder.AbstractModelBuilder
 
AbstractModelQuery<F,V> - Class in ambit2.db.update.model
 
AbstractModelQuery() - Constructor for class ambit2.db.update.model.AbstractModelQuery
 
AbstractModelQuery._models_criteria - Enum in ambit2.db.update.model
 
AbstractModelStatistics<U extends Bin> - Class in ambit2.similarity.stats
 
AbstractModelStatistics(String) - Constructor for class ambit2.similarity.stats.AbstractModelStatistics
 
AbstractMoleculeAction - Class in ambit2.jchempaint.editor
An abstract action to perform smth on a molecule
AbstractMoleculeAction(IAtomContainer) - Constructor for class ambit2.jchempaint.editor.AbstractMoleculeAction
 
AbstractMoleculeAction(IAtomContainer, String) - Constructor for class ambit2.jchempaint.editor.AbstractMoleculeAction
 
AbstractMoleculeAction(IAtomContainer, String, Icon) - Constructor for class ambit2.jchempaint.editor.AbstractMoleculeAction
 
AbstractMopacShell - Class in ambit2.mopac
Runs OpenMopac as an external executable and reads the results back.
AbstractMopacShell() - Constructor for class ambit2.mopac.AbstractMopacShell
 
AbstractObjectUpdate<Target> - Class in ambit2.db.update
 
AbstractObjectUpdate(Target) - Constructor for class ambit2.db.update.AbstractObjectUpdate
 
AbstractObjectUpdate() - Constructor for class ambit2.db.update.AbstractObjectUpdate
 
AbstractPanel<T> - Class in ambit2.ui
 
AbstractPanel() - Constructor for class ambit2.ui.AbstractPanel
 
AbstractPanel(T) - Constructor for class ambit2.ui.AbstractPanel
 
AbstractPropertyGenerator<P> - Class in ambit2.core.processors.structure
Transforms IStructureRecord into IAtomContainer , calculates some property and assigns it to IStructureRecord
AbstractPropertyGenerator() - Constructor for class ambit2.core.processors.structure.AbstractPropertyGenerator
 
AbstractPropertyRetrieval<F,T,C extends net.idea.modbcum.i.IQueryCondition> - Class in ambit2.db.search.property
 
AbstractPropertyRetrieval() - Constructor for class ambit2.db.search.property.AbstractPropertyRetrieval
 
AbstractPropertyRetrieval._PROPERTY_TYPE - Enum in ambit2.db.search.property
 
AbstractPropertyRetrieval.ANNOTATIONS_TABLE - Enum in ambit2.db.search.property
 
AbstractPropertyRetrieval.PROPERTY_TABLE - Enum in ambit2.db.search.property
 
AbstractPropertyRetrieval.REFERENCE_TABLE - Enum in ambit2.db.search.property
 
AbstractPropertyRetrieval.SearchMode - Enum in ambit2.db.search.property
 
AbstractPropertyWriter<Target,Result> - Class in ambit2.db.processors
 
AbstractPropertyWriter() - Constructor for class ambit2.db.processors.AbstractPropertyWriter
 
AbstractPropertyWriter.mode - Enum in ambit2.db.processors
 
AbstractQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition,ResultType> - Class in ambit2.db.search
Abstract class for a query.
AbstractQuery() - Constructor for class ambit2.db.search.AbstractQuery
 
AbstractReadDataset<T,M extends ISourceDataset> - Class in ambit2.db.update.dataset
 
AbstractReadDataset() - Constructor for class ambit2.db.update.dataset.AbstractReadDataset
 
AbstractReadDataset._fields - Enum in ambit2.db.update.dataset
 
AbstractReadSubstance<F,T> - Class in ambit2.db.substance
 
AbstractReadSubstance() - Constructor for class ambit2.db.substance.AbstractReadSubstance
 
AbstractReadSubstance._sqlids - Enum in ambit2.db.substance
 
AbstractRelation<RELATION_TYPE,RELATION_METRIC extends Serializable,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord> - Class in ambit2.base.relation
Abstract class to represent relationship between compounds
AbstractRelation(FIRSTSTRUC, SECONDSTRUC, RELATION_METRIC) - Constructor for class ambit2.base.relation.AbstractRelation
 
AbstractRepositoryAccess - Class in ambit2.db
 
AbstractRepositoryAccess(Connection) - Constructor for class ambit2.db.AbstractRepositoryAccess
 
AbstractRepositoryWriter<Target,Result> - Class in ambit2.db.processors
 
AbstractRepositoryWriter() - Constructor for class ambit2.db.processors.AbstractRepositoryWriter
 
AbstractRepositoryWriter.OP - Enum in ambit2.db.processors
 
AbstractResource<Q,T extends Serializable,P extends net.idea.modbcum.i.processors.IProcessor<Q,org.restlet.representation.Representation>> - Class in ambit2.rest
Abstract class for resources
AbstractResource() - Constructor for class ambit2.rest.AbstractResource
 
AbstractSearchRequest<R> - Class in ambit2.search.chemidplus
 
AbstractSearchRequest() - Constructor for class ambit2.search.chemidplus.AbstractSearchRequest
 
AbstractSimilarityModel<ID,Features,ResultType extends Comparable<?>> - Class in ambit2.similarity
 
AbstractSimilarityModel() - Constructor for class ambit2.similarity.AbstractSimilarityModel
 
AbstractSmartsPattern<T> - Class in ambit2.smarts.query
 
AbstractSmartsPattern() - Constructor for class ambit2.smarts.query.AbstractSmartsPattern
 
AbstractStaxRDFWriter<INPUT,OUTPUT> - Class in ambit2.rest.dataset
 
AbstractStaxRDFWriter() - Constructor for class ambit2.rest.dataset.AbstractStaxRDFWriter
 
AbstractStructureProcessor - Class in ambit2.core.processors
Parent class for processors
AbstractStructureProcessor(Logger) - Constructor for class ambit2.core.processors.AbstractStructureProcessor
 
AbstractStructureProcessor<Predictor> - Class in ambit2.rest.model.predictor
TODO rename - there is same name class in ambiot2-core!
AbstractStructureProcessor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.AbstractStructureProcessor
 
AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition> - Class in ambit2.db.search.structure
 
AbstractStructureQuery() - Constructor for class ambit2.db.search.structure.AbstractStructureQuery
 
AbstractStructureQuery.FIELD_NAMES - Enum in ambit2.db.search.structure
 
AbstractStructureRecordReporter<Result> - Class in ambit2.db.reporters
 
AbstractStructureRecordReporter(Profile, Template) - Constructor for class ambit2.db.reporters.AbstractStructureRecordReporter
 
AbstractStructureRecordReporter(Result, Profile, Template) - Constructor for class ambit2.db.reporters.AbstractStructureRecordReporter
 
AbstractStructureRetrieval<R> - Class in ambit2.db.readers
Retrieve structures, given a chemical or structure ID.
AbstractStructureRetrieval() - Constructor for class ambit2.db.readers.AbstractStructureRetrieval
 
AbstractStructureRetrieval._sqlids - Enum in ambit2.db.readers
 
AbstractStructuresModelBuilder<DATA> - Class in ambit2.rest.model.builder
 
AbstractStructuresModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String) - Constructor for class ambit2.rest.model.builder.AbstractStructuresModelBuilder
 
AbstractStructuresModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String[], String[], String) - Constructor for class ambit2.rest.model.builder.AbstractStructuresModelBuilder
 
AbstractUpdateProcessor<Group,Target> - Class in ambit2.db.processors
Generic processor to execute IQueryUpdate
AbstractUpdateProcessor() - Constructor for class ambit2.db.processors.AbstractUpdateProcessor
 
AbstractUpdateProcessor(AbstractRepositoryWriter.OP, IQueryUpdate<Group, Target>) - Constructor for class ambit2.db.processors.AbstractUpdateProcessor
 
AbstractUpdateStructureRelation<S extends IStructureRecord,O extends IStructureRecord,RELATION,METRIC> - Class in ambit2.db.chemrelation
 
AbstractUpdateStructureRelation() - Constructor for class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
AbstractUpdateStructureRelation(S, O, RELATION, METRIC) - Constructor for class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
AbstractXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters.xlsx
 
AbstractXLSXReporter(String, boolean, Template, Profile, SubstanceEndpointsBundle[], String, boolean) - Constructor for class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
accept(File) - Method in class ambit2.base.io.AmbitFileFilter
 
accept(File) - Method in class ambit2.base.io.MolFileFilter
 
accept(float, float) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
accept(float, float) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixBitset
 
accept(float, float) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
accept(T) - Method in class ambit2.similarity.stats.Bin
 
accept(List<IAtom>) - Method in interface ambit2.smarts.IAcceptable
 
acceptChanges() - Method in class ambit2.db.results.AmbitRows
 
acceptChanges(Connection) - Method in class ambit2.db.results.AmbitRows
 
accepted(ITask<ITaskResult, USERID>) - Method in class ambit2.rest.task.FilteredTasksIterator
 
acceptLastRecord() - Method in class ambit2.core.io.pdb.RawIteratingPDBReader
 
acceptLastRecord() - Method in class ambit2.core.io.RawIteratingMOLReader
 
acceptLastRecord() - Method in class ambit2.core.io.RawIteratingReader
 
acceptLastRecord() - Method in class ambit2.some.SOMERawReader
 
accepts(Class) - Method in class ambit2.core.io.ArffWriter
 
accepts(Class) - Method in class ambit2.core.io.DelimitedFileReader
 
accepts(Class) - Method in class ambit2.core.io.DelimitedFileWriter
 
accepts(Class<? extends IChemObject>) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
accepts(Class) - Method in class ambit2.core.io.IteratingFileReader
 
accepts(Class) - Method in class ambit2.core.io.MDLReader
 
accepts(Class) - Method in class ambit2.core.io.PDFWriter
 
accepts(Class) - Method in class ambit2.core.io.RawIteratingWrapper
 
accepts(Class) - Method in class ambit2.core.io.XLSFileWriter
 
accepts(Class) - Method in class ambit2.mopac.Mopac7Reader
 
accepts(Class) - Method in class ambit2.mopac.Mopac7Writer
 
accepts(Class<? extends IChemObject>) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
ACCURACY - Static variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
acidName - Variable in class ambit2.structure2name.rules.CarbonData
 
action(JTable, int, Object) - Method in interface ambit2.ui.table.IHeaderAction
 
actionPerformed(ActionEvent) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
actionPerformed(ActionEvent) - Method in class ambit2.ui.editors.FileSelector
 
actionPerformed(ActionEvent) - Method in class ambit2.ui.editors.SelectFieldsPanel
 
actions - Variable in class ambit2.ui.HeaderComboBoxModel
 
activateChlorineRules(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
activateRingChainRules(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
activateRule(String, boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
activeList - Variable in class ambit2.core.groups.FilteredList
 
acyclicAtoms - Variable in class ambit2.structure2name.IUPACNameGenerator
 
AcyclicComponent - Class in ambit2.structure2name.components
 
AcyclicComponent() - Constructor for class ambit2.structure2name.components.AcyclicComponent
 
acyclicComponents - Variable in class ambit2.structure2name.IUPACNameGenerator
 
add(P) - Method in class ambit2.base.data.Profile
 
add(Profile<P>, boolean) - Method in class ambit2.base.data.Profile
 
add(String, String, Class) - Method in class ambit2.base.data.Template
 
add(T) - Method in class ambit2.core.groups.FilteredList
 
add(int, T) - Method in class ambit2.core.groups.FilteredList
 
add(IAtomContainer) - Method in class ambit2.core.groups.SuppleAtomContainer
 
add(int, P) - Method in class ambit2.db.processors.DBProcessorsChain
 
add(P) - Method in class ambit2.db.processors.DBProcessorsChain
 
add(IQueryRetrieval<T>) - Method in class ambit2.db.search.QueryCombined
 
add(AtomEnvironment) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
add(T) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
add(OTContainers<T>) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
add(OTRemoteTask) - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
add(DistanceComparable<T>) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
add1ImplicitHAtom(IAtom) - Static method in class ambit2.core.data.MoleculeTools
 
addAll(Collection<? extends T>) - Method in class ambit2.core.groups.FilteredList
 
addAll(int, Collection<? extends T>) - Method in class ambit2.core.groups.FilteredList
 
addAll(Collection<? extends AtomEnvironment>) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
AddAllChemicalsperSubstanceToBundle - Class in ambit2.db.update.bundle.chemicals
Adds all chemicals , defined as substance components to a bundle Used by DBSubstanceWriter when importing a file as a bundle
AddAllChemicalsperSubstanceToBundle(SubstanceEndpointsBundle, SubstanceRecord) - Constructor for class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
AddAllChemicalsperSubstanceToBundle(SubstanceRecord) - Constructor for class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
AddAllChemicalsperSubstanceToBundle() - Constructor for class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
addAllowedValue(Comparable) - Method in class ambit2.base.data.Property
 
addArgument(boolean) - Method in class ambit2.sln.SLNLogicalExpression
 
addArgument(boolean) - Method in class ambit2.smarts.SmartsLogicalExpression
 
addAtom(IAtom) - Method in class ambit2.core.groups.AbstractGroup
 
addAtom(IAtom) - Method in interface ambit2.core.groups.ISGroup
 
addAtom(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addBatch(Q) - Method in class ambit2.db.PreparedStatementBatchExecutor
 
addBond(IBond) - Method in class ambit2.core.groups.AbstractGroup
 
addBond(IBond) - Method in interface ambit2.core.groups.ISGroup
 
addBond(IBond) - Method in class ambit2.core.groups.SuperAtom
 
addBond(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addBond(int, int, IBond.Order) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addBondsConnected2Atoms(IAtomContainer, List<IAtom>, List<IBond>) - Method in class ambit2.core.groups.AbstractGroup
 
addBrackets(double, double, double, double) - Method in class ambit2.core.groups.AbstractGroup
 
addBrackets(double, double, double, double) - Method in interface ambit2.core.groups.ISGroup
 
AddChemicalToBundle - Class in ambit2.db.update.bundle.chemicals
 
AddChemicalToBundle(SubstanceEndpointsBundle, IStructureRecord) - Constructor for class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
AddChemicalToBundle(IStructureRecord) - Constructor for class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
AddChemicalToBundle() - Constructor for class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.IteratingFileReader
 
addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RawIteratingWrapper
 
addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
addColumns(OTFeatures) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Add features to the dataset
addColumns(OTFeatures) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
addColumns(OTFeature) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
addComponentToCombination(int[], Stack<int[]>) - Method in class ambit2.smarts.ComponentMapping
 
AddCompoundAsSubstanceToBundle - Class in ambit2.db.update.bundle.substance
 
AddCompoundAsSubstanceToBundle() - Constructor for class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
AddCompoundAsSubstanceToBundle(SubstanceEndpointsBundle, SubstanceRecord) - Constructor for class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
addCondition(ICondition) - Method in class ambit2.rules.conditions.ConditionExpression
 
addControls() - Method in class ambit2.ui.QueryBrowser
 
addCorrectionFactor(ICorrectionFactor) - Method in class ambit2.groupcontribution.GroupContributionModel
 
addDashes(String) - Static method in class ambit2.base.data.I5Utils
http://docs.oracle.com/javase/6/docs/api/java/util/UUID.html#toString()
addDescriptor(String) - Method in class ambit2.rules.conditions.AbstractDescriptorSolver
 
AddDimensionedImage - Class in ambit2.db.reporters.xlsx
 
AddDimensionedImage() - Constructor for class ambit2.db.reporters.xlsx.AddDimensionedImage
 
AddDimensionedImage.ClientAnchorDetail - Class in ambit2.db.reporters.xlsx
The HSSFClientAnchor class accepts eight arguments.
AddDimensionedImage.ConvertImageUnits - Class in ambit2.db.reporters.xlsx
Utility methods used to convert Excels character based column and row size measurements into pixels and/or millimetres.
addEexplicitHydrogens - Variable in class ambit2.core.processors.structure.HydrogenAdderProcessor
 
addEffect(EffectRecord<ENDPOINT, CONDITIONS, UNIT>) - Method in class ambit2.base.data.study.ProtocolApplication
 
addElectronContainer(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addElement(Property, Boolean) - Method in class ambit2.base.data.ProfileListModel
 
addEndpointSynonym(String) - Method in class ambit2.base.data.study.EffectRecord
 
AddEndpointToBundle - Class in ambit2.db.update.bundle.endpoints
 
AddEndpointToBundle(SubstanceEndpointsBundle, SubstanceProperty) - Constructor for class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
AddEndpointToBundle(SubstanceProperty) - Constructor for class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
AddEndpointToBundle() - Constructor for class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
adder - Static variable in class ambit2.core.data.MoleculeTools
 
adder - Variable in class ambit2.core.processors.structure.HydrogenAdderProcessor
 
addEvaluation(IEvaluation<EVCONTENT>) - Method in class ambit2.core.data.model.ModelWrapper
 
addExecutable(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutable(String, String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutableFreeBSD(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutableLinux(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutableLinux64(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutableMac(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExecutableWin(String, String[]) - Method in class ambit2.base.external.CommandShell
 
addExplcitHNeighbours(IAtom, IAtomContainer, int) - Static method in class ambit2.smarts.smirks.Transformations
 
addFacet(IFacet) - Method in class ambit2.base.data.StructureRecord
 
addFacet(IFacet) - Method in interface ambit2.base.interfaces.IStructureRecord
 
addFacet(IFacet) - Method in class ambit2.base.relation.composition.CompositionRelation
 
addFacet(BundleRoleFacet) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
addField(T, int, int, V) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
addFields(String, String, boolean, boolean) - Method in class ambit2.base.data.Template
 
addFilterRule(String, int) - Method in class ambit2.tautomers.KnowledgeBase
 
addGenericTypes - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
addGroup(String) - Method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
addGroup(IGroup) - Method in class ambit2.groupcontribution.GroupContributionModel
 
addGroupAtom(ISGroup, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addGroupBond(ISGroup, IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addGuideline(String) - Method in class ambit2.base.data.study.Protocol
 
addHeaderColumn(String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
addHeaderColumn(String) - Method in class ambit2.core.io.ToxcastAssayReader
 
addImageToSheet(String, Sheet, Drawing, byte[], int, int, int, int) - Method in class ambit2.db.reporters.xlsx.AddDimensionedImage
Add an image to a worksheet.
addImageToSheet(int, int, Sheet, Drawing, byte[], int, int, int, int) - Method in class ambit2.db.reporters.xlsx.AddDimensionedImage
Add an image to a worksheet.
Additive - Class in ambit2.base.relation.composition
Substance composition: additives
Additive(SubstanceRecord, IStructureRecord, Proportion) - Constructor for class ambit2.base.relation.composition.Additive
 
addJob(Reference, List<String>) - Method in class ambit2.rest.task.CallableDatasetCreator
 
addLigands0 - Variable in class ambit2.smarts.StereoChange
 
addLigands1 - Variable in class ambit2.smarts.StereoChange
 
addLigandsAtoms - Variable in class ambit2.smarts.StereoChange
 
addLocalDescriptor(ILocalDescriptor) - Method in class ambit2.groupcontribution.GroupContributionModel
 
addLogOperation(int) - Method in class ambit2.sln.SLNLogicalExpression
 
addLogOperation(int) - Method in class ambit2.smarts.SmartsLogicalExpression
 
addLonePair(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addMeasurement(ProtocolApplication) - Method in class ambit2.base.data.SubstanceRecord
 
addMolecule(IAtomContainer, ReactionSequenceStep, IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
addMouseListener(MouseListener) - Method in class ambit2.ui.editors.ListEditor
 
addNew - Variable in class ambit2.db.readers.RetrieveField
 
addNew - Variable in class ambit2.db.readers.RetrieveProfileValues
 
addNew - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
addNewReaction(ReactionData) - Method in class ambit2.reactions.sets.ReactionGroup
 
addNewReaction(ReactionData) - Method in class ambit2.reactions.sets.ReactionSet
 
addObject(T, int) - Method in class ambit2.domain.stats.datastructures.Histogram
 
addObject(T) - Method in class ambit2.domain.stats.datastructures.Histogram
 
addObject(T) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
null property
addObject(T, Object) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
addObject(T, int) - Method in class ambit2.similarity.stats.Histogram
 
addObject(T) - Method in class ambit2.similarity.stats.Histogram
 
addParameter(Parameter) - Method in class ambit2.core.data.model.Algorithm
 
addParameters(int, List<QueryParam>) - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
addParameters(int, List<QueryParam>) - Method in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
addParameters(int, List<QueryParam>) - Method in class ambit2.db.substance.study.UpdateSubstanceStudy
 
addParameters(int, List<QueryParam>) - Method in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
addParentAtom(IAtom) - Method in class ambit2.core.groups.MultipleGroup
 
addPicture(IStructureRecord, int, int) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
addPicture(byte[], int, int) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
addPoint(Comparable, ResultType, ResultType) - Method in interface ambit2.model.IModelStatistics
 
addPoint(Comparable, Double, Double) - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
addPoint(Comparable, T, T) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
addPoint(Comparable, Double, Double) - Method in class ambit2.similarity.stats.PredictionModelStatistics
 
addPreconditionAtom(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
addPreconditionAtomtype(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
addProperties(Map) - Method in class ambit2.core.io.MolPropertiesIOSetting
 
addPropertiesToTemplate - Variable in class ambit2.db.readers.RetrieveTemplateStructure
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.data.Profile
 
addPropertyChangeListener(PropertyChangeListener) - Method in class ambit2.rest.task.CallableDatasetCreator
 
addPropertyChangeListener(PropertyChangeListener) - Method in class ambit2.ui.table.BrowsableTableModel
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IBrowserMode
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IFindNavigator
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IPageNavigator
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IRecordNavigator
 
addRankingRule(String, int) - Method in class ambit2.tautomers.KnowledgeBase
 
addRecordProperties(Map) - Method in class ambit2.base.data.StructureRecord
 
addRecordProperties(Map) - Method in interface ambit2.base.interfaces.IStructureRecord
 
addRecordProperties(Map) - Method in class ambit2.base.relation.composition.CompositionRelation
 
address - Variable in class ambit2.base.data.AmbitUser
 
address - Variable in class ambit2.export.isa.v1_0.objects.Person
 
address - Variable in class ambit2.ui.editors.AmbitUserEditor
 
addRowSetListener(RowSetListener) - Method in class ambit2.db.results.AmbitRows
 
addRule(String, int) - Method in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
addRule(String, int) - Method in class ambit2.tautomers.KnowledgeBase
 
addScore(double) - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
addScore(double) - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
addSeparator - Static variable in class ambit2.export.isa.base.ISAConst
 
addSetting(IOSetting) - Method in class ambit2.core.io.IteratingFileReader
 
addSetting(IOSetting) - Method in class ambit2.core.io.RawIteratingWrapper
 
addSetting(IOSetting) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
addSettings(Collection<IOSetting>) - Method in class ambit2.core.io.IteratingFileReader
 
addSettings(Collection<IOSetting>) - Method in class ambit2.core.io.RawIteratingWrapper
 
addSettings(Collection<IOSetting>) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
addSingleElectron(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addSMILEScolumn - Variable in class ambit2.core.io.FilesWithHeaderWriter
 
addSolver(IDescriptorSolver) - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
addStatementToCache(String, PreparedStatement) - Method in class ambit2.db.StatementExecutor
 
addStereoElement(IStereoElement) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addStructureParam(List<QueryParam>) - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
addStructureParam(List<QueryParam>) - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds
 
addStructureParam(List<QueryParam>) - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset
 
addStructureParam(List<QueryParam>) - Method in class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults
 
addStructureRelation(CompositionRelation) - Method in class ambit2.base.data.SubstanceRecord
 
addStructureRelation(String, IStructureRecord, STRUCTURE_RELATION, Proportion) - Method in class ambit2.base.data.SubstanceRecord
 
addStudyDescriptionContent(Study, String) - Static method in class ambit2.export.isa.v1_0.ISAJsonUtils1_0
 
AddSubstanceToBundle - Class in ambit2.db.update.bundle.substance
 
AddSubstanceToBundle(SubstanceEndpointsBundle, SubstanceRecord) - Constructor for class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
AddSubstanceToBundle(SubstanceRecord) - Constructor for class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
AddSubstanceToBundle() - Constructor for class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
addTask(String, ICallableTask, Reference, USERID, boolean) - Method in class ambit2.rest.task.TaskStorage
 
addTask(String, ICallableTask, Reference, USERID) - Method in class ambit2.rest.TaskApplication
 
addTask(String, ICallableTask, Reference, boolean, USERID) - Method in class ambit2.rest.TaskApplication
 
addToFilter(T) - Method in class ambit2.core.groups.FilteredList
 
addToFilter(int) - Method in class ambit2.core.groups.FilteredList
 
addToFilter(T) - Method in interface ambit2.core.groups.IFiltered
 
addToFilter(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addToFilter(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
addToReport(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
addToResult(String, boolean, int, Result) - Method in class ambit2.descriptors.processors.AbstractDescriptorFactory
 
addToResult(String, boolean, int, Profile<Property>) - Method in class ambit2.descriptors.processors.DescriptorsFactory
 
addValue(Comparable, Object, ResultType) - Method in interface ambit2.model.IModelStatistics
 
addValue(Comparable, Object, T) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
addValues(SubstanceRecord, Property, Value, Object) - Static method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
addVector(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
addVectorEqual(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
addWidgets() - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
addWidgets(IChemModel) - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
addWidgets(Preferences.VTAGS) - Method in class ambit2.ui.editors.PreferencesPanel
 
addWidgets(T) - Method in class ambit2.ui.QueryBrowser
 
adminAAEnabled - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
adminPass - Variable in class ambit2.db.processors.DbCreateDatabase
 
ADomainMethodType - Enum in ambit2.model.numeric
Applicability domain method type
ae_sql - Variable in class ambit2.db.update.fpae.CreateAtomEnvironment
 
aeDescriptor - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
aeParams - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
AESimilarity - Static variable in class ambit2.core.config.AmbitCONSTANTS
Atom environment similarity
affiliation - Variable in class ambit2.base.data.AmbitUser
 
affiliation - Variable in class ambit2.export.isa.v1_0.objects.Person
 
affiliation - Variable in class ambit2.ui.editors.AmbitUserEditor
 
afterHandle(Request, Response) - Method in class ambit2.rest.OriginFilter
 
afterLast() - Method in class ambit2.db.results.AmbitRows
 
afterProcessing(Target, Iterator<ItemInput>) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
afterProcessing(IQueryRetrieval<ResultType>, Iterator<ResultType>) - Method in class ambit2.db.DbReader
 
afterProcessing(IInputState, Iterator<ITEMTYPE>) - Method in class ambit2.db.processors.BatchDBProcessor
 
afterProcessing(Reference, Iterator<Item>) - Method in class ambit2.rest.RDFBatchParser
 
agent - Variable in class ambit2.rest.task.CallableQueryProcessor
 
agent - Variable in class ambit2.smarts.SMIRKSReaction
 
agentFlags - Variable in class ambit2.smarts.SMIRKSReaction
 
agents - Variable in class ambit2.smarts.SMIRKSReaction
 
agentsCLG - Variable in class ambit2.smarts.SMIRKSReaction
 
agentsSmarts - Variable in class ambit2.smarts.SMIRKSReaction
 
AGGLO_AGGR_DIAM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
AGGLO_AGGR_SIZE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
AGGLO_AGGR_SIZE_DIST - Static variable in class ambit2.base.ro.I5CONSTANTS
 
AGGLO_AGGREGATION_IDX - Static variable in class ambit2.base.ro.I5CONSTANTS
 
AJAX_TIMEOUT - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
alchoholName - Variable in class ambit2.structure2name.rules.CarbonData
 
aldehydeName - Variable in class ambit2.structure2name.rules.CarbonData
 
alg_reporter - Variable in class ambit2.rest.model.builder.ModelBuilder
 
Algorithm<T extends Serializable> - Class in ambit2.core.data.model
Quick implementation of OpenTox Algorithm spec
Algorithm() - Constructor for class ambit2.core.data.model.Algorithm
 
Algorithm(String) - Constructor for class ambit2.core.data.model.Algorithm
 
algorithm - Variable in class ambit2.core.data.model.ModelWrapper
 
algorithm - Static variable in class ambit2.rest.algorithm.MLResources
 
algorithm(String, String) - Static method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
algorithm - Variable in class ambit2.rest.legacy.OTFeature
Deprecated.
 
algorithm() - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
Retrieve algorithms from ot:hasSource property
algorithm - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
algorithm - Variable in class ambit2.rest.model.task.CallableModelCreator
 
Algorithm.AlgorithmFormat - Enum in ambit2.core.data.model
 
Algorithm.requires - Enum in ambit2.core.data.model
 
algorithmKey - Static variable in class ambit2.rest.algorithm.MLResources
 
algorithms(String, String) - Static method in class ambit2.rest.legacy.OTAlgorithms
Deprecated.
 
algorithms - Variable in class ambit2.rest.task.CallableDatasetCreator
 
AlgorithmType - Enum in ambit2.core.data.model
 
AlgorithmURIReporter - Class in ambit2.rest.algorithm
Generates URI from algorithm ID
AlgorithmURIReporter() - Constructor for class ambit2.rest.algorithm.AlgorithmURIReporter
 
AlgorithmURIReporter(Request) - Constructor for class ambit2.rest.algorithm.AlgorithmURIReporter
 
AliphaticSymbolQueryAtom - Class in ambit2.smarts
 
AliphaticSymbolQueryAtom(IChemObjectBuilder) - Constructor for class ambit2.smarts.AliphaticSymbolQueryAtom
 
ALKANES_CH3 - Static variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
alkaneSufix - Variable in class ambit2.structure2name.rules.IUPACRuleDataBase
 
ALL - Static variable in class ambit2.db.search.structure.QueryMissingDescriptor
 
ALL - Static variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
ALL - Static variable in class ambit2.similarity.stats.PredictionModelStatistics
 
allCorrectionFactorsToJsonString(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
allDescriptorList - Variable in class ambit2.rules.conditions.DescriptorSolverSet
 
allGroupInfoToJsonString(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
allowDatabaseCreate() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
allowDBCreate() - Method in class ambit2.rest.DBConnection
 
ALLOWED_ORIGINS - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
allowedOrigins - Variable in class ambit2.rest.OriginFilter
 
allowedProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
allowedProducts - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
allowedValues - Variable in class ambit2.base.data.Property
 
allPages - Variable in class ambit2.ui.table.PageNavigator
 
allPages - Variable in class ambit2.ui.table.RecordNavigator
 
AllSourcesFinder - Class in ambit2.search
 
AllSourcesFinder(Template) - Constructor for class ambit2.search.AllSourcesFinder
 
AllSourcesFinder(Template, IProcessor<String, String>, AbstractFinder.MODE) - Constructor for class ambit2.search.AllSourcesFinder
 
ambit2.balloon - package ambit2.balloon
 
ambit2.base.config - package ambit2.base.config
 
ambit2.base.data - package ambit2.base.data
Base data structures; no chemistry.
ambit2.base.data.study - package ambit2.base.data.study
Detailed description of experimental data, linked to substances
ambit2.base.data.substance - package ambit2.base.data.substance
Chemical substances, with complex composition (including nanomaterials)
ambit2.base.exceptions - package ambit2.base.exceptions
 
ambit2.base.external - package ambit2.base.external
 
ambit2.base.facet - package ambit2.base.facet

Facets

ambit2.base.interfaces - package ambit2.base.interfaces

Format independent IO utilities

ambit2.base.io - package ambit2.base.io

Interfaces

ambit2.base.io.format - package ambit2.base.io.format
 
ambit2.base.json - package ambit2.base.json

JSON utilities

ambit2.base.processors - package ambit2.base.processors

Processors (similar to a processing node in a workflow engine)

ambit2.base.processors.batch - package ambit2.base.processors.batch
 
ambit2.base.processors.search - package ambit2.base.processors.search
 
ambit2.base.relation - package ambit2.base.relation

Classes to describe relations between chemical structures

ambit2.base.relation.composition - package ambit2.base.relation.composition

Classes to describe chemical composition

ambit2.base.ro - package ambit2.base.ro
Ro did not begin with attempting to rival or supplant any other language whatever, either natural or artificial, nor was it suggested by any of them.
ambit2.chebi - package ambit2.chebi
 
ambit2.core.config - package ambit2.core.config

User preferences and other configuration options

ambit2.core.data - package ambit2.core.data
 
ambit2.core.data.distances - package ambit2.core.data.distances
 
ambit2.core.data.model - package ambit2.core.data.model
 
ambit2.core.external - package ambit2.core.external

Launching external applications by command shell

ambit2.core.filter - package ambit2.core.filter
 
ambit2.core.groups - package ambit2.core.groups
 
ambit2.core.helper - package ambit2.core.helper
 
ambit2.core.i - package ambit2.core.i
 
ambit2.core.io - package ambit2.core.io
Input output support.
ambit2.core.io.bcf - package ambit2.core.io.bcf
 
ambit2.core.io.dx - package ambit2.core.io.dx
 
ambit2.core.io.fp - package ambit2.core.io.fp
 
ambit2.core.io.json - package ambit2.core.io.json
 
ambit2.core.io.pdb - package ambit2.core.io.pdb
 
ambit2.core.io.sj - package ambit2.core.io.sj
 
ambit2.core.io.study - package ambit2.core.io.study
 
ambit2.core.json - package ambit2.core.json
 
ambit2.core.processors - package ambit2.core.processors
 
ambit2.core.processors.batch - package ambit2.core.processors.batch
 
ambit2.core.processors.quality - package ambit2.core.processors.quality
 
ambit2.core.processors.structure - package ambit2.core.processors.structure
 
ambit2.core.processors.structure.key - package ambit2.core.processors.structure.key
 
ambit2.core.smiles - package ambit2.core.smiles

SMILES tools, additional to CDK smiles functionality

ambit2.db - package ambit2.db
 
ambit2.db.cache - package ambit2.db.cache
 
ambit2.db.chart - package ambit2.db.chart
 
ambit2.db.chemrelation - package ambit2.db.chemrelation
 
ambit2.db.facets.bookmarks - package ambit2.db.facets.bookmarks
 
ambit2.db.facets.bundle - package ambit2.db.facets.bundle
 
ambit2.db.facets.compounds - package ambit2.db.facets.compounds
 
ambit2.db.facets.datasets - package ambit2.db.facets.datasets
 
ambit2.db.facets.propertyvalue - package ambit2.db.facets.propertyvalue
 
ambit2.db.facets.qlabel - package ambit2.db.facets.qlabel
 
ambit2.db.model - package ambit2.db.model
 
ambit2.db.processors - package ambit2.db.processors
 
ambit2.db.processors.quality - package ambit2.db.processors.quality
 
ambit2.db.readers - package ambit2.db.readers
 
ambit2.db.reporters - package ambit2.db.reporters
 
ambit2.db.reporters.xlsx - package ambit2.db.reporters.xlsx
 
ambit2.db.results - package ambit2.db.results
 
ambit2.db.search - package ambit2.db.search
 
ambit2.db.search.property - package ambit2.db.search.property
 
ambit2.db.search.qlabel - package ambit2.db.search.qlabel
 
ambit2.db.search.structure - package ambit2.db.search.structure
 
ambit2.db.search.structure.byproperty - package ambit2.db.search.structure.byproperty
 
ambit2.db.search.structure.pairwise - package ambit2.db.search.structure.pairwise
 
ambit2.db.simiparity.space - package ambit2.db.simiparity.space
 
ambit2.db.substance - package ambit2.db.substance
 
ambit2.db.substance.ids - package ambit2.db.substance.ids
 
ambit2.db.substance.processor - package ambit2.db.substance.processor
 
ambit2.db.substance.properties - package ambit2.db.substance.properties
 
ambit2.db.substance.relation - package ambit2.db.substance.relation
 
ambit2.db.substance.study - package ambit2.db.substance.study
 
ambit2.db.substance.study.facet - package ambit2.db.substance.study.facet
 
ambit2.db.update - package ambit2.db.update
 
ambit2.db.update.bookmark - package ambit2.db.update.bookmark
 
ambit2.db.update.bundle - package ambit2.db.update.bundle
 
ambit2.db.update.bundle.chemicals - package ambit2.db.update.bundle.chemicals
 
ambit2.db.update.bundle.effects - package ambit2.db.update.bundle.effects
 
ambit2.db.update.bundle.endpoints - package ambit2.db.update.bundle.endpoints
 
ambit2.db.update.bundle.matrix - package ambit2.db.update.bundle.matrix
 
ambit2.db.update.bundle.substance - package ambit2.db.update.bundle.substance
 
ambit2.db.update.chemical - package ambit2.db.update.chemical
 
ambit2.db.update.dataset - package ambit2.db.update.dataset
 
ambit2.db.update.dictionary - package ambit2.db.update.dictionary
 
ambit2.db.update.fp - package ambit2.db.update.fp
 
ambit2.db.update.fpae - package ambit2.db.update.fpae
 
ambit2.db.update.model - package ambit2.db.update.model
 
ambit2.db.update.property - package ambit2.db.update.property
 
ambit2.db.update.propertyannotations - package ambit2.db.update.propertyannotations
 
ambit2.db.update.qlabel - package ambit2.db.update.qlabel
 
ambit2.db.update.qlabel.smarts - package ambit2.db.update.qlabel.smarts
 
ambit2.db.update.queryfolder - package ambit2.db.update.queryfolder
 
ambit2.db.update.reference - package ambit2.db.update.reference
 
ambit2.db.update.storedquery - package ambit2.db.update.storedquery
 
ambit2.db.update.structure - package ambit2.db.update.structure
 
ambit2.db.update.value - package ambit2.db.update.value
 
ambit2.db.version - package ambit2.db.version
 
ambit2.dbui - package ambit2.dbui
 
ambit2.dbui.dictionary - package ambit2.dbui.dictionary
 
ambit2.descriptors - package ambit2.descriptors
 
ambit2.descriptors.constitutional - package ambit2.descriptors.constitutional
 
ambit2.descriptors.fingerprints - package ambit2.descriptors.fingerprints
 
ambit2.descriptors.geometrical - package ambit2.descriptors.geometrical
 
ambit2.descriptors.processors - package ambit2.descriptors.processors
 
ambit2.descriptors.simmatrix - package ambit2.descriptors.simmatrix
 
ambit2.descriptors.topological - package ambit2.descriptors.topological
 
ambit2.descriptors.utils - package ambit2.descriptors.utils
 
ambit2.domain.stats - package ambit2.domain.stats

Basic statistics classes

ambit2.domain.stats.datastructures - package ambit2.domain.stats.datastructures

Datastructures for the statistics classes

ambit2.domain.stats.transforms - package ambit2.domain.stats.transforms

Statistics : Transformations Fast Fourie Transform

ambit2.domain.stats.transforms.densityestimation - package ambit2.domain.stats.transforms.densityestimation

Statistics : Density estimation Non parametric kernel density estimation

ambit2.domain.stats.transforms.transformfilters - package ambit2.domain.stats.transforms.transformfilters

Data transformations (PCA and more)

ambit2.dragon - package ambit2.dragon
 
ambit2.export.isa - package ambit2.export.isa
TODO documentation
ambit2.export.isa.base - package ambit2.export.isa.base
 
ambit2.export.isa.json - package ambit2.export.isa.json
 
ambit2.export.isa.tab - package ambit2.export.isa.tab
 
ambit2.export.isa.v1_0 - package ambit2.export.isa.v1_0
 
ambit2.export.isa.v1_0.objects - package ambit2.export.isa.v1_0.objects
 
ambit2.featureselection - package ambit2.featureselection
 
ambit2.groupcontribution - package ambit2.groupcontribution
 
ambit2.groupcontribution.cli - package ambit2.groupcontribution.cli
 
ambit2.groupcontribution.correctionfactors - package ambit2.groupcontribution.correctionfactors
 
ambit2.groupcontribution.dataset - package ambit2.groupcontribution.dataset
 
ambit2.groupcontribution.descriptors - package ambit2.groupcontribution.descriptors
 
ambit2.groupcontribution.fragmentation - package ambit2.groupcontribution.fragmentation
 
ambit2.groupcontribution.groups - package ambit2.groupcontribution.groups
 
ambit2.groupcontribution.io - package ambit2.groupcontribution.io
 
ambit2.groupcontribution.nmr - package ambit2.groupcontribution.nmr
 
ambit2.groupcontribution.nmr.nmr_1h - package ambit2.groupcontribution.nmr.nmr_1h
 
ambit2.groupcontribution.rules - package ambit2.groupcontribution.rules
 
ambit2.groupcontribution.transformations - package ambit2.groupcontribution.transformations
 
ambit2.groupcontribution.utils - package ambit2.groupcontribution.utils
 
ambit2.groupcontribution.utils.math - package ambit2.groupcontribution.utils.math
 
ambit2.jchempaint.editor - package ambit2.jchempaint.editor
 
ambit2.markush - package ambit2.markush
 
ambit2.ml.io - package ambit2.ml.io
 
ambit2.ml.io.app - package ambit2.ml.io.app
 
ambit2.ml.mlib - package ambit2.ml.mlib
 
ambit2.model - package ambit2.model
 
ambit2.model.builder - package ambit2.model.builder
 
ambit2.model.dataset - package ambit2.model.dataset
 
ambit2.model.evaluation - package ambit2.model.evaluation
 
ambit2.model.numeric - package ambit2.model.numeric
 
ambit2.model.numeric.distance - package ambit2.model.numeric.distance
 
ambit2.model.structure - package ambit2.model.structure
 
ambit2.mopac - package ambit2.mopac
 
ambit2.namestructure - package ambit2.namestructure
 
ambit2.pubchem - package ambit2.pubchem
 
ambit2.pubchem.rest - package ambit2.pubchem.rest
 
ambit2.reactions - package ambit2.reactions
 
ambit2.reactions.cli - package ambit2.reactions.cli
 
ambit2.reactions.fragmentation - package ambit2.reactions.fragmentation
 
ambit2.reactions.generator - package ambit2.reactions.generator
 
ambit2.reactions.generator.score - package ambit2.reactions.generator.score
 
ambit2.reactions.generator.score.components - package ambit2.reactions.generator.score.components
 
ambit2.reactions.io - package ambit2.reactions.io
 
ambit2.reactions.mapping - package ambit2.reactions.mapping
 
ambit2.reactions.mmp.analysis - package ambit2.reactions.mmp.analysis
 
ambit2.reactions.reactor - package ambit2.reactions.reactor
 
ambit2.reactions.retrosynth - package ambit2.reactions.retrosynth
 
ambit2.reactions.rules - package ambit2.reactions.rules
 
ambit2.reactions.rules.conditions - package ambit2.reactions.rules.conditions
 
ambit2.reactions.rules.scores - package ambit2.reactions.rules.scores
 
ambit2.reactions.sets - package ambit2.reactions.sets
 
ambit2.reactions.syntheticaccessibility - package ambit2.reactions.syntheticaccessibility
 
ambit2.rendering - package ambit2.rendering
 
ambit2.rest - package ambit2.rest
 
ambit2.rest.aa.opensso - package ambit2.rest.aa.opensso
 
ambit2.rest.algorithm - package ambit2.rest.algorithm
 
ambit2.rest.config - package ambit2.rest.config
 
ambit2.rest.dataset - package ambit2.rest.dataset
 
ambit2.rest.exception - package ambit2.rest.exception
 
ambit2.rest.freemarker - package ambit2.rest.freemarker
 
ambit2.rest.legacy - package ambit2.rest.legacy
 
ambit2.rest.model - package ambit2.rest.model
 
ambit2.rest.model.builder - package ambit2.rest.model.builder
 
ambit2.rest.model.predictor - package ambit2.rest.model.predictor
 
ambit2.rest.model.task - package ambit2.rest.model.task
 
ambit2.rest.property - package ambit2.rest.property
 
ambit2.rest.rdf - package ambit2.rest.rdf
 
ambit2.rest.rdf.chembl - package ambit2.rest.rdf.chembl
 
ambit2.rest.rdf.sparql - package ambit2.rest.rdf.sparql
 
ambit2.rest.reporters - package ambit2.rest.reporters
 
ambit2.rest.structure - package ambit2.rest.structure
 
ambit2.rest.study - package ambit2.rest.study
 
ambit2.rest.substance - package ambit2.rest.substance
 
ambit2.rest.task - package ambit2.rest.task
 
ambit2.rest.task.dsl - package ambit2.rest.task.dsl
 
ambit2.rest.task.weka - package ambit2.rest.task.weka
 
ambit2.rest.wrapper - package ambit2.rest.wrapper
 
ambit2.rules - package ambit2.rules
 
ambit2.rules.actions - package ambit2.rules.actions
 
ambit2.rules.conditions - package ambit2.rules.conditions
 
ambit2.rules.conditions.parser - package ambit2.rules.conditions.parser
 
ambit2.rules.conditions.solvers - package ambit2.rules.conditions.solvers
 
ambit2.rules.conditions.value - package ambit2.rules.conditions.value
 
ambit2.rules.functions - package ambit2.rules.functions
 
ambit2.rules.json - package ambit2.rules.json
 
ambit2.rules.miscellaneous - package ambit2.rules.miscellaneous
 
ambit2.rules.weight - package ambit2.rules.weight
 
ambit2.search - package ambit2.search
 
ambit2.search.chemidplus - package ambit2.search.chemidplus
 
ambit2.search.csls - package ambit2.search.csls
 
ambit2.search.opentox - package ambit2.search.opentox
 
ambit2.similarity - package ambit2.similarity
 
ambit2.similarity.knn - package ambit2.similarity.knn
 
ambit2.similarity.measure - package ambit2.similarity.measure
 
ambit2.similarity.stats - package ambit2.similarity.stats
 
ambit2.sln - package ambit2.sln
 
ambit2.sln.dictionary - package ambit2.sln.dictionary
 
ambit2.sln.io - package ambit2.sln.io
 
ambit2.sln.reaction - package ambit2.sln.reaction
 
ambit2.sln.search - package ambit2.sln.search
 
ambit2.smarts - package ambit2.smarts

SMARTS parser

ambit2.smarts.groups - package ambit2.smarts.groups
 
ambit2.smarts.processors - package ambit2.smarts.processors
 
ambit2.smarts.query - package ambit2.smarts.query
Ambit implementation of SMARTS parser
ambit2.smarts.smirks - package ambit2.smarts.smirks
 
ambit2.smi23d - package ambit2.smi23d
 
ambit2.some - package ambit2.some
 
ambit2.structure2name - package ambit2.structure2name
 
ambit2.structure2name.components - package ambit2.structure2name.components
 
ambit2.structure2name.helpers - package ambit2.structure2name.helpers
 
ambit2.structure2name.rules - package ambit2.structure2name.rules
 
ambit2.structure2name.rules.parser - package ambit2.structure2name.rules.parser
 
ambit2.tautomers - package ambit2.tautomers
 
ambit2.tautomers.processor - package ambit2.tautomers.processor
 
ambit2.tautomers.ranking - package ambit2.tautomers.ranking
 
ambit2.tautomers.rules - package ambit2.tautomers.rules
 
ambit2.tautomers.tools - package ambit2.tautomers.tools
 
ambit2.tautomers.zwitterion - package ambit2.tautomers.zwitterion
 
ambit2.ui - package ambit2.ui
 
ambit2.ui.editors - package ambit2.ui.editors
 
ambit2.ui.jmol - package ambit2.ui.jmol
 
ambit2.ui.table - package ambit2.ui.table
 
ambit2.vega - package ambit2.vega
 
AMBIT_DESCRIPTORS_ONTOLOGY - Static variable in class ambit2.base.data.Property
 
AMBIT_IDSTRUCTURE - Static variable in class ambit2.core.config.AmbitCONSTANTS
the database field structure.idstructure
AMBIT_IDSUBSTANCE - Static variable in class ambit2.core.config.AmbitCONSTANTS
the database field substance.idsubstance
AMBIT_uri - Static variable in class ambit2.base.data.LiteratureEntry
 
AMBITAppConfigInternal - Class in ambit2.rest.config
 
AMBITAppConfigInternal() - Constructor for class ambit2.rest.config.AMBITAppConfigInternal
No config overriding at all
AMBITAppConfigProperties - Class in ambit2.rest.config
 
AMBITAppConfigProperties() - Constructor for class ambit2.rest.config.AMBITAppConfigProperties
 
AMBITAppConfigProperties(File) - Constructor for class ambit2.rest.config.AMBITAppConfigProperties
 
AmbitBean - Class in ambit2.base.data
 
AmbitBean() - Constructor for class ambit2.base.data.AmbitBean
 
AMBITConfig - Enum in ambit2.base.config
 
AMBITConfigProperties - Class in ambit2.base.config
 
AMBITConfigProperties() - Constructor for class ambit2.base.config.AMBITConfigProperties
 
AMBITConfigProperties(File) - Constructor for class ambit2.base.config.AMBITConfigProperties
 
AmbitCONSTANTS - Class in ambit2.core.config
Constants TODO : move to ambit2-base
AMBITDB_VERSION_MAJOR - Static variable in interface ambit2.db.DBVersion
 
AMBITDB_VERSION_MINOR - Static variable in interface ambit2.db.DBVersion
 
AmbitDBVersion - Class in ambit2.db.version
 
AmbitDBVersion() - Constructor for class ambit2.db.version.AmbitDBVersion
 
AmbitFileFilter - Class in ambit2.base.io
Customized file filter
AmbitFileFilter() - Constructor for class ambit2.base.io.AmbitFileFilter
 
AmbitFileFilter(String, String) - Constructor for class ambit2.base.io.AmbitFileFilter
 
AmbitIOException - Exception in ambit2.base.exceptions
TODO add description
AmbitIOException() - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(String) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(String, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(Throwable) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(Throwable, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(String, Throwable) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitIOException(String, Throwable, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException
 
AmbitML - Class in ambit2.ml.io.app
 
AmbitML() - Constructor for class ambit2.ml.io.app.AmbitML
 
AmbitML.out_formats - Enum in ambit2.ml.io.app
 
ambitProperties - Static variable in class ambit2.base.config.AMBITConfigProperties
 
AmbitRows<T> - Class in ambit2.db.results
 
AmbitRows() - Constructor for class ambit2.db.results.AmbitRows
 
AmbitRowsPanel<T,Rows extends AmbitRows<T>> - Class in ambit2.dbui.dictionary
 
AmbitRowsPanel() - Constructor for class ambit2.dbui.dictionary.AmbitRowsPanel
 
AmbitSettingsListener - Class in ambit2.ui
An implementation of IReaderListener and IWriterListener.
AmbitSettingsListener(IOSetting.Importance) - Constructor for class ambit2.ui.AmbitSettingsListener
 
AmbitSmirksCli - Class in ambit2.reactions.cli
 
AmbitSmirksCli() - Constructor for class ambit2.reactions.cli.AmbitSmirksCli
 
AmbitUser - Class in ambit2.base.data
Contains all information about an AMBIT database user.
AmbitUser() - Constructor for class ambit2.base.data.AmbitUser
 
AmbitUser(String) - Constructor for class ambit2.base.data.AmbitUser
 
AmbitUser(String, AmbitUser.USER_TYPE) - Constructor for class ambit2.base.data.AmbitUser
 
AmbitUser.USER_TYPE - Enum in ambit2.base.data
 
AmbitUserEditor - Class in ambit2.ui.editors
Editor for AmbitUser
AmbitUserEditor() - Constructor for class ambit2.ui.editors.AmbitUserEditor
 
AminoGroup - Class in ambit2.tautomers.zwitterion
 
AminoGroup() - Constructor for class ambit2.tautomers.zwitterion.AminoGroup
 
analyse() - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
analyseTautomerDescriptors(String, String, int, int) - Method in class ambit2.tautomers.Tautomer2DescriptorUtils
 
analyzeAtomExpression(String) - Method in class ambit2.sln.SLNParser
 
analyzeBondExpression(String) - Method in class ambit2.sln.SLNParser
 
analyzeSubExpressionsFromLowAnd(SmartsAtomExpression, SmartsAtomExpression) - Method in class ambit2.smarts.SmartsToChemObject
 
analyzeSubExpressionsFromLowAnd(SmartsBondExpression, SmartsBondExpression) - Method in class ambit2.smarts.SmartsToChemObject
 
analyzeSubExpressionsFromLowAnd(SmartsAtomExpression, SmartsAtomExpression) - Static method in class ambit2.smarts.StereoFromSmartsAtomExpression
 
analyzeSubstance(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
 
and - Variable in class ambit2.dbui.QueryInfoEditor
 
annotate(Properties, String) - Method in class ambit2.base.ro.AbstractAnnotator
 
annotate(EffectRecord<String, IParams, String>) - Method in class ambit2.db.substance.study.facet.FacetAnnotator
 
annotate(ProtocolApplication<Protocol, IParams, String, IParams, String>) - Method in class ambit2.db.substance.study.facet.FacetAnnotator
 
annotateConditions(String) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotateEndpoint(String) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotateGuideline(String) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotateParam(String) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotateSubstance(SubstanceRecord) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotateUnits(String) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
annotation - Variable in class ambit2.base.data.study.Value
 
annotations - Variable in class ambit2.base.data.Property
 
annotationsWriter - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
annotationsWriter - Variable in class ambit2.rest.model.task.CallableModelCreator
 
annotationValue - Variable in class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
Annotea - Class in ambit2.rest.rdf
 
Annotea() - Constructor for class ambit2.rest.rdf.Annotea
 
Annotea.AnnoteaProperty - Enum in ambit2.rest.rdf
 
Annotea.Bookmark - Enum in ambit2.rest.rdf
 
Annotea.BookmarkProperty - Enum in ambit2.rest.rdf
 
answer - Variable in class ambit2.ui.WizardPanel
 
AP_a - Static variable in class ambit2.smarts.SmartsConst
 
AP_A - Static variable in class ambit2.smarts.SmartsConst
 
AP_ANY - Static variable in class ambit2.smarts.SmartsConst
 
AP_AtNum - Static variable in class ambit2.smarts.SmartsConst
 
AP_Charge - Static variable in class ambit2.smarts.SmartsConst
 
AP_Chiral - Static variable in class ambit2.smarts.SmartsConst
 
AP_D - Static variable in class ambit2.smarts.SmartsConst
 
AP_GMOE - Static variable in class ambit2.smarts.SmartsConst
 
AP_H - Static variable in class ambit2.smarts.SmartsConst
 
AP_h - Static variable in class ambit2.smarts.SmartsConst
 
AP_iMOE - Static variable in class ambit2.smarts.SmartsConst
 
AP_Mass - Static variable in class ambit2.smarts.SmartsConst
 
AP_NMOE - Static variable in class ambit2.smarts.SmartsConst
 
AP_OB_Hybr - Static variable in class ambit2.smarts.SmartsConst
 
AP_R - Static variable in class ambit2.smarts.SmartsConst
 
AP_r - Static variable in class ambit2.smarts.SmartsConst
 
AP_Recursive - Static variable in class ambit2.smarts.SmartsConst
 
AP_v - Static variable in class ambit2.smarts.SmartsConst
 
AP_vMOE - Static variable in class ambit2.smarts.SmartsConst
 
AP_X - Static variable in class ambit2.smarts.SmartsConst
 
AP_x - Static variable in class ambit2.smarts.SmartsConst
 
AP_XMOE - Static variable in class ambit2.smarts.SmartsConst
 
app - Variable in class ambit2.rest.freemarker.FreeMarkerStatusService
 
appDomainMethodType - Variable in class ambit2.model.numeric.DataCoverage
 
ApplicabilityDomain - Class in ambit2.groupcontribution.utils.math
 
ApplicabilityDomain() - Constructor for class ambit2.groupcontribution.utils.math.ApplicabilityDomain
 
applicable(IAtom) - Method in class ambit2.core.processors.AbstractStructureProcessor
Used as criteria whether to assign atom types as properties e.g.
applicable(IAtom) - Method in class ambit2.core.processors.IsotopesProcessor
 
applicable - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
application - Variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
application - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
application - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
application_root - Variable in class ambit2.rest.task.LauncherResource
 
applicationConditions - Variable in class ambit2.reactions.GenericReaction
 
applicationConditionsStatus - Variable in class ambit2.reactions.GenericReactionInstance
 
applicationRoot - Variable in class ambit2.rest.task.CallableDatasetCreator
 
applicationRootReference - Variable in class ambit2.rest.model.builder.ModelBuilder
 
applicationRootReference - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
applicationRootReference - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
applicationRootReference - Variable in class ambit2.rest.task.CallablePOST
 
apply(IAtomContainer) - Method in class ambit2.reactions.fragmentation.Fragmentation
 
apply(double) - Method in class ambit2.rules.functions.ValueTransformation
 
apply(Object) - Method in interface ambit2.rules.IActionRule
 
applyArg - Variable in class ambit2.reactions.cli.AmbitSmirksCli
 
applyAromaticityTransformAtLocation(IAtomContainer, List<IAtom>, List<IAtom>, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyAtInstance(IAtomContainer, List<IAtom>, SMIRKSManager) - Method in class ambit2.reactions.GenericReaction
 
applyAtInstance(IAtomContainer, List<IAtom>, SMIRKSManager, boolean) - Method in class ambit2.reactions.GenericReaction
 
applyAtInstancesSimultaneously(IAtomContainer, List<List<IAtom>>, SMIRKSManager, boolean) - Method in class ambit2.reactions.GenericReaction
 
applyEvenIfDisconnected(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
applyHAtomTransformAtLocation(IAtomContainer, List<IAtom>, List<IAtom>, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyRule(ILocalDescriptor) - Method in interface ambit2.groupcontribution.rules.ILocalDescriptorRule
 
applyRule(IAtomContainer) - Method in class ambit2.reactions.fragmentation.FragmentationRule
 
applyRule(IAtomContainer) - Method in class ambit2.tautomers.Rule
 
applyStereoTransformAtLocation(IAtomContainer, List<IAtom>, List<IAtom>, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyStrategy(IAtomContainer, ArrayList<IRetroSynthRuleInstance>) - Method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
applyTransformation(SMIRKSManager, IAtomContainer) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
applyTransformation(IAtomContainer, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformation(IAtomContainer, IAcceptable, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformationsAtLocationsWithCloning(IAtomContainer, List<List<IAtom>>, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformationWithCombinedOverlappedPos(IAtomContainer, IAcceptable, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformationWithSingleCopyForEachPos(IAtomContainer, IAcceptable, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformationWithSingleCopyForEachPos(IAtomContainer, IAcceptable, SMIRKSReaction, SmartsConst.SSM_MODE) - Method in class ambit2.smarts.SMIRKSManager
 
applyTransformAtLocation(IAtomContainer, List<IAtom>, SMIRKSReaction) - Method in class ambit2.smarts.SMIRKSManager
 
arff - Variable in class ambit2.ml.io.OutputARFF
 
ARFF3ColReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
ARFF3ColReporter() - Constructor for class ambit2.db.reporters.ARFF3ColReporter
 
ARFF3ColReporter(Template) - Constructor for class ambit2.db.reporters.ARFF3ColReporter
 
ARFF3ColReporter(Template, Profile) - Constructor for class ambit2.db.reporters.ARFF3ColReporter
 
ARFFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
ARFFReporter() - Constructor for class ambit2.db.reporters.ARFFReporter
 
ARFFReporter(Template) - Constructor for class ambit2.db.reporters.ARFFReporter
 
ARFFReporter(Template, Profile, IProcessor...) - Constructor for class ambit2.db.reporters.ARFFReporter
 
ArffWriter - Class in ambit2.core.io
 
ArffWriter(Writer) - Constructor for class ambit2.core.io.ArffWriter
 
arffWriter - Variable in class ambit2.ml.io.OutputARFF
 
aromaticAtomEnergy - Static variable in class ambit2.tautomers.PredefinedKnowledgeBase
 
aromaticDetector - Variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
AromaticSymbolQueryAtom - Class in ambit2.smarts
 
AromaticSymbolQueryAtom(IChemObjectBuilder) - Constructor for class ambit2.smarts.AromaticSymbolQueryAtom
 
arrayBuffer - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
ArrayResult<T> - Class in ambit2.core.data
 
ArrayResult() - Constructor for class ambit2.core.data.ArrayResult
 
ArrayResult(T[]) - Constructor for class ambit2.core.data.ArrayResult
 
arrayToString(double[]) - Static method in class ambit2.model.structure.DataCoverageFingerprints
 
ArrayUtils - Class in ambit2.groupcontribution.utils.math
 
ArrayUtils() - Constructor for class ambit2.groupcontribution.utils.math.ArrayUtils
 
asBooleanQuery(int) - Method in class ambit2.core.data.HashIntDescriptorResult
 
asJSON() - Method in class ambit2.base.data.study.EffectRecord
 
asJSON() - Method in class ambit2.base.data.study.Params
 
asJSON() - Method in class ambit2.base.data.study.Value
 
Assay - Class in ambit2.export.isa.v1_0.objects
Assay JSON Schema JSON Schema describing an Assay
Assay() - Constructor for class ambit2.export.isa.v1_0.objects.Assay
 
assayFilePrefix - Static variable in class ambit2.export.isa.base.ISAConst
 
assays - Variable in class ambit2.export.isa.v1_0.objects.Study
 
assayUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
assess(Matrix) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
assessTransformed(double[], int) - Method in class ambit2.model.numeric.DataCoverageDescriptors
does not perform transformation (e.g.
assign(Property) - Method in class ambit2.base.data.Property
 
assign(SubstanceRecord, Object) - Method in class ambit2.core.io.StringArrayHeader
 
assignCASRN(IStructureRecord) - Method in class ambit2.core.io.RawIteratingFolderReader
 
assignEINECS(IStructureRecord) - Method in class ambit2.core.io.RawIteratingFolderReader
 
AssignHPDLevels(double[][]) - Method in interface ambit2.domain.stats.transforms.densityestimation.HighestDensityRegions
 
AssignHPDLevels(int) - Method in interface ambit2.domain.stats.transforms.densityestimation.HighestDensityRegions
 
AssignHPDLevels(double[][]) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
AssignHPDLevels HighestDensityRegions interface
AssignHPDLevels(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
AssignHPDLevels HighestDensityRegions interface
assignName(IStructureRecord) - Method in class ambit2.core.io.RawIteratingFolderReader
 
assignProperties - Variable in class ambit2.db.processors.AbstractDescriptorCalculator
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.model.predictor.CoveragePredictor
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
assignResults(IStructureRecord, Object) - Method in class ambit2.rest.task.weka.WekaPredictor
 
assignTitle(ObjectNode, ObjectNode, String) - Method in class ambit2.core.io.study.StudyFormatter
 
assignTransformedInstance(IStructureRecord, Instance, double) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
assignTransformedInstance(IStructureRecord, Instance, double) - Method in class ambit2.rest.task.weka.WekaPredictor
 
associateStep(int, ReactionSequenceStep) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
at1 - Variable in class ambit2.smarts.ClosureBond
 
at2 - Variable in class ambit2.smarts.ClosureBond
 
at_property - Static variable in class ambit2.core.processors.AbstractStructureProcessor
 
at_property_added - Static variable in class ambit2.core.processors.AbstractStructureProcessor
 
at_property_removed - Static variable in class ambit2.core.processors.AbstractStructureProcessor
 
AtmPressure - Static variable in class ambit2.base.ro.I5CONSTANTS
 
atom - Variable in class ambit2.core.groups.AbstractGroup.SelfIterable
 
atom - Variable in class ambit2.smarts.AtomSmartsNode
 
ATOM_ANNOTATION - Static variable in class ambit2.rendering.CompoundImageTools
 
atom_environment - Variable in class ambit2.descriptors.AtomEnvironment
 
AtomAnnotationGenerator - Class in ambit2.rendering
 
AtomAnnotationGenerator() - Constructor for class ambit2.rendering.AtomAnnotationGenerator
 
atomAttributeToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
atomClasses - Variable in class ambit2.smarts.EquivalenceTester
 
AtomClusteringCoefficient(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
atomColIndices - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
atomComplexities - Variable in class ambit2.reactions.rules.scores.MolecularComplexity
 
atomComplexity - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
AtomComplexity - Class in ambit2.reactions.rules.scores
 
AtomComplexity() - Constructor for class ambit2.reactions.rules.scores.AtomComplexity
 
atomComplexityCalculator - Variable in class ambit2.reactions.rules.scores.MolecularComplexity
 
AtomCondition - Class in ambit2.tautomers.rules
 
AtomCondition() - Constructor for class ambit2.tautomers.rules.AtomCondition
 
atomConditions - Variable in class ambit2.tautomers.rules.EnergyCorrection
 
AtomConfigurator - Class in ambit2.core.processors.structure
 
AtomConfigurator() - Constructor for class ambit2.core.processors.structure.AtomConfigurator
 
atomContainer - Variable in class ambit2.ui.Panel2D
 
atomContainers - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
atomContainerToSLNContainer(IAtomContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
atomCount - Variable in class ambit2.smarts.StructInfo
 
atomCount - Variable in class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
AtomCountHybridizationDescriptor - Class in ambit2.descriptors.constitutional
Atomistic topological indices.
AtomCountHybridizationDescriptor() - Constructor for class ambit2.descriptors.constitutional.AtomCountHybridizationDescriptor
 
AtomCountRelativeDescriptor - Class in ambit2.descriptors.constitutional
Relative atom-type count.
AtomCountRelativeDescriptor() - Constructor for class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
AtomDistance - Class in ambit2.core.data.distances
 
AtomDistance() - Constructor for class ambit2.core.data.distances.AtomDistance
 
AtomDistanceProcessor - Class in ambit2.core.data.distances
 
AtomDistanceProcessor() - Constructor for class ambit2.core.data.distances.AtomDistanceProcessor
 
AtomEnvironentMatrix - Class in ambit2.descriptors
 
AtomEnvironentMatrix() - Constructor for class ambit2.descriptors.AtomEnvironentMatrix
 
AtomEnvironentMatrix(IAtomTypeMatcher, String, int) - Constructor for class ambit2.descriptors.AtomEnvironentMatrix
 
AtomEnvironentMatrix._param - Enum in ambit2.descriptors
 
AtomEnvironment - Static variable in class ambit2.core.config.AmbitCONSTANTS
Atom environment (circular fingerprints)
AtomEnvironment - Class in ambit2.descriptors
An atom environment.
AtomEnvironment() - Constructor for class ambit2.descriptors.AtomEnvironment
3-levels
AtomEnvironment(int) - Constructor for class ambit2.descriptors.AtomEnvironment
 
AtomEnvironment(int, String, int[], int, long, int) - Constructor for class ambit2.descriptors.AtomEnvironment
 
AtomEnvironmentDescriptor - Class in ambit2.descriptors
implements atom environment fingerprint following Xing, L., Glen, R.C.
AtomEnvironmentDescriptor() - Constructor for class ambit2.descriptors.AtomEnvironmentDescriptor
 
AtomEnvironmentDescriptor._param - Enum in ambit2.descriptors
 
AtomEnvironmentDistanceType - Enum in ambit2.model.structure
Defines how to compare ambit2.data.descriptors.AtomEnvironmentDescriptor.
AtomEnvironmentGenerator - Class in ambit2.descriptors.processors
A processor to generate atom environments.
AtomEnvironmentGenerator() - Constructor for class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
AtomEnvironmentList - Class in ambit2.descriptors.processors
A list of ambit2.descriptors.data.descriptors.AtomEnvironment.
AtomEnvironmentList() - Constructor for class ambit2.descriptors.processors.AtomEnvironmentList
 
AtomEnvironmentList(int) - Constructor for class ambit2.descriptors.processors.AtomEnvironmentList
 
AtomEnvironmentList(Collection) - Constructor for class ambit2.descriptors.processors.AtomEnvironmentList
 
AtomEnvironmentMatrixDescriptor - Class in ambit2.descriptors
 
AtomEnvironmentMatrixDescriptor() - Constructor for class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
AtomEnvironmentMatrixDescriptor(IAtomTypeMatcher, String, int) - Constructor for class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
AtomEnvironmentMatrixGenerator - Class in ambit2.descriptors.processors
A processor to generate atom environments.
AtomEnvironmentMatrixGenerator() - Constructor for class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
AtomEnvironmentMatrixGenerator(int) - Constructor for class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
AtomEnvironmentMatrixWriter<S> - Class in ambit2.db.update.fpae
 
AtomEnvironmentMatrixWriter() - Constructor for class ambit2.db.update.fpae.AtomEnvironmentMatrixWriter
 
AtomEnvironmentsDistance - Class in ambit2.similarity.measure
 
AtomEnvironmentsDistance() - Constructor for class ambit2.similarity.measure.AtomEnvironmentsDistance
 
AtomEnvironmentWriter<S> - Class in ambit2.db.update.fpae
Deprecated.
AtomEnvironmentWriter() - Constructor for class ambit2.db.update.fpae.AtomEnvironmentWriter
Deprecated.
 
AtomEquivalenceInfo - Class in ambit2.smarts
 
AtomEquivalenceInfo() - Constructor for class ambit2.smarts.AtomEquivalenceInfo
 
atomExpression - Variable in class ambit2.sln.SLNAtom
 
atomFingerprintToString(int[], char) - Static method in class ambit2.descriptors.AtomEnvironment
 
AtomGroup - Class in ambit2.groupcontribution.groups
 
AtomGroup() - Constructor for class ambit2.groupcontribution.groups.AtomGroup
 
atomID - Variable in class ambit2.sln.SLNAtom
 
atomID - Variable in class ambit2.sln.SLNAtomExpression
 
atomIndex - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
AtomLabelGenerator - Class in ambit2.rendering
 
AtomLabelGenerator() - Constructor for class ambit2.rendering.AtomLabelGenerator
 
atomLayersCode - Variable in class ambit2.smarts.AtomEquivalenceInfo
 
atomName - Variable in class ambit2.sln.SLNAtom
 
atomno - Variable in class ambit2.descriptors.AtomEnvironment
 
atomNums - Variable in class ambit2.smarts.QuerySequenceElement
 
AtomPairCorrectionFactor - Class in ambit2.groupcontribution.correctionfactors
 
AtomPairCorrectionFactor(String, String, int, SmartsParser, IsomorphismTester) - Constructor for class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
AtomPairCorrectionFactor(String, String, SmartsParser, IsomorphismTester) - Constructor for class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
AtomPairCorrectionFactor(String, String, int, SmartsParser, IsomorphismTester, IValueTransformation) - Constructor for class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
AtomPrimChars - Static variable in class ambit2.smarts.SmartsConst
 
atomPropertiesToString(IAtom) - Static method in class ambit2.smarts.SmartsHelper
 
atomrendermode - Variable in class ambit2.ui.Panel2D
 
atomRingNumbers - Variable in class ambit2.structure2name.IUPACNameGenerator
 
atoms - Variable in class ambit2.core.groups.AbstractGroup
 
atoms - Variable in class ambit2.core.groups.SuppleAtomContainer
 
atoms() - Method in class ambit2.core.groups.SuppleAtomContainer
 
atoms - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironmentInstance
 
atoms - Variable in class ambit2.groupcontribution.nmr.SubstituentInstance
 
atoms - Variable in class ambit2.smarts.Node
 
atoms - Variable in class ambit2.smarts.QuerySequenceElement
 
atoms - Variable in class ambit2.smarts.TopLayer
 
atoms - Variable in class ambit2.structure2name.components.AbstractComponent
 
atoms - Variable in class ambit2.tautomers.RuleInstance
 
AtomSmartsNode - Class in ambit2.smarts
 
AtomSmartsNode() - Constructor for class ambit2.smarts.AtomSmartsNode
 
atomSpinAttrToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
atomStereoChemAttrToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
atomSymbol - Variable in class ambit2.structure2name.rules.FunctionalGroupData
 
atomToSLNAtom(IAtom) - Method in class ambit2.sln.io.SLN2ChemObject
 
atomToString(IAtom) - Static method in class ambit2.smarts.SmartsHelper
 
atomType - Variable in class ambit2.sln.SLNAtom
 
atomtypeasproperties - Variable in class ambit2.core.processors.AbstractStructureProcessor
 
atomTypes - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
atomTypes - Variable in class ambit2.descriptors.AtomEnvironmentDescriptor
 
atomtypes2properties(IAtomContainer) - Static method in class ambit2.core.processors.AbstractStructureProcessor
 
atomtypes2properties_init(IAtomContainer) - Static method in class ambit2.core.processors.AbstractStructureProcessor
 
atomtypes2property(IAtomContainer, Object, boolean) - Method in class ambit2.core.processors.AbstractStructureProcessor
 
atomtypes2property(String, IAtomContainer, Object, boolean) - Method in class ambit2.core.processors.AbstractStructureProcessor
 
atomTypeToString(int) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
atomTypeToString(int) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
AtomTypeVerifierDescriptor - Class in ambit2.descriptors
 
AtomTypeVerifierDescriptor() - Constructor for class ambit2.descriptors.AtomTypeVerifierDescriptor
 
atomtypingonsmiles - Variable in class ambit2.core.processors.structure.MoleculeReader
 
attachDepict - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
attachDepictRouter() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
attachGroupToAllStructures(String, int, ArrayList<String>, int) - Method in class ambit2.smarts.ChemObjectFactory
 
attachInvestigation - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
attachInvestigationRouter() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
attachment - Variable in class ambit2.core.io.I5ReaderSimple
 
attachSubstance - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
attachSubstanceOwner - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
attachSubstanceOwnerRouter() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
attachSubstanceRouter() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
attachToxmatch - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
attachToxmatchRouter() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
attributes - Variable in class ambit2.core.io.ToXMLReaderSimple
 
attributes - Variable in class ambit2.rest.rdf.RDFInstancesIterator
 
attributeSelection - Variable in class ambit2.model.AbstractModel
 
attributeSelection - Variable in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
attrName - Variable in class ambit2.sln.SLNExpressionToken
 
authorList - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
autosizecolumn - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
AverageMolecularWeightDescriptor - Class in ambit2.descriptors.constitutional
Average molecular weight.
AverageMolecularWeightDescriptor() - Constructor for class ambit2.descriptors.constitutional.AverageMolecularWeightDescriptor
 
avg - Variable in class ambit2.base.data.PropertyStats
 
AWTDrawVisitorWithImageMap - Class in ambit2.rendering
Implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing.
AWTDrawVisitorWithImageMap(Graphics2D) - Constructor for class ambit2.rendering.AWTDrawVisitorWithImageMap
Constructs a new IDrawVisitor using the AWT widget toolkit, taking a Graphics2D object to which the chemical content is drawn.

B

b - Variable in class ambit2.db.simiparity.space.QMapSpace
 
b - Static variable in class ambit2.similarity.stats.DoubleValuesHistogram
 
b64search_param - Static variable in class ambit2.rest.AbstractResource
 
B_ATTR_s - Static variable in class ambit2.sln.SLNConst
 
B_ATTR_USER_DEFINED - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_C - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_E - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_I - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_N - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_T - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_U - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_U_ - Static variable in class ambit2.sln.SLNConst
 
B_STEREO_Z - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_1 - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_2 - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_3 - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_ANY - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_aromatic - Static variable in class ambit2.sln.SLNConst
 
B_TYPE_USER_DEFINED - Static variable in class ambit2.sln.SLNConst
 
babel - Variable in class ambit2.core.smiles.SmilesParserWrapper
 
back(ActionEvent) - Method in class ambit2.ui.WizardPanel
 
background - Variable in class ambit2.rendering.CompoundImageTools
 
BALLOON_EXE - Static variable in class ambit2.balloon.ShellBalloon
 
BALLOON_HOME - Static variable in class ambit2.balloon.ShellBalloon
 
Bandwidth - Class in ambit2.domain.stats.transforms.densityestimation
Bandwidth calculation for Kernel density estimation ambit2.stats.transforms.densityestimation.KDensity1D
Bandwidth() - Constructor for class ambit2.domain.stats.transforms.densityestimation.Bandwidth
 
bar - Variable in class ambit2.ui.editors.ListEditor
 
BarChartGenerator<T extends ISourceDataset> - Class in ambit2.db.chart
 
BarChartGenerator() - Constructor for class ambit2.db.chart.BarChartGenerator
 
BarChartGeneratorDataset - Class in ambit2.db.chart
 
BarChartGeneratorDataset() - Constructor for class ambit2.db.chart.BarChartGeneratorDataset
 
base_sql - Static variable in class ambit2.db.search.property.AbstractPropertyRetrieval
 
base_sql_type_confidence - Static variable in class ambit2.db.search.property.PropertiesByDataset
 
baseRef - Variable in class ambit2.rest.reporters.TaskRDFReporter
 
baseReference - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
baseReference - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
baseReference - Variable in class ambit2.rest.RDFBatchParser
 
baseReference - Variable in class ambit2.rest.reporters.CatalogURIReporter
 
BASEURL_DEPTH - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
basic4Permutation - Static variable in class ambit2.smarts.ChiralPermutations
 
basicScore - Variable in class ambit2.reactions.GenericReaction
 
basicScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
basicScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
batch - Variable in class ambit2.base.processors.batch.BatchReporter
 
batch - Variable in class ambit2.rest.task.CallableQueryProcessor
 
BatchDBProcessor<ITEMTYPE> - Class in ambit2.db.processors
Reads file
BatchDBProcessor() - Constructor for class ambit2.db.processors.BatchDBProcessor
 
BatchDBProcessor(ProcessorsChain<ITEMTYPE, IBatchStatistics, IProcessor>) - Constructor for class ambit2.db.processors.BatchDBProcessor
 
BatchProcessor<INPUT,Target> - Class in ambit2.base.processors.batch
 
BatchProcessor() - Constructor for class ambit2.base.processors.batch.BatchProcessor
 
BatchProcessor(ProcessorsChain<Target, IBatchStatistics, IProcessor>) - Constructor for class ambit2.base.processors.batch.BatchProcessor
 
BatchReporter<Item,ItemList,Output> - Class in ambit2.base.processors.batch
Batch reporter
BatchReporter() - Constructor for class ambit2.base.processors.batch.BatchReporter
 
BatchRetrievePubChem - Class in ambit2.pubchem
 
BatchRetrievePubChem() - Constructor for class ambit2.pubchem.BatchRetrievePubChem
 
BatchStructuresListProcessor - Class in ambit2.db.processors
 
BatchStructuresListProcessor() - Constructor for class ambit2.db.processors.BatchStructuresListProcessor
 
BeanEditor<L> - Class in ambit2.ui.editors
Generic editor
BeanEditor(L, String[], String) - Constructor for class ambit2.ui.editors.BeanEditor
 
BeanEditor(L, String[], String[], String) - Constructor for class ambit2.ui.editors.BeanEditor
 
beforeFirst() - Method in class ambit2.db.results.AmbitRows
 
beforeHandle(Request, Response) - Method in class ambit2.rest.OriginFilter
 
beforeProcessing(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
beforeProcessing(IQueryRetrieval<ResultType>) - Method in class ambit2.db.DbReader
 
beforeProcessing(Reference) - Method in class ambit2.rest.RDFBatchParser
 
beginState - Variable in class ambit2.tautomers.RuleInstance
 
biboPrefix - Static variable in class ambit2.base.data.ChEMBLProperties
 
BibTex - Class in ambit2.rest.rdf
 
BibTex() - Constructor for class ambit2.rest.rdf.BibTex
 
BibTex.BTClass - Enum in ambit2.rest.rdf
 
BIG_INTEGER - Static variable in class ambit2.core.filter.MoleculeFilter
 
Bin<T extends Comparable> - Class in ambit2.similarity.stats
 
Bin(T, T) - Constructor for class ambit2.similarity.stats.Bin
 
BinaryCombinations - Class in ambit2.smarts
 
BinaryCombinations() - Constructor for class ambit2.smarts.BinaryCombinations
 
BinaryKernelDistance - Class in ambit2.similarity.measure
Binary Kernel Discrimination method applied to fingerprints (bitset).
BinaryKernelDistance() - Constructor for class ambit2.similarity.measure.BinaryKernelDistance
 
binNumber - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
bins(int) - Static method in class ambit2.domain.stats.Tools
 
binWidth - Variable in class ambit2.db.chart.XTabChartGenerator
 
bitmap - Variable in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
bitset2bigint16(BitSet, int, BigInteger[]) - Static method in class ambit2.core.data.MoleculeTools
 
bitset2Long(BitSet) - Static method in class ambit2.core.data.MoleculeTools
 
bitset2params(BitSet, List<QueryParam>) - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
bitset2String(BitSet) - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
TODO this is inefficient, convert to hex or use org.openscience.cdk.fingerprint.io.FPSWriter
bitSetCheck(BitSet, BitSet) - Method in class ambit2.smarts.Screening
Every bit set on in the query shouldbe present inthe target but the target can have more bits set on compared to the query
bitSetCheck(BitSet, BitSet, int) - Method in class ambit2.smarts.Screening
 
BitSetGenerator - Class in ambit2.descriptors.processors
Given IStructureRecord generates fingerprint and assigns it to the relevant properties of IStructureRecord
BitSetGenerator() - Constructor for class ambit2.descriptors.processors.BitSetGenerator
 
BitSetGenerator(FPTable) - Constructor for class ambit2.descriptors.processors.BitSetGenerator
 
bitsets - Variable in class ambit2.rest.model.predictor.FingerprintsPredictor
 
blackFont - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
blackFont - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
blank - Variable in class ambit2.mopac.Mopac7Writer
 
blocks - Variable in class ambit2.dragon.DragonDescriptorDictionary
 
blueFont - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
blueFont - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
blueStyle - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
BOILINGPOINT - Static variable in class ambit2.base.ro.I5CONSTANTS
 
BonchevCentricInformationIndicesDescriptor - Class in ambit2.descriptors.topological
 
BonchevCentricInformationIndicesDescriptor() - Constructor for class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
bondAtomNumbersToString(IAtomContainer, IBond) - Static method in class ambit2.smarts.SmartsHelper
 
bondAttributeToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
bondChange(IAtom, IAtom, IBond.Order, IBond.Order, IAtomContainer, TetrahedralChirality, StereoChange) - Static method in class ambit2.smarts.smirks.StereoTransformation
 
bondChange(IAtom, IAtom, IBond.Order, IBond.Order, IAtomContainer, DoubleBondStereochemistry, StereoChange) - Static method in class ambit2.smarts.smirks.StereoTransformation
 
bondChange(IAtom, IAtom, IBond.Order, IBond.Order, IAtomContainer, TetrahedralChirality) - Static method in class ambit2.smarts.StereoChemUtils
 
bondChange(IAtom, IAtom, IBond.Order, IBond.Order, IAtomContainer, ExtendedTetrahedral) - Static method in class ambit2.smarts.StereoChemUtils
 
bondChange(IAtom, IAtom, IBond.Order, IBond.Order, IAtomContainer, DoubleBondStereochemistry, StereoChange) - Static method in class ambit2.smarts.StereoChemUtils
 
BondChars - Static variable in class ambit2.smarts.SmartsConst
 
bondCount - Variable in class ambit2.smarts.StructInfo
 
bondCount - Variable in class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
bondDirectionToString(int) - Static method in class ambit2.smarts.SmartsConst
 
bondExpression - Variable in class ambit2.sln.SLNBond
 
BondGroup - Class in ambit2.groupcontribution.groups
 
BondGroup() - Constructor for class ambit2.groupcontribution.groups.BondGroup
 
bondOrder - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
bondOrderToIntValue(IBond) - Static method in class ambit2.smarts.SmartsHelper
 
bondPropertiesReader - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
bondPropertiesReader - Variable in class ambit2.descriptors.processors.BitSetGenerator
 
bonds - Variable in class ambit2.core.groups.AbstractGroup
 
bonds - Variable in class ambit2.core.groups.SuppleAtomContainer
 
bonds() - Method in class ambit2.core.groups.SuppleAtomContainer
 
bonds - Variable in class ambit2.smarts.QuerySequenceElement
 
bonds - Variable in class ambit2.smarts.TopLayer
 
bonds - Variable in class ambit2.tautomers.RuleInstance
 
bondStereoChemistryAttributeToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
bondToSLNBond(IBond) - Method in class ambit2.sln.io.SLN2ChemObject
 
bondToString(IBond) - Static method in class ambit2.smarts.SmartsHelper
 
bondToStringExhaustive(IQueryAtomContainer, IBond) - Static method in class ambit2.smarts.SmartsHelper
 
bondType - Variable in class ambit2.sln.SLNBond
 
bondTypeAttributeToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
bondTypeAttributeToSLNString(int, boolean) - Static method in class ambit2.sln.SLNConst
 
Bookmark - Class in ambit2.base.data
http://www.w3.org/2003/07/Annotea/BookmarkSchema-20030707
Bookmark() - Constructor for class ambit2.base.data.Bookmark
 
Bookmark(String) - Constructor for class ambit2.base.data.Bookmark
 
Bookmark._fields - Enum in ambit2.base.data
 
Bookmark.ResourceType - Enum in ambit2.base.data
 
BookmarksByTopicFacet - Class in ambit2.db.facets.bookmarks
 
BookmarksByTopicFacet() - Constructor for class ambit2.db.facets.bookmarks.BookmarksByTopicFacet
 
BookmarksByTopicFacetQuery - Class in ambit2.db.facets.bookmarks
 
BookmarksByTopicFacetQuery(String) - Constructor for class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
bootStrap - Variable in class ambit2.groupcontribution.GCMTestConfig
 
bootStrapIterations - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
border - Variable in class ambit2.ui.DelimitersPanel
 
borderColor - Variable in class ambit2.rendering.CompoundImageTools
 
BorderColor - Static variable in class ambit2.ui.editors.ClassHolderEditor
 
borderWidth - Variable in class ambit2.rendering.CompoundImageTools
 
boxcox - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
boxes - Variable in class ambit2.ui.DelimitersPanel
 
bracketLeft - Static variable in class ambit2.core.data.MoleculeTools
 
bracketRight - Static variable in class ambit2.core.data.MoleculeTools
 
branches - Variable in class ambit2.core.io.ToXMLReaderSimple
 
BrowsableTableModel - Class in ambit2.ui.table
 
BrowsableTableModel() - Constructor for class ambit2.ui.table.BrowsableTableModel
 
BrowsableTableModel(TableModel) - Constructor for class ambit2.ui.table.BrowsableTableModel
 
browse - Variable in class ambit2.ui.editors.FileSelector
 
browser - Variable in class ambit2.dbui.dictionary.AmbitRowsPanel
 
browser_table - Variable in class ambit2.ui.QueryBrowser
 
browserMode - Variable in class ambit2.ui.table.BrowsableTableModel
 
BrowserModeCellRenderer - Class in ambit2.ui
 
BrowserModeCellRenderer(IBrowserMode.BrowserMode) - Constructor for class ambit2.ui.BrowserModeCellRenderer
 
BrowserModeNavigator - Class in ambit2.ui.table
 
BrowserModeNavigator(IBrowserMode) - Constructor for class ambit2.ui.table.BrowserModeNavigator
 
bt - Variable in class ambit2.smarts.ClosureBond
 
BT_ANY - Static variable in class ambit2.smarts.SmartsConst
 
BT_AROMATIC - Static variable in class ambit2.smarts.SmartsConst
 
BT_CIS - Static variable in class ambit2.smarts.SmartsConst
 
BT_CISUNSPEC - Static variable in class ambit2.smarts.SmartsConst
 
BT_DOUBLE - Static variable in class ambit2.smarts.SmartsConst
 
BT_DOWN - Static variable in class ambit2.smarts.SmartsConst
 
BT_DOWNUNSPEC - Static variable in class ambit2.smarts.SmartsConst
 
BT_RING - Static variable in class ambit2.smarts.SmartsConst
 
BT_SINGLE - Static variable in class ambit2.smarts.SmartsConst
 
BT_TRANS - Static variable in class ambit2.smarts.SmartsConst
 
BT_TRANSUNSPEC - Static variable in class ambit2.smarts.SmartsConst
 
BT_TRIPLE - Static variable in class ambit2.smarts.SmartsConst
 
BT_UNDEFINED - Static variable in class ambit2.smarts.SmartsConst
 
BT_UP - Static variable in class ambit2.smarts.SmartsConst
 
BT_UPUNSPEC - Static variable in class ambit2.smarts.SmartsConst
 
BucketJson2CSVConvertor - Class in ambit2.rest.study
 
BucketJson2CSVConvertor(String) - Constructor for class ambit2.rest.study.BucketJson2CSVConvertor
 
BucketJson2CSVConvertor(String[], String[], String[], String[]) - Constructor for class ambit2.rest.study.BucketJson2CSVConvertor
 
BucketJson2CSVConvertor(String[], String[], String[], String[], String) - Constructor for class ambit2.rest.study.BucketJson2CSVConvertor
 
build() - Method in interface ambit2.base.data.IModel
Builds (trains) the model.
build(Matrix) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
build(Matrix) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
build(Matrix) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
build(DATA) - Method in interface ambit2.model.numeric.IDataCoverage
 
build(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
build2D - Variable in class ambit2.core.processors.StructureNormalizer
 
build2d(IAtomContainer, IStructureRecord.STRUC_TYPE) - Method in class ambit2.core.processors.StructureNormalizer
 
buildCenter(String, Component) - Method in class ambit2.ui.WizardPanel
 
buildDataset(String, String, String[], Form, String) - Method in class ambit2.rest.task.CallableBuilder
 
buildDocument() - Method in class ambit2.base.data.Template
 
builder - Variable in class ambit2.core.processors.StructureNormalizer
 
builder - Variable in class ambit2.db.search.structure.QuerySMARTS
 
builder - Variable in class ambit2.rest.model.task.CallableModelCreator
 
builder - Variable in class ambit2.smarts.SmartsManager
 
builder - Variable in class ambit2.smarts.SmartsToChemObject
 
builder - Variable in class ambit2.smarts.SMIRKSReaction
 
buildFields(PanelBuilder, CellConstraints) - Method in class ambit2.ui.editors.BeanEditor
 
buildGraphicsPanel() - Method in class ambit2.ui.WizardPanel
 
buildHelpPanel(String) - Method in class ambit2.ui.WizardPanel
 
buildInitialize() - Method in class ambit2.similarity.AbstractSimilarityModel
 
buildInitialize() - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
buildLeft(String) - Method in class ambit2.ui.WizardPanel
 
buildMainPanel(String, Component) - Method in class ambit2.ui.WizardPanel
 
buildNavigation(boolean, String) - Method in class ambit2.ui.WizardPanel
 
buildPanel() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
buildPanel(String) - Method in class ambit2.dbui.dictionary.OntologyEditor
 
buildPanel() - Method in class ambit2.dbui.QueryDatasetEditor
 
buildPanel() - Method in class ambit2.dbui.QueryEditor
 
buildPanel() - Method in class ambit2.dbui.QueryFieldEditor
 
buildPanel() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
buildPanel() - Method in class ambit2.dbui.QueryFunctionalGroupsEditor
 
buildPanel() - Method in class ambit2.dbui.QueryInfoEditor
 
buildPanel() - Method in class ambit2.dbui.QuerySimilarityEditor
 
buildPanel() - Method in class ambit2.dbui.QuerySmartsEditor
 
buildPanel() - Method in class ambit2.dbui.QueryStoredResultsEditor
 
buildPanel(T) - Method in class ambit2.ui.AbstractPanel
 
buildPanel(L, String[], String[]) - Method in class ambit2.ui.editors.BeanEditor
 
buildPanel() - Method in class ambit2.ui.editors.FileSelector
 
buildPanel() - Method in class ambit2.ui.editors.ListEditor
 
buildPanel(String) - Method in class ambit2.ui.editors.SelectFieldsPanel
 
buildPanel(IBrowserMode) - Method in class ambit2.ui.table.BrowserModeNavigator
 
buildPanel(IFindNavigator) - Method in class ambit2.ui.table.FindNavigator
 
buildPanel(IPageNavigator) - Method in class ambit2.ui.table.PageNavigator
 
buildPanel(IRecordNavigator) - Method in class ambit2.ui.table.RecordNavigator
 
buildPanel(Component, Component, Component) - Method in class ambit2.ui.WizardPanel
 
buildPanel(FormLayout) - Method in class ambit2.ui.WizardPanel
 
buildPopupMenu(Component, Object, int, int, JPopupMenu) - Method in class ambit2.ui.QueryBrowser
 
buildStart() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
built - Variable in class ambit2.model.AbstractModel
 
bundle - Variable in class ambit2.db.substance.processor.DBBundleStudyWriter
 
bundle - Variable in class ambit2.db.substance.QueryCountProtocolApplications
 
bundle - Variable in class ambit2.db.substance.relation.ReadSubstanceComposition
 
bundle - Variable in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
bundle - Variable in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
bundle - Variable in class ambit2.db.update.bundle.effects.ReadEffectRecordByBundle
 
bundle - Variable in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
bundle_number - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
bundleDescriptionLoc - Variable in class ambit2.export.isa.ISAExportConfig
 
bundleDescriptionLocString - Variable in class ambit2.export.isa.ISAExportConfig
 
BundleOwnerByNumber - Class in ambit2.db.update.bundle
Query to check bundle owner by bundle number
BundleOwnerByNumber() - Constructor for class ambit2.db.update.bundle.BundleOwnerByNumber
 
bundleRole - Variable in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
BundleRoleFacet - Class in ambit2.base.facet
 
BundleRoleFacet(String) - Constructor for class ambit2.base.facet.BundleRoleFacet
 
bundles - Variable in class ambit2.db.reporters.CSVReporter
 
bundles - Variable in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
BundleStudyFacetQuery - Class in ambit2.db.update.bundle.effects
 
BundleStudyFacetQuery(String) - Constructor for class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
BundleSummaryFacet - Class in ambit2.db.facets.bundle
 
BundleSummaryFacet(String) - Constructor for class ambit2.db.facets.bundle.BundleSummaryFacet
 
BundleSummaryQuery - Class in ambit2.db.facets.bundle
 
BundleSummaryQuery(String) - Constructor for class ambit2.db.facets.bundle.BundleSummaryQuery
 
bundleTitleLoc - Variable in class ambit2.export.isa.ISAExportConfig
 
bundleTitleLocString - Variable in class ambit2.export.isa.ISAExportConfig
 
button - Variable in class ambit2.ui.table.BrowserModeNavigator
 
buttons - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
buttons - Variable in class ambit2.ui.editors.SelectFieldsPanel
 

C

c - Variable in class ambit2.db.simiparity.space.QMapSpace
 
c1 - Static variable in class ambit2.smarts.BinaryCombinations
 
c2 - Static variable in class ambit2.smarts.BinaryCombinations
 
c3 - Static variable in class ambit2.smarts.BinaryCombinations
 
cache(String, String, ResultType, boolean) - Method in class ambit2.db.DbReader
Does nothing, otherwise should cache the query result
cache - Variable in class ambit2.db.DbReaderStructure
 
cache(String, String, IStructureRecord, boolean) - Method in class ambit2.db.DbReaderStructure
 
cache - Variable in class ambit2.db.reporters.AbstractImageReporter
 
cache(IStructureRecord, BufferedImage) - Method in class ambit2.db.reporters.AbstractImageReporter
 
cache - Variable in class ambit2.db.StatementExecutor
 
cache - Variable in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
CachedImage<MORE> - Class in ambit2.rendering
 
CachedImage(BufferedImage, String) - Constructor for class ambit2.rendering.CachedImage
 
CachedRowSetFactory - Class in ambit2.db
 
CachedRowSetFactory() - Constructor for class ambit2.db.CachedRowSetFactory
 
CachedRowSetTableModel - Class in ambit2.dbui
 
CachedRowSetTableModel() - Constructor for class ambit2.dbui.CachedRowSetTableModel
 
cacheUpdater - Variable in class ambit2.db.DbReaderStructure
 
cacheUpdater - Variable in class ambit2.db.reporters.AbstractImageReporter
 
CACTVS_ENERGY_RANK - Static variable in class ambit2.tautomers.TautomerConst
 
CACTVSRanking - Class in ambit2.tautomers
 
CACTVSRanking() - Constructor for class ambit2.tautomers.CACTVSRanking
 
calc - Variable in class ambit2.db.processors.DescriptorsCalculator
 
calcAlkeneHShifts(HAtomEnvironmentInstance, int) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
calcAllTautomersAndAllRanks(IAtomContainer) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
calcAtomComplexity(String, boolean) - Static method in class ambit2.reactions.cli.ComplexityCli
 
calcAtomComplexity(IAtom, IAtomContainer) - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
calcAtomFragments(Fragmentation, DataSetObject, Map<IAtom, int[]>, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcAtomGroup(IAtom, IAtomContainer, GroupContributionModel) - Static method in class ambit2.groupcontribution.Calculator
 
calcAtomLocalDescriptors(IAtomContainer, List<ILocalDescriptor>) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcAtomTopDegrees(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
calcAtomTopDegrees(IAtomContainer, boolean) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
calcBondFragments(Fragmentation, DataSetObject, Map<IAtom, int[]>, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcBondGroup(IBond, IAtomContainer, GroupContributionModel) - Static method in class ambit2.groupcontribution.Calculator
 
calcCACTVSEnergyRanks(List<IAtomContainer>) - Static method in class ambit2.tautomers.TautomerManager
 
calcCorrectionFactors(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcDecriptorValuesForMolecule(IAtomContainer, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
calcDescritptor(IAtomContainer, IMolecularDescriptor, int) - Static method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
calcDGroupFragments(Fragmentation, DataSetObject, Map<IAtom, int[]>, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcDistance(double[], double[], int) - Method in class ambit2.model.numeric.DataCoverageDistance
 
calcDistribution(IQueryAtomContainer) - Method in class ambit2.tautomers.RuleStateBondDistribution
 
calcForAtom(IAtom, IAtomContainer) - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
calcForAtom(IAtom, IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
calcForAtoms(IAtom[], IAtomContainer) - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
calcForAtoms(IAtom[], IAtomContainer) - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
calcGGroupFragments(Fragmentation, DataSetObject, Map<IAtom, int[]>, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcHomoLumo(IAtomContainer) - Method in class ambit2.mopac.Mopac7Reader
 
calcHShift(HAtomEnvironmentInstance) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
calcLGroupFragments(Fragmentation, DataSetObject, Map<IAtom, int[]>, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calcModelValue(IAtomContainer, boolean) - Method in class ambit2.groupcontribution.GroupContributionModel
 
calcModelValue(IAtomContainer) - Method in class ambit2.groupcontribution.GroupContributionModel
 
calcModelValue(DataSetObject, boolean) - Method in class ambit2.groupcontribution.GroupContributionModel
 
calcMolecularComplexity01() - Method in class ambit2.reactions.rules.scores.MolecularComplexity
Proudfood paper, CM = sum{CA_i}
calcMolecularComplexity02() - Method in class ambit2.reactions.rules.scores.MolecularComplexity
Proudfood paper, CM* = log(sum{2^CA_i})
calcNodeHash() - Method in class ambit2.reactions.reactor.ReactorNode
 
calcReactionScore(GenericReactionInstance) - Method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
calcRingSet() - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
calcScoreRank(IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
calcSmartsDataForTarget(IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
calcSyntheticAccessibility(IAtomContainer) - Method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
calcTautomerRankCorrCoeff(double[], double[]) - Static method in class ambit2.tautomers.tools.TautomerAnalysis
 
calcTautomerRankingMeasure(double[], double[]) - Static method in class ambit2.tautomers.tools.TautomerAnalysis
This is a measure for the tautomer ranking based on a comparison with tautomers energies
calcTautomerRankSpearmanCorrCoeff(double[], double[], boolean) - Static method in class ambit2.tautomers.tools.TautomerAnalysis
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
This method calculates the atom environment of an atom.
calculate(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
This method calculates the atom environment of an atom.
calculate(IAtomContainer) - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.constitutional.DerivedMolecularWeightDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.CrossSectionalDiameterDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.InChI
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.MaximumDiameterDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.MolecularWeight
Calculate the weight of specified element type in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class ambit2.descriptors.PKASmartsDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.PlanarityDescriptor
 
calculate(ITEM) - Method in class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.SizeDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.SpherosityDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.topological.CTIDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
calculate(IAtomContainer) - Method in class ambit2.dragon.DescriptorDragonShell
 
calculate(IAtomContainer) - Method in class ambit2.mopac.DescriptorMopacShell
 
calculate(IAtomContainer) - Method in class ambit2.some.DescriptorSOMEShell
 
calculateAverageDistance(Features, List<DistanceComparable<Features>>) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
Weighted average Sum((1/distance)*property).
calculateConditionsStatus() - Method in class ambit2.reactions.GenericReactionInstance
 
calculateCounts(IAtomContainer) - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
calculateCounts(IAtomContainer) - Method in class ambit2.descriptors.constitutional.AtomCountHybridizationDescriptor
 
calculateCounts(IAtomContainer) - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
calculateCounts(IAtomContainer) - Method in class ambit2.descriptors.constitutional.HeteroAtomCountDescriptor
 
calculatedDescrData - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
calculateDerivedValue(IAtomContainer, double) - Method in class ambit2.descriptors.constitutional.AverageMolecularWeightDescriptor
 
calculateDerivedValue(IAtomContainer, double) - Method in class ambit2.descriptors.constitutional.CubicRootMolecularWeightDescriptor
 
calculateDerivedValue(IAtomContainer, double) - Method in class ambit2.descriptors.constitutional.DerivedMolecularWeightDescriptor
 
calculateDerivedValue(IAtomContainer, double) - Method in class ambit2.descriptors.constitutional.SquareRootMolecularWeightDescriptor
 
calculateDescriptor(String, Object) - Method in class ambit2.reactions.reactor.ReactorDescriptorSolver
 
calculateDescriptor(String, Object) - Method in class ambit2.reactions.rules.SyntheticStrategyDescriptorSolver
 
calculateDescriptor(String, Object) - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
calculateDescriptor(String, Object) - Method in interface ambit2.rules.conditions.IDescriptorSolver
 
calculateDescriptor(String, Object) - Method in class ambit2.rules.conditions.solvers.CDKDescriptorSolver
 
calculateDescriptors(OTDataset) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Identify which descriptors are used as independent variables and have valid ot:algorithm entry and run the calculations
calculateDescriptors(OTFeatures, OTDataset) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Run descriptor calculations for specified set of features
calculateDescriptors(OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
calculateDescriptors(OTFeatures, OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
calculateError(Double, Double) - Method in class ambit2.similarity.stats.PredictionModelStatistics
 
calculateExprValue(Object) - Method in class ambit2.rules.conditions.DescriptorExpression
 
calculateFor(IAtomContainer) - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
calculateFor(IAtomContainer) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
calculateFor(IAtomContainer) - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
calculateFor(IAtomContainer) - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
calculateHMatrixUsingInvC(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.ApplicabilityDomain
 
calculateHShifts() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
calculateLocalDescriptors(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
calculateMaxMinProperty(NearestNeighborsSearch<T>) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
calculateMetric(T) - Method in class ambit2.db.cache.QueryCachedResults
 
calculateMetric(StructureRelation) - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
calculateMetric(BookmarksByTopicFacet) - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
calculateMetric(BundleSummaryFacet) - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
calculateMetric(BundleRoleFacet) - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
calculateMetric(BundleRoleFacet) - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
calculateMetric(BundleRoleFacet) - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
calculateMetric(IFacet<String>) - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
calculateMetric(EndpointCompoundFacet) - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
calculateMetric(FACET) - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
calculateMetric(PropertyDatasetFacet<Property, SourceDataset>) - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
calculateMetric(DatasetConsensusLabelFacet) - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
calculateMetric(DatasetStructureQLabelFacet) - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
calculateMetric(DatasetStrucTypeFacet) - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
calculateMetric(R) - Method in class ambit2.db.readers.AbstractStructureRetrieval
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.readers.ReadChemicalIds
 
calculateMetric(SourceDataset) - Method in class ambit2.db.readers.RetrieveDatasets
 
calculateMetric(DescriptorValue) - Method in class ambit2.db.readers.RetrieveDescriptor
 
calculateMetric(Object) - Method in class ambit2.db.readers.RetrieveField
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
calculateMetric(ResultType) - Method in class ambit2.db.readers.RetrieveModelTemplates
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.readers.RetrieveProfileValues
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
calculateMetric(ResultType) - Method in class ambit2.db.readers.RetrieveTemplate
 
calculateMetric(Dictionary) - Method in class ambit2.db.search.DictionaryQuery
 
calculateMetric(Property) - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
calculateMetric(PropertyStats<T>) - Method in class ambit2.db.search.property.FilteredCount
 
calculateMetric(PropertyTemplateStats) - Method in class ambit2.db.search.property.PropertyCount
 
calculateMetric(Range) - Method in class ambit2.db.search.property.PropertyRange
 
calculateMetric(PropertyStats) - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
calculateMetric(String) - Method in class ambit2.db.search.property.PropertyStatsString
 
calculateMetric(Range<Double>) - Method in class ambit2.db.search.property.QueryMetricRange
 
calculateMetric(Property) - Method in class ambit2.db.search.property.QueryOntology
 
calculateMetric(SimilarityRelation) - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
calculateMetric(QLabel) - Method in class ambit2.db.search.qlabel.QueryConsensus
 
calculateMetric(String) - Method in class ambit2.db.search.qlabel.QueryConsensus
 
calculateMetric(QLabel) - Method in class ambit2.db.search.qlabel.QueryQLabel
 
calculateMetric(T) - Method in class ambit2.db.search.QueryCombined
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.QuerySmilesByID
 
calculateMetric(AmbitUser) - Method in class ambit2.db.search.QueryUser
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
calculateMetric(ChemSpaceCell) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
calculateMetric(IStructureRecord[]) - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairs
 
calculateMetric(IStructureRecord[]) - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QuerySimilarityBitset
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QuerySMARTS
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.search.structure.ScopeQuery
 
calculateMetric(QMap) - Method in class ambit2.db.simiparity.space.QueryQMap
 
calculateMetric(QMapSpace) - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
calculateMetric(SubstanceRecord) - Method in class ambit2.db.substance.AbstractReadSubstance
 
calculateMetric(ExternalIdentifier) - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
calculateMetric(CompositionRelation) - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
calculateMetric(IStructureRecord) - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
calculateMetric(OwnerFacet) - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
calculateMetric(SubstanceStudyFacet) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
calculateMetric(ER) - Method in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
calculateMetric(ProtocolApplication) - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
calculateMetric(List<ProtocolApplication>) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
calculateMetric(Bookmark) - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
calculateMetric(Bookmark) - Method in class ambit2.db.update.bookmark.ReadBookmark
 
calculateMetric(Integer) - Method in class ambit2.db.update.bundle.BundleOwnerByNumber
 
calculateMetric(SubstanceByCategoryFacet) - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
calculateMetric(M) - Method in class ambit2.db.update.dataset.AbstractReadDataset
 
calculateMetric(FACET) - Method in class ambit2.db.update.dataset.QueryCount
 
calculateMetric(String) - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
calculateMetric(IFingerprint<FPTable, String>) - Method in class ambit2.db.update.fp.QueryFingerprints
 
calculateMetric(ModelQueryResults) - Method in class ambit2.db.update.model.QueryModel
 
calculateMetric(ModelQueryResults) - Method in class ambit2.db.update.model.ReadModel
 
calculateMetric(PropertyAnnotation) - Method in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
calculateMetric(SessionID) - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
calculateMetric(ILiteratureEntry) - Method in class ambit2.db.update.reference.ReadReference
 
calculateMetric(ISourceDataset) - Method in class ambit2.db.update.storedquery.ReadStoredQuery
 
calculateMetric(IStoredQuery) - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
calculateMetric(AmbitDBVersion) - Method in class ambit2.db.version.DBVersionQuery
 
calculateRank(TautomerIncrementStep, IAtomContainer) - Method in class ambit2.tautomers.ranking.EnergyRanking
 
calculateRank(IAtomContainer, KnowledgeBase) - Method in class ambit2.tautomers.ranking.EnergyRanking
 
calculateRank(TautomerIncrementStep, IAtomContainer) - Method in class ambit2.tautomers.RuleManager
 
calculateRank(TautomerIncrementStep, IAtomContainer, TautomerManager) - Static method in class ambit2.tautomers.RuleManager
 
calculateRegion(IAtomContainer) - Method in class ambit2.tautomers.rules.TautomerRegion
 
Calculator - Class in ambit2.groupcontribution
 
Calculator() - Constructor for class ambit2.groupcontribution.Calculator
 
calculator - Variable in class ambit2.rest.model.predictor.DescriptorPredictor
 
call() - Method in class ambit2.rest.task.CallableDatasetCreator
 
call() - Method in class ambit2.rest.task.CallableProtectedTask
 
CallableBuilder<USERID> - Class in ambit2.rest.task
http://opentox.org/dev/apis/api-1.2/Algorithm
CallableBuilder(Form, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallableBuilder
 
CallableBuilder(MediaType, Representation, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallableBuilder
 
CallableBuilder(MediaType, Representation, long, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallableBuilder
 
CallableDatasetCreator - Class in ambit2.rest.task
Creates a compatible dataset, given a model and a dataset of compounds 1)Retrieve model representation 2)Retrieve independent features representation.
CallableDatasetCreator(Form, Reference, Reference, String) - Constructor for class ambit2.rest.task.CallableDatasetCreator
 
CallableMockup<USERID> - Class in ambit2.rest.task
Mockup class.
CallableMockup(Form, USERID) - Constructor for class ambit2.rest.task.CallableMockup
 
CallableModelCreator<DATA,Item,Builder extends ModelBuilder<DATA,Algorithm,ModelQueryResults>,USERID> - Class in ambit2.rest.model.task
 
CallableModelCreator(Form, Context, Algorithm, Builder, USERID, String, ClientInfo) - Constructor for class ambit2.rest.model.task.CallableModelCreator
 
CallableModelPredictor<ModelItem,Predictor extends ModelPredictor,USERID> - Class in ambit2.rest.model.task
 
CallableModelPredictor(Form, Reference, Context, Predictor, USERID, String, ClientInfo) - Constructor for class ambit2.rest.model.task.CallableModelPredictor
 
CallableNumericalModelCreator<USERID> - Class in ambit2.rest.task
 
CallableNumericalModelCreator(Form, Reference, Context, Algorithm, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, USERID, String, ClientInfo) - Constructor for class ambit2.rest.task.CallableNumericalModelCreator
 
CallablePOST<USERID> - Class in ambit2.rest.task
Wrapper for remote tasks to be used as super service
CallablePOST(Form, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallablePOST
 
CallablePOST(MediaType, Representation, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallablePOST
 
CallablePOST(MediaType, Representation, long, Reference, USERID, String) - Constructor for class ambit2.rest.task.CallablePOST
 
CallableProtectedTask<USERID> - Class in ambit2.rest.task
 
CallableProtectedTask(USERID) - Constructor for class ambit2.rest.task.CallableProtectedTask
 
CallableQueryProcessor<Target,Result,USERID> - Class in ambit2.rest.task
 
CallableQueryProcessor(Form, Context, USERID, String, ClientInfo) - Constructor for class ambit2.rest.task.CallableQueryProcessor
 
CallableQueryProcessor(Reference, Form, Context, USERID, String, ClientInfo) - Constructor for class ambit2.rest.task.CallableQueryProcessor
 
CallableWekaModelCreator<USERID> - Class in ambit2.rest.task.weka
Creates a model, given an algorithm
CallableWekaModelCreator(Form, Reference, Context, Algorithm, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, USERID, String, ClientInfo) - Constructor for class ambit2.rest.task.weka.CallableWekaModelCreator
 
CallableWekaPredictor<T,USERID> - Class in ambit2.rest.task.weka
 
CallableWekaPredictor(Form, Reference, Context, ModelPredictor<T, Instance>, USERID, String, ClientInfo) - Constructor for class ambit2.rest.task.weka.CallableWekaPredictor
 
callback - Variable in class ambit2.tautomers.processor.TautomerProcessor
 
callInternal() - Method in class ambit2.rest.task.CallableDatasetCreator
 
canApply(IAtomContainer) - Method in class ambit2.dragon.AbstractDescriptorShell
 
canApply(IAtomContainer) - Method in class ambit2.some.SOMEShell
 
cancel() - Method in interface ambit2.base.interfaces.IBatchProcessor
 
cancel() - Method in class ambit2.base.processors.batch.BatchProcessor
 
cancel(boolean) - Method in class ambit2.rest.task.ExecutableTask
 
cancel(ActionEvent) - Method in class ambit2.ui.WizardPanel
 
cancelAction() - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
cancelled - Variable in class ambit2.base.processors.batch.BatchProcessor
 
cancelled - Variable in class ambit2.pubchem.HTTPRequest
 
cancelRowUpdates() - Method in class ambit2.db.results.AmbitRows
 
cancelTasks() - Method in class ambit2.rest.task.TaskStorage
 
CanonicTautomer - Class in ambit2.tautomers.ranking
 
CanonicTautomer(TautomerManager) - Constructor for class ambit2.tautomers.ranking.CanonicTautomer
 
capitalizeFirstLetter(String) - Static method in class ambit2.ui.editors.BeanEditor
 
captions - Variable in class ambit2.ui.editors.BeanEditor
 
CarbonData - Class in ambit2.structure2name.rules
 
CarbonData() - Constructor for class ambit2.structure2name.rules.CarbonData
 
carbonData - Variable in class ambit2.structure2name.rules.IUPACRuleDataBase
 
CarboxylicGroup - Class in ambit2.tautomers.zwitterion
 
CarboxylicGroup() - Constructor for class ambit2.tautomers.zwitterion.CarboxylicGroup
 
CAS - Static variable in class ambit2.base.data.Property
 
CAS_num - Static variable in class ambit2.base.data.LiteratureEntry
 
caseSensitive - Variable in class ambit2.db.search.structure.QueryFieldAbstract
 
caseSensitive - Static variable in class ambit2.rest.AbstractResource
 
CASKey - Class in ambit2.core.processors.structure.key
Returns CAS number given the structure and its properties
CASKey() - Constructor for class ambit2.core.processors.structure.key.CASKey
 
CASProcessor - Class in ambit2.base.processors
Transform a string to CAS number format XXXXX-XX-X
CASProcessor() - Constructor for class ambit2.base.processors.CASProcessor
 
casProcessor - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
casProcessor - Variable in class ambit2.core.io.I5ReaderSimple
 
casProperty - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
casProperty - Static variable in class ambit2.core.io.I5ReaderSimple
 
casProperty - Variable in class ambit2.core.io.RawIteratingFolderReader
 
CASRN - Static variable in class ambit2.core.config.AmbitCONSTANTS
CAS RN
casTransformer - Variable in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
casTransformer - Variable in class ambit2.core.io.RawIteratingFolderReader
 
casTransformer - Variable in class ambit2.core.processors.structure.MoleculeReader
 
CatalogRDFReporter<T> - Class in ambit2.rest.reporters
RDF output for non DB based objects
CatalogRDFReporter(Request, MediaType) - Constructor for class ambit2.rest.reporters.CatalogRDFReporter
 
CatalogURIReporter<T> - Class in ambit2.rest.reporters
 
CatalogURIReporter(Request) - Constructor for class ambit2.rest.reporters.CatalogURIReporter
 
CatalogURIReporter(Reference) - Constructor for class ambit2.rest.reporters.CatalogURIReporter
 
CatalogURIReporter() - Constructor for class ambit2.rest.reporters.CatalogURIReporter
 
categories - Variable in class ambit2.core.io.dx.DXParser
 
category - Variable in class ambit2.db.cache.QueryCachedResults
 
category - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
category - Variable in class ambit2.export.isa.v1_0.objects.FactorValue
 
category - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttributeValue
 
category - Variable in class ambit2.export.isa.v1_0.objects.ProcessParameterValue
 
cBasisForEffect - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cBioaccBasis - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cConcType - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cDegradationParameter - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CDKDescriptorInfo - Class in ambit2.groupcontribution.descriptors
 
CDKDescriptorInfo() - Constructor for class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
CDKDescriptorManager - Class in ambit2.groupcontribution.descriptors
 
CDKDescriptorManager() - Constructor for class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
CDKDescriptorSolver - Class in ambit2.rules.conditions.solvers
 
CDKDescriptorSolver() - Constructor for class ambit2.rules.conditions.solvers.CDKDescriptorSolver
 
CDKHueckelAromaticityDetector - Class in ambit2.core.helper
For compatibility .
CDKHueckelAromaticityDetector() - Constructor for class ambit2.core.helper.CDKHueckelAromaticityDetector
 
CdkJmolAdapter - Class in ambit2.ui.jmol
Provides an interface to CDK IO and CDK data classes.
CdkJmolAdapter(String) - Constructor for class ambit2.ui.jmol.CdkJmolAdapter
 
CdkJmolAdapter.StructureIterator - Class in ambit2.ui.jmol
 
cdkParser - Variable in class ambit2.core.smiles.SmilesParserWrapper
 
cDoses - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cEffect - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cEffectType - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cell - Variable in class ambit2.core.io.PDFWriter
 
cell - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
CELL_BORDER_WIDTH_MILLIMETRES - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
cellEditor - Variable in class ambit2.ui.EditableHeader
 
cellRenderer - Variable in class ambit2.ui.QueryBrowser
 
cellToRecord(int, int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
center - Variable in class ambit2.smarts.QuerySequenceElement
 
centerNum - Variable in class ambit2.smarts.QuerySequenceElement
 
central_atom - Variable in class ambit2.descriptors.AtomEnvironment
 
cExposure - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cfg - Variable in class ambit2.db.processors.DescriptorsCalculator
 
cfg - Variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
cGeneration - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CGIDescriptor - Class in ambit2.descriptors.geometrical
Charge-related Geometrical Index (CGI TODO: reference
CGIDescriptor() - Constructor for class ambit2.descriptors.geometrical.CGIDescriptor
 
Chain - Class in ambit2.structure2name.components
 
Chain() - Constructor for class ambit2.structure2name.components.Chain
 
changeExtension(File) - Method in class ambit2.base.io.AmbitFileFilter
 
changeLineSeparators - Variable in class ambit2.db.reporters.SDFReporter
 
channelCopy2(ReadableByteChannel, WritableByteChannel) - Static method in class ambit2.base.io.DownloadTool
Channel copy method 2.
characteristicCategories - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
characteristicCategories - Variable in class ambit2.export.isa.v1_0.objects.Study
 
characteristics - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
characteristics - Variable in class ambit2.export.isa.v1_0.objects.Material
 
characteristics - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
characteristics - Variable in class ambit2.export.isa.v1_0.objects.Sample
 
characteristics - Variable in class ambit2.export.isa.v1_0.objects.Source
 
characteristicType - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttribute
 
charStructInfo - Variable in class ambit2.smarts.StructureSetAnalyzer
 
CharStructInfo() - Constructor for class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
ChartGenerator<T> - Class in ambit2.db.chart
 
ChartGenerator() - Constructor for class ambit2.db.chart.ChartGenerator
 
ChartGenerator(int, int) - Constructor for class ambit2.db.chart.ChartGenerator
 
ChC_AntiClock - Static variable in class ambit2.smarts.SmartsConst
 
ChC_Clock - Static variable in class ambit2.smarts.SmartsConst
 
ChC_R - Static variable in class ambit2.smarts.SmartsConst
 
ChC_S - Static variable in class ambit2.smarts.SmartsConst
 
ChC_Unspec - Static variable in class ambit2.smarts.SmartsConst
 
ChEBIClient - Class in ambit2.chebi
http://www.ebi.ac.uk/chebi/webServices.do
ChEBIClient(String, SearchCategory) - Constructor for class ambit2.chebi.ChEBIClient
 
ChebiFinder - Class in ambit2.chebi
 
ChebiFinder(Template, AbstractFinder.MODE) - Constructor for class ambit2.chebi.ChebiFinder
 
check() - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
check() - Method in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
check() - Method in class ambit2.db.substance.study.UpdateSubstanceStudy
 
check() - Method in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
check(double, double) - Method in enum ambit2.rules.conditions.value.IValue.Relation
 
checkAssay(Study, int) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
checkAssayProcess(Assay, int) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
checkColumnIndices(Map<String, Integer>) - Method in class ambit2.reactions.ReactionDataBase
 
checkComponentInCombination(int, int[]) - Method in class ambit2.smarts.ComponentMapping
 
checkComponentInCombination(int, int[]) - Method in class ambit2.smarts.SmartsManager
 
checkComponentMapings() - Method in class ambit2.smarts.ComponentMapping
 
checkConditionForAtom(IAtomContainer, int) - Method in class ambit2.tautomers.rules.AtomCondition
 
checkConditionForAtom(IAtomContainer, int, IsomorphismTester) - Method in class ambit2.tautomers.rules.AtomCondition
 
checkConditionsForTarget(Object) - Method in class ambit2.reactions.GenericReaction
 
checkCurStateInstanceValidity() - Method in class ambit2.tautomers.RuleInstance
 
checkDoubleBondStereochemistry(DoubleBondStereochemistry, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
checkForZeroColumn(int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
checkForZeroRow(int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
checkInvalidatedDBStereo(IAtomContainer, List<IStereoElement>, Map<IStereoElement, StereoChange>) - Method in class ambit2.smarts.SMIRKSManager
 
checkIsomorphismAtPosition(IAtomContainer, int) - Method in class ambit2.smarts.IsomorphismTester
 
checkIsomorphismAtPosition(IQueryAtomContainer, int) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
checkIsStructureOnly() - Method in class ambit2.sln.SLNContainer
 
checkIsTerminalFragment(IAtomContainer) - Static method in class ambit2.reactions.retrosynth.NodeComponent
 
checkMappings() - Method in class ambit2.smarts.SMIRKSReaction
 
checkMethylGroup(IAtom, IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
checkMolecule(IAtomContainer) - Method in class ambit2.tautomers.FilterTautomers
 
checkNewAlleneAtoms(IAtomContainer, boolean, boolean) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
checkOximAciNitro(IAtom, IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
checkPSSeTeH(IAtom, IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
checkStereoElements(IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
checkStudy(int) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
checkStudyProcess(Study, int) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
checkSubstituentMapping(List<IAtom>, HAtomEnvironmentInstance, int, int) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
checkTarget(ScreeningData) - Method in class ambit2.smarts.Screening
PreScreening - run this after the query is set
checkTetrahedralChirality(TetrahedralChirality, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
chembl - Static variable in class ambit2.base.data.ChEMBLProperties
 
ChEMBLCompoundURI - Class in ambit2.core.processors.structure.key
 
ChEMBLCompoundURI() - Constructor for class ambit2.core.processors.structure.key.ChEMBLCompoundURI
 
chemblPrefix - Static variable in class ambit2.base.data.ChEMBLProperties
 
ChEMBLProperties - Class in ambit2.base.data
 
ChEMBLProperties.ChEMBL_Class - Enum in ambit2.base.data
 
ChEMBLProperties.ChEMBL_Property - Enum in ambit2.base.data
 
ChEMBLRawReader - Class in ambit2.rest.rdf.chembl
Reads SPARQL results from http://rdf.farmbio.uu.se/chembl/ into iterator
ChEMBLRawReader() - Constructor for class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
chemblSparql - Static variable in class ambit2.base.data.ChEMBLProperties
 
ChemComplexityUtils - Class in ambit2.reactions.rules.scores
 
ChemComplexityUtils() - Constructor for class ambit2.reactions.rules.scores.ChemComplexityUtils
 
chemical - Variable in class ambit2.db.update.structure.CreateStructure
 
ChemicalByDataset - Class in ambit2.db.update.structure
idchemical by dataset
ChemicalByDataset(SourceDataset) - Constructor for class ambit2.db.update.structure.ChemicalByDataset
 
ChemicalByDataset() - Constructor for class ambit2.db.update.structure.ChemicalByDataset
 
ChemicalByDataset(Integer) - Constructor for class ambit2.db.update.structure.ChemicalByDataset
 
ChemicalByQueryFolder - Class in ambit2.db.search.structure
Retrieves chemicals from set of datasets, defined in the query table restricted by sessions.title
ChemicalByQueryFolder(String[]) - Constructor for class ambit2.db.search.structure.ChemicalByQueryFolder
 
ChemicalBySubstanceRelation - Class in ambit2.db.substance.relation
Returns all chemicals which are component of a substance.
ChemicalBySubstanceRelation() - Constructor for class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
ChemicalBySubstanceRelation(STRUCTURE_RELATION) - Constructor for class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
ChemicalName - Class in ambit2.export.isa.v1_0.objects
 
ChemicalName() - Constructor for class ambit2.export.isa.v1_0.objects.ChemicalName
 
chemicalName - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
ChemicalRoleByBundle - Class in ambit2.db.facets.compounds
 
ChemicalRoleByBundle(String) - Constructor for class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
chemicalsOnly - Variable in class ambit2.db.readers.RetrieveField
 
chemicalsOnly - Variable in class ambit2.db.readers.RetrieveModelTemplates
 
chemicalsOnly - Variable in class ambit2.db.readers.RetrieveProfileValues
 
chemicalsOnly - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
chemicalsOnly - Variable in class ambit2.db.readers.RetrieveTemplate
 
chemicalsOnly - Variable in class ambit2.db.search.property.AbstractPropertyRetrieval
 
chemicalsOnly - Variable in class ambit2.db.search.structure.AbstractStructureQuery
 
chemicalsOnly - Variable in class ambit2.db.search.structure.QueryCombinedStructure
 
chemicalsOnly - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
ChemicalSpaceQuery - Class in ambit2.db.search.structure.pairwise
 
ChemicalSpaceQuery() - Constructor for class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
ChemicalSpaceQuery.ChemSpaceMethod - Enum in ambit2.db.search.structure.pairwise
 
ChemicalStructureQualityCheck - Class in ambit2.core.processors.quality
Verifies consistency between multiple structures, coming from different origins 2)coherence of multiple origins - compare all structures of same idchemical - assign OK if same, notOK if not same retrieve a chemical (by idchemical) retrieve structures per chemical calculate fingerprints per structure compare structure fingerprints with fingerprints from fp1024 (per chemical), if different, assign "ERROR", otherwise assign "ProbablyOK" (slow) select one structure and compare all other structures (same chemical) with isomrphism test; assign "ERROR" if not same.
ChemicalStructureQualityCheck() - Constructor for class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
CHEMIDPLUS_URL - Static variable in class ambit2.search.chemidplus.ChemIdPlusRequest
 
ChemIdPlusRequest - Class in ambit2.search.chemidplus
 
ChemIdPlusRequest() - Constructor for class ambit2.search.chemidplus.ChemIdPlusRequest
 
chemObject - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
ChemObjectFactory - Class in ambit2.smarts
Utilities for generation of different types of chemical objects: molecules, fragments, queries
ChemObjectFactory(IChemObjectBuilder) - Constructor for class ambit2.smarts.ChemObjectFactory
 
ChemObjectToSmiles - Class in ambit2.smarts
 
ChemObjectToSmiles() - Constructor for class ambit2.smarts.ChemObjectToSmiles
 
chemShift0 - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
chemShifts - Variable in class ambit2.groupcontribution.nmr.Substituent
 
ChemSpaceCell - Class in ambit2.db.search.structure.pairwise
 
ChemSpaceCell() - Constructor for class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
ChiralPermutations - Class in ambit2.smarts
 
ChiralPermutations() - Constructor for class ambit2.smarts.ChiralPermutations
 
chunkQuery - Variable in class ambit2.db.reporters.QueryPacketReporter
 
CircularFingerprintInterpretable - Class in ambit2.descriptors.fingerprints
 
CircularFingerprintInterpretable() - Constructor for class ambit2.descriptors.fingerprints.CircularFingerprintInterpretable
 
city - Variable in class ambit2.base.data.AmbitUser
 
city - Variable in class ambit2.ui.editors.AmbitUserEditor
 
classcScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
classcScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
ClassHolder - Class in ambit2.base.data
A place holder for class name and description, in order to allow display of light list of objects, instantiated on demand only.
ClassHolder(String, String, String, String) - Constructor for class ambit2.base.data.ClassHolder
 
ClassHolder(String, String, String, ImageIcon) - Constructor for class ambit2.base.data.ClassHolder
 
ClassHolderEditor - Class in ambit2.ui.editors
 
ClassHolderEditor() - Constructor for class ambit2.ui.editors.ClassHolderEditor
 
ClassificationModelStatistics<U extends Bin> - Class in ambit2.similarity.stats
 
ClassificationModelStatistics(String) - Constructor for class ambit2.similarity.stats.ClassificationModelStatistics
 
classifier - Variable in class ambit2.rest.task.weka.FilteredWekaPredictor
 
classifier - Variable in class ambit2.rest.task.weka.WekaModelBuilder
 
classifier - Variable in class ambit2.rest.task.weka.WekaPredictor
 
classifyQuery(Features, List<DistanceComparable<Features>>) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
classIndex - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
classUnknown - Variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
clazz - Variable in class ambit2.base.data.ClassHolder
 
clazz - Variable in class ambit2.base.data.Property
 
cleanedResourceRef(Reference) - Method in class ambit2.rest.freemarker.FreeMarkerSupport
 
cleanedResourceRef(Reference) - Method in class ambit2.rest.ProtectedResource
 
cleanHeader(String) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
cleanKekuleBonds - Variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
cleanPropertyRefs() - Method in class ambit2.core.io.dx.DXParser
 
cleanup() - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
cleanupCompletedTasks - Variable in class ambit2.rest.task.TaskStorage
 
cleanUpTasks() - Method in class ambit2.rest.task.TaskStorage
 
cleanupTimer - Variable in class ambit2.rest.task.TaskStorage
 
clear() - Method in class ambit2.base.data.Profile
 
clear() - Method in class ambit2.base.data.SelectionBean
 
clear() - Method in class ambit2.base.data.StructureRecord
 
clear() - Method in class ambit2.base.data.study.EffectRecord
 
clear() - Method in class ambit2.base.data.study.Params
 
clear() - Method in class ambit2.base.data.study.ProtocolApplication
 
clear() - Method in class ambit2.base.data.SubstanceRecord
 
clear() - Method in class ambit2.base.facet.BundleRoleFacet
 
clear() - Method in interface ambit2.base.interfaces.IStructureRecord
 
clear() - Method in interface ambit2.base.processors.IAmbitResult
Clears te object
clear() - Method in class ambit2.base.relation.AbstractRelation
 
clear() - Method in class ambit2.base.relation.composition.Proportion
 
clear() - Method in class ambit2.core.groups.FilteredList
 
clear() - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
clear() - Method in class ambit2.db.simiparity.space.QMap
 
clear() - Method in class ambit2.db.simiparity.space.QMapSpace
 
clear() - Method in class ambit2.descriptors.FunctionalGroup
 
clear() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
clear()
clear() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
Clear() deallocates kdeList
clear() - Method in interface ambit2.model.IModelStatistics
 
clear(Comparable) - Method in interface ambit2.model.IModelStatistics
 
clear() - Method in class ambit2.model.numeric.DataCoverage
 
clear() - Method in class ambit2.model.numeric.DataCoverageDensity
 
clear() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
clear() - Method in class ambit2.model.numeric.DataCoverageDistance
 
clear() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
clear() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
clear() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
clear() - Method in class ambit2.similarity.stats.AbstractModelStatistics
 
clear(Comparable) - Method in class ambit2.similarity.stats.AbstractModelStatistics
 
clear(Comparable) - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
clear() - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
clear() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
clear(Comparable) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
clearAllErrorsAndWarnings() - Method in class ambit2.sln.io.SLN2ChemObject
 
clearAllErrorsAndWarnings() - Method in class ambit2.sln.io.SLN2Substance
 
clearAtomIDs(SLNContainer) - Static method in class ambit2.sln.SLNHelper
 
clearCalculationErrors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
clearComposition - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
clearFacets() - Method in class ambit2.base.data.StructureRecord
 
clearFacets() - Method in interface ambit2.base.interfaces.IStructureRecord
 
clearFacets() - Method in class ambit2.base.relation.composition.CompositionRelation
 
clearFacets() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
clearFilter() - Method in class ambit2.core.groups.FilteredList
 
clearFilter() - Method in interface ambit2.core.groups.IFiltered
 
clearFilter() - Method in class ambit2.core.groups.SuppleAtomContainer
 
clearFlag() - Method in class ambit2.domain.stats.datastructures.Histogram
 
clearFlag() - Method in class ambit2.similarity.stats.Histogram
 
clearGroups() - Method in class ambit2.groupcontribution.GroupContributionModel
 
clearIsotopes - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
clearKDEList() - Method in class ambit2.model.numeric.DataCoverageDensity
 
clearMeasurements - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
clearParameters() - Method in class ambit2.db.results.AmbitRows
 
clearProfile(double[]) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
clearProperties() - Method in class ambit2.base.data.StructureRecord
 
clearProperties() - Method in interface ambit2.base.interfaces.IStructureRecord
 
clearProperties() - Method in class ambit2.base.relation.composition.CompositionRelation
 
clearProperties(IChemObject) - Static method in class ambit2.core.data.MoleculeTools
 
clearWarnings() - Method in class ambit2.db.results.AmbitRows
 
client - Variable in class ambit2.chebi.ChEBIClient
 
ClientAnchorDetail(int, int, int) - Constructor for class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
Create a new instance of the ClientAnchorDetail class using the following parameters.
clone() - Method in class ambit2.base.data.AmbitBean
 
clone() - Method in class ambit2.base.data.AmbitUser
 
clone() - Method in class ambit2.base.data.StructureRecord
 
clone() - Method in interface ambit2.base.interfaces.IStructureRecord
 
clone() - Method in class ambit2.base.relation.composition.CompositionRelation
 
clone() - Method in class ambit2.core.groups.SuppleAtomContainer
 
clone() - Method in class ambit2.model.numeric.DataCoverage
 
clone() - Method in class ambit2.reactions.reactor.ReactorNode
 
clone() - Method in class ambit2.reactions.retrosynth.RetroSynthNode
 
clone() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
cloneAndCheckStereo(IAtomContainer, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
cloneDoubleBondStereochemistry(DoubleBondStereochemistry, IAtomContainer, IAtomContainer, IAtom[], IBond[]) - Static method in class ambit2.smarts.StereoChemUtils
 
cloneDoubleBondStereochemistry(DoubleBondStereochemistry, IAtomContainer, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
cloneNode() - Method in class ambit2.smarts.Node
 
CloneProcessor - Class in ambit2.core.processors.structure
Clones IAtomContainer.
CloneProcessor() - Constructor for class ambit2.core.processors.structure.CloneProcessor
 
cloneTetrahedralChirality(TetrahedralChirality, IAtomContainer, IAtomContainer, IAtom[]) - Static method in class ambit2.smarts.StereoChemUtils
 
cloneTetrahedralChirality(TetrahedralChirality, IAtomContainer, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
close() - Method in class ambit2.base.external.CommandShell
 
close() - Method in class ambit2.core.io.ArffWriter
 
close() - Method in class ambit2.core.io.DelimitedFileReader
 
close() - Method in class ambit2.core.io.DelimitedFileWriter
 
close() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
close() - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
close() - Method in class ambit2.core.io.I5ReaderSimple
 
close() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
close() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
close() - Method in class ambit2.core.io.IteratingFileReader
 
close() - Method in class ambit2.core.io.IteratingFolderReader
 
close() - Method in class ambit2.core.io.IteratingXLSReader
 
close() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
close() - Method in class ambit2.core.io.MDLReader
 
close() - Method in class ambit2.core.io.PDFWriter
 
close() - Method in class ambit2.core.io.RawIteratingCSVReader
 
close() - Method in class ambit2.core.io.RawIteratingReader
 
close() - Method in class ambit2.core.io.RawIteratingWrapper
 
close() - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
close() - Method in class ambit2.core.io.ToXMLReaderSimple
 
close() - Method in class ambit2.core.io.XLSFileWriter
 
close() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
close() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
close() - Method in class ambit2.db.AbstractRepositoryAccess
 
close() - Method in class ambit2.db.DbReader
 
close() - Method in class ambit2.db.DbReaderStructure
 
close() - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
close() - Method in class ambit2.db.processors.DBProcessorsChain
 
close() - Method in class ambit2.db.processors.DbStructureWriter
 
close() - Method in class ambit2.db.processors.DescriptorsCalculator
 
close() - Method in class ambit2.db.processors.FP1024Writer
 
close() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
close() - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
close() - Method in class ambit2.db.processors.PropertyImporter
 
close() - Method in class ambit2.db.processors.RepositoryWriter
 
close() - Method in class ambit2.db.processors.ValueWriter
 
close() - Method in class ambit2.db.processors.ValueWriterNew
 
close() - Method in class ambit2.db.reporters.AbstractImageReporter
 
close() - Method in class ambit2.db.reporters.PDFReporter
 
close() - Method in class ambit2.db.reporters.QueryPacketReporter
 
close() - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
close() - Method in class ambit2.db.RepositoryReader
 
close() - Method in class ambit2.db.results.AmbitRows
 
close() - Method in class ambit2.db.search.property.ValuesReader
 
close() - Method in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
close() - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
close() - Method in class ambit2.db.StatementExecutor
 
close() - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
close() - Method in class ambit2.db.substance.processor.DBMatrixValueMarker
 
close() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
close() - Method in class ambit2.db.UpdateExecutor
 
close() - Method in class ambit2.dbui.ProfileEditor
 
close() - Method in class ambit2.descriptors.FunctionalGroup
 
close() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
close() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
close() - Method in class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
close() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
close() - Method in interface ambit2.ml.io.IMLOutput
 
close() - Method in class ambit2.ml.io.OutputARFF
 
close() - Method in class ambit2.ml.io.OutputVW
 
close() - Method in class ambit2.ml.io.OutputVW_LDA
 
close() - Method in class ambit2.mopac.Mopac7Reader
 
close() - Method in class ambit2.mopac.Mopac7Writer
 
close() - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
close() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
close() - Method in class ambit2.rest.dataset.RDFFileWriter
 
close() - Method in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
close() - Method in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
close() - Method in class ambit2.rest.model.predictor.ExternalModel
 
close() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
close() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
close() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
close() - Method in class ambit2.rest.reporters.CatalogRDFReporter
 
close() - Method in class ambit2.rest.reporters.CatalogURIReporter
 
close() - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
close() - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
close() - Method in class ambit2.some.SOMEVisualizer
 
closeBracket - Static variable in class ambit2.core.filter.MoleculeFilter
 
closeItemReader(ItemReader) - Method in class ambit2.core.io.IteratingFolderReader
 
closeIterator(Iterator) - Method in class ambit2.base.processors.batch.BatchProcessor
 
ClosenessCentrality(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
closeReader(RandomAccessFile) - Static method in class ambit2.reactions.io.ReactionWriteUtils
 
closeResults(ResultSet) - Method in class ambit2.db.search.QueryExecutor
 
closeResults(Results) - Method in class ambit2.db.StatementExecutor
 
closeWriter(FileWriter) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
closeWriter(FileWriter) - Static method in class ambit2.reactions.io.ReactionWriteUtils
 
closeWriters() - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
ClosureBond - Class in ambit2.smarts
 
ClosureBond() - Constructor for class ambit2.smarts.ClosureBond
 
clusterer - Variable in class ambit2.rest.task.weka.FilteredWekaPredictor
 
clusterer - Variable in class ambit2.rest.task.weka.WekaModelBuilder
 
clusterer - Variable in class ambit2.rest.task.weka.WekaPredictor
 
ClusteringApp - Class in ambit2.ml.mlib
 
ClusteringApp() - Constructor for class ambit2.ml.mlib.ClusteringApp
 
cMaxScore - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cMeasuredConcentration - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cMEDIUM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cMetabolicActivation - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cMetabolicActivationSystem - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CMLReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
Writes query results as CML .
CMLReporter() - Constructor for class ambit2.db.reporters.CMLReporter
 
CMLUtilities - Class in ambit2.smarts
SMARTSProp is a per atom property & hvnNrrrrrrrrRRRRRRRR extractSMARTSProperties(IAtomContainer mol) setCMLSMARTSProperties(IAtomContainer mol) mol.getAtom(i).setProperty("SMARTSProp", prop); if already set,
CMLUtilities() - Constructor for class ambit2.smarts.CMLUtilities
 
CO_DIFFERS - Static variable in class ambit2.sln.SLNConst
 
CO_EQUALS - Static variable in class ambit2.sln.SLNConst
 
CO_GREATER_OR_EQUALS - Static variable in class ambit2.sln.SLNConst
 
CO_GREATER_THAN - Static variable in class ambit2.sln.SLNConst
 
CO_LESS_OR_EQUALS - Static variable in class ambit2.sln.SLNConst
 
CO_LESS_THAN - Static variable in class ambit2.sln.SLNConst
 
CO_NO_COMPARISON - Static variable in class ambit2.sln.SLNConst
 
cOCContent - Static variable in class ambit2.base.ro.I5CONSTANTS
 
code - Variable in exception ambit2.base.exceptions.HttpException
 
col_batch - Static variable in class ambit2.core.io.sj.MalariaHTSDataDelimitedReader
 
col_SAMPLE - Static variable in class ambit2.core.io.sj.MalariaHTSDataDelimitedReader
 
CollectionsByChemical - Class in ambit2.db.facets.compounds
Returns number of collections (within a folder), where idchemical is a member of collections = query table; folder = sessions table
CollectionsByChemical(String) - Constructor for class ambit2.db.facets.compounds.CollectionsByChemical
 
Color - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ColorTableCellRenderer - Class in ambit2.ui
 
ColorTableCellRenderer() - Constructor for class ambit2.ui.ColorTableCellRenderer
 
column - Variable in class ambit2.ui.HeaderComboBoxModel
 
columnFiltrationthreshold - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
columnNorm(int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
columns - Variable in class ambit2.base.data.PropertiesTableModel
 
columns - Variable in class ambit2.core.io.study.StudyFormatter
 
columns - Variable in class ambit2.ui.editors.BeanEditor
 
columnsScProd(MatrixDouble, int, MatrixDouble, int) - Static method in class ambit2.groupcontribution.utils.math.MathUtilities
 
columnUpdated(int) - Method in class ambit2.db.results.AmbitRows
 
columnUpdated(String) - Method in class ambit2.db.results.AmbitRows
 
combine - Variable in class ambit2.db.search.QueryInfo
 
COMBINE_ALL - Static variable in class ambit2.db.search.QueryInfo
 
COMBINE_ANY - Static variable in class ambit2.db.search.QueryInfo
 
combine_options - Static variable in class ambit2.db.search.QueryInfo
 
combine_queries - Variable in class ambit2.db.search.QueryCombined
 
CombinedRuleInstance - Class in ambit2.tautomers
 
CombinedRuleInstance() - Constructor for class ambit2.tautomers.CombinedRuleInstance
 
combRI - Variable in class ambit2.tautomers.RuleInstance
 
comma - Variable in class ambit2.rendering.CompoundImageTools
 
comma - Variable in class ambit2.rest.task.TaskJSONReporter
 
Command - Class in ambit2.base.external
 
Command(String) - Constructor for class ambit2.base.external.Command
 
Command(String, String[]) - Constructor for class ambit2.base.external.Command
 
command - Variable in class ambit2.rendering.StructureEditorProcessor
 
CommandShell<INPUT,OUTPUT> - Class in ambit2.base.external
A wrapper for an external executable (OS dependent).
CommandShell() - Constructor for class ambit2.base.external.CommandShell
 
Comment - Class in ambit2.export.isa.v1_0.objects
ISA comment schema - it corresponds to ISA Comment[] construct JSON-schema representing a comment in the ISA model
Comment() - Constructor for class ambit2.export.isa.v1_0.objects.Comment
 
commentChar - Variable in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Data
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Factor
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
comments - Variable in class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
comments - Variable in class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Person
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Process
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
comments - Variable in class ambit2.export.isa.v1_0.objects.Study
 
commit() - Method in class ambit2.db.results.AmbitRows
 
comp - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
companyName - Variable in class ambit2.base.data.study.ProtocolApplication
 
companyUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
compare(GenericReactionInstance, GenericReactionInstance, ReactionSequence.SortingMethod) - Static method in class ambit2.reactions.retrosynth.ReactionSequence
 
compare(int, int, int) - Static method in class ambit2.sln.SLNConst
 
compare(double, double, int) - Static method in class ambit2.sln.SLNConst
 
compare(String, String, int) - Static method in class ambit2.sln.SLNConst
 
compareIgnoreCase(String, String, int) - Static method in class ambit2.sln.SLNConst
 
compareTo(AbstractLabel<LABEL>) - Method in class ambit2.base.data.AbstractLabel
 
compareTo(Property) - Method in class ambit2.base.data.Property
 
compareTo(SourceDataset) - Method in class ambit2.base.data.SourceDataset
 
compareTo(Algorithm<T>) - Method in class ambit2.core.data.model.Algorithm
 
compareTo(ISGroup) - Method in class ambit2.core.groups.AbstractGroup
 
compareTo(AtomEnvironment) - Method in class ambit2.descriptors.AtomEnvironment
 
compareTo(OTObject) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
compareTo(DistanceComparable) - Method in class ambit2.similarity.measure.DistanceComparable
 
compareTo(Bin<T>) - Method in class ambit2.similarity.stats.Bin
 
compareTo(Bin<T>) - Method in class ambit2.similarity.stats.SelfBin
 
compareTo(ValuePair) - Method in class ambit2.similarity.stats.ValuePair
 
compareTo(SMIRKSTransformation) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
comparisonOperation - Variable in class ambit2.sln.SLNExpressionToken
 
comparisonOperationToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
completed - Variable in class ambit2.rest.task.Task
 
completeTheHeader() - Method in class ambit2.db.reporters.ARFF3ColReporter
 
completeTheHeader() - Method in class ambit2.db.reporters.ARFFReporter
 
completionService_external - Variable in class ambit2.rest.task.TaskStorage
 
completionService_internal - Variable in class ambit2.rest.task.TaskStorage
 
ComplexityCli - Class in ambit2.reactions.cli
 
ComplexityCli() - Constructor for class ambit2.reactions.cli.ComplexityCli
 
component - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
component - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
Component - Class in ambit2.export.isa.v1_0.objects
 
Component() - Constructor for class ambit2.export.isa.v1_0.objects.Component
 
component - Variable in class ambit2.ui.editors.BeanEditor
 
component - Variable in class ambit2.ui.editors.EditorPanel
 
component - Variable in class ambit2.ui.editors.ListEditor
 
component - Variable in class ambit2.ui.editors.PreferencesPanel
 
componentAtoms - Variable in class ambit2.structure2name.components.ComponentConnection
 
ComponentConnection - Class in ambit2.structure2name.components
 
ComponentConnection() - Constructor for class ambit2.structure2name.components.ComponentConnection
 
ComponentConnection.ConType - Enum in ambit2.structure2name.components
 
ComponentGroup - Class in ambit2.core.groups
 
ComponentGroup(String, int) - Constructor for class ambit2.core.groups.ComponentGroup
 
componentHidden(ComponentEvent) - Method in class ambit2.ui.Panel2D
 
ComponentMapping - Class in ambit2.smarts
 
ComponentMapping() - Constructor for class ambit2.smarts.ComponentMapping
 
componentMoved(ComponentEvent) - Method in class ambit2.ui.Panel2D
 
componentName - Variable in class ambit2.export.isa.v1_0.objects.Component
 
ComponentRelationship - Class in ambit2.reactions.mapping
 
ComponentRelationship() - Constructor for class ambit2.reactions.mapping.ComponentRelationship
 
componentResized(ComponentEvent) - Method in class ambit2.ui.Panel2D
 
components - Variable in class ambit2.core.groups.ContainerGroup
 
components - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
components - Variable in class ambit2.reactions.retrosynth.RetroSynthNode
 
components - Variable in class ambit2.smarts.ComponentMapping
 
components - Variable in class ambit2.structure2name.components.ComponentConnection
 
components - Variable in class ambit2.structure2name.IUPACNameGenerator
 
componentShown(ComponentEvent) - Method in class ambit2.ui.Panel2D
 
componentsMatch - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
componentType - Variable in class ambit2.export.isa.v1_0.objects.Component
 
ComponentUtils - Class in ambit2.structure2name.components
 
ComponentUtils() - Constructor for class ambit2.structure2name.components.ComponentUtils
 
ComponentUtils.Comparison - Enum in ambit2.structure2name.components
 
composeSeparator - Static variable in class ambit2.groupcontribution.transformations.TransformationComposition
 
compositionName - Variable in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
CompositionRelation - Class in ambit2.base.relation.composition
Substance composition
CompositionRelation(SubstanceRecord, IStructureRecord, Proportion) - Constructor for class ambit2.base.relation.composition.CompositionRelation
 
CompositionRelation(SubstanceRecord, IStructureRecord, STRUCTURE_RELATION, Proportion) - Constructor for class ambit2.base.relation.composition.CompositionRelation
 
CompositionRelation.jsonFeature - Enum in ambit2.base.relation.composition
 
compositionRelationToSLNContainer(CompositionRelation) - Method in class ambit2.sln.io.SLN2Substance
 
compositionUUID - Variable in class ambit2.base.relation.composition.CompositionRelation
 
compositionUUID - Variable in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
compositionUUID - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
compositionUUID - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
compositionUUID_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
compound(Reference) - Static method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
compound(String) - Static method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
compound_resource - Static variable in class ambit2.rest.DataResources
 
compoundAAEnabled - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
compoundID_resource - Static variable in class ambit2.rest.DataResources
 
CompoundImageTools - Class in ambit2.rendering
Generates BufferedImage from smiles or compound.
CompoundImageTools() - Constructor for class ambit2.rendering.CompoundImageTools
 
CompoundImageTools(Dimension) - Constructor for class ambit2.rendering.CompoundImageTools
 
CompoundImageTools.Mode2D - Enum in ambit2.rendering
 
compoundInDatasetPrefix - Variable in class ambit2.rest.QueryStaXReporter
 
compoundReporter - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
compoundReporter - Variable in class ambit2.rest.substance.SubstanceRDFReporter
 
compounds - Variable in class ambit2.core.io.ToXMLReaderSimple
 
compounds - Variable in class ambit2.db.reporters.ARFF3ColReporter
 
compoundTemplate - Variable in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
CompoundURI - Static variable in class ambit2.rest.rdf.RDFInstancesIterator
 
CompoundURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.rest.structure
MediaType.TEXT_URI_LIST
CompoundURIReporter(String, Reference) - Constructor for class ambit2.rest.structure.CompoundURIReporter
 
CompoundURIReporter(Reference) - Constructor for class ambit2.rest.structure.CompoundURIReporter
 
CompoundURIReporter(Request) - Constructor for class ambit2.rest.structure.CompoundURIReporter
 
CompoundURIReporter(String, Request, boolean) - Constructor for class ambit2.rest.structure.CompoundURIReporter
 
CompoundURIReporter(String) - Constructor for class ambit2.rest.structure.CompoundURIReporter
 
compress(boolean) - Method in class ambit2.dragon.DragonDescriptorDictionary
 
cond1 - Variable in class ambit2.dbui.QueryInfoEditor
 
cond2 - Variable in class ambit2.dbui.QueryInfoEditor
 
cond3 - Variable in class ambit2.dbui.QueryInfoEditor
 
condenseStructures(String, int, int, String, int, int) - Method in class ambit2.smarts.ChemObjectFactory
 
condenseStructures(IAtomContainer, int, int, IAtomContainer, int, int) - Method in class ambit2.smarts.ChemObjectFactory
 
condition - Variable in class ambit2.db.search.AbstractQuery
 
condition - Variable in class ambit2.db.simiparity.space.QueryQMap
 
condition - Variable in class ambit2.db.substance.ReadSubstanceByName
 
condition - Static variable in class ambit2.rest.AbstractResource
 
condition1 - Variable in class ambit2.db.search.QueryInfo
 
condition2 - Variable in class ambit2.db.search.QueryInfo
 
condition3 - Variable in class ambit2.db.search.QueryInfo
 
ConditionExpression - Class in ambit2.rules.conditions
 
ConditionExpression() - Constructor for class ambit2.rules.conditions.ConditionExpression
 
conditionHeaders - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
ConditionJsonParser - Class in ambit2.rules.conditions.parser
 
ConditionJsonParser() - Constructor for class ambit2.rules.conditions.parser.ConditionJsonParser
 
ConditionParsingUtils - Class in ambit2.rules.conditions.parser
 
ConditionParsingUtils() - Constructor for class ambit2.rules.conditions.parser.ConditionParsingUtils
 
conditions - Variable in class ambit2.base.data.study.EffectRecord
 
conditions - Variable in class ambit2.reactions.GenericReaction
 
conditions2annotations(ProtocolEffectRecord<String, IParams, String>) - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
conditionScores - Variable in class ambit2.reactions.GenericReaction
 
conditionsScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
conditionsScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
conditionsStatus - Variable in class ambit2.reactions.GenericReactionInstance
 
conditionString - Variable in class ambit2.db.simiparity.space.QueryQMapSpace
 
confidenceLinks - Variable in class ambit2.rest.rdf.RDFPropertyIterator
 
config - Variable in class ambit2.core.processors.structure.FingerprintGenerator
 
config - Variable in class ambit2.sln.io.SLN2Substance
 
config - Variable in class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
config - Variable in class ambit2.vega.VegaShell
 
config_changeLineSeparators - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
configErrors - Variable in class ambit2.groupcontribution.io.GCM2Json
 
configFile - Variable in class ambit2.groupcontribution.cli.HNMRPredictCli
 
configFile - Variable in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
configProperties - Static variable in class ambit2.base.config.AMBITConfigProperties
 
configStatus - Variable in class ambit2.reactions.GenericReaction
 
configurator - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
configurator - Variable in class ambit2.db.search.structure.QuerySMARTS
 
configurator - Variable in class ambit2.db.search.structure.QueryStructure
 
configurator - Variable in class ambit2.descriptors.processors.BitSetGenerator
 
configure(IAtom) - Method in class ambit2.descriptors.IsotopeFactory
Configures an atom.
configure(IAtom, IIsotope) - Method in class ambit2.descriptors.IsotopeFactory
Configures an atom to have all the data of the given isotope.
configure() - Method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
configure(HAtomEnvironment, int) - Method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
configure(SMIRKSManager) - Method in class ambit2.reactions.GenericReaction
 
configure() - Method in class ambit2.smarts.groups.GroupMatch
 
configure(SMIRKSManager) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
configureAtoms(IAtomContainer) - Method in class ambit2.descriptors.IsotopeFactory
Configures atoms in an AtomContainer to carry all the correct data according to their element type.
configureCollectionProcessors(String) - Method in class ambit2.db.reporters.CSVReporter
 
configureGenericReactions(SMIRKSManager) - Method in class ambit2.reactions.ReactionDataBase
 
configureProcessors(String, boolean) - Method in class ambit2.db.reporters.QueryHeaderReporter
 
configureProcessors(String, boolean) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
configurePropertyProcessors() - Method in class ambit2.db.reporters.CSVReporter
 
configurePropertyProcessors() - Method in class ambit2.db.reporters.QueryHeaderReporter
 
configureQuery(SubstanceRecord, IParameterizedQuery<SubstanceRecord, List<ProtocolApplication>, IQueryCondition>) - Method in class ambit2.db.substance.study.SubstanceStudyDetailsProcessor
 
configureReactions(SMIRKSManager) - Method in class ambit2.smarts.processors.NeutraliseProcessor
 
configureReactions(SMIRKSManager) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
configureReader(RawIteratingCSVReader, IInputState, File) - Method in class ambit2.db.processors.BatchDBProcessor
 
configureStructureRecord(StructureRecord, InChIGeneratorFactory, List<INCHI_OPTION>) - Static method in class ambit2.reactions.reactor.ReactorStrategy
 
configureTemplateMap(Map<String, Object>, Request, IFreeMarkerApplication) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
configureTemplateMap(Map<String, Object>, Request, IFreeMarkerApplication) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
configureTemplateMap(Map<String, Object>, Request, IFreeMarkerApplication) - Method in class ambit2.rest.freemarker.FreeMarkerSupport
 
configureToolBar(JToolBar) - Method in class ambit2.ui.editors.ListEditor
 
configWarnings - Variable in class ambit2.groupcontribution.io.GCM2Json
 
confirm() - Method in interface ambit2.base.interfaces.IAmbitEditor
 
confirm() - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
confirm() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
confirm() - Method in class ambit2.dbui.dictionary.OntologyEditor
 
confirm() - Method in class ambit2.dbui.ProfileEditor
 
confirm() - Method in class ambit2.dbui.QueryCombinedEditor
 
confirm() - Method in class ambit2.dbui.QueryEditor
 
confirm() - Method in class ambit2.dbui.QueryInfoEditor
 
confirm() - Method in class ambit2.dbui.QueryScopeEditor
 
confirm() - Method in class ambit2.dbui.QuerySimilarityEditor
 
confirm() - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
confirm() - Method in class ambit2.ui.editors.BeanEditor
 
confirm() - Method in class ambit2.ui.editors.FileSelector
 
confirm() - Method in class ambit2.ui.editors.ListEditor
 
confirm() - Method in class ambit2.ui.editors.PreferencesPanel
 
confirm() - Method in class ambit2.ui.editors.SelectFieldsPanel
 
confirm() - Method in class ambit2.ui.editors.TemplateEditor
 
confirm() - Method in class ambit2.ui.jmol.Panel3D
 
confirm() - Method in class ambit2.ui.Panel2D
 
confirm() - Method in class ambit2.ui.QueryBrowser
 
conformation - Variable in class ambit2.smarts.DoubleBondStereoInfo
 
conformer_resource - Static variable in class ambit2.rest.DataResources
 
conformerID_resource - Static variable in class ambit2.rest.DataResources
 
conformerKey_resource - Static variable in class ambit2.rest.DataResources
 
conformerTemplate - Variable in class ambit2.rest.rdf.RDFDataEntryIterator
 
conformerTemplate - Variable in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
ConformerURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.rest.structure
Generates conformer URI as /compound/{id}/conformer/{id}
ConformerURIReporter(String) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(String, Request) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(Request) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(String, Request, boolean) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(Request, boolean) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(String, Reference) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConformerURIReporter(Reference) - Constructor for class ambit2.rest.structure.ConformerURIReporter
 
ConfusionMatrix - Class in ambit2.similarity.stats
 
ConfusionMatrix(Histogram<SelfBin<ValuePair>>) - Constructor for class ambit2.similarity.stats.ConfusionMatrix
 
connection - Variable in class ambit2.db.AbstractRepositoryAccess
 
connection - Variable in class ambit2.db.processors.DBProcessorsChain
 
connection - Variable in class ambit2.db.results.ResultSetTableModel
 
connectionBondOrder - Variable in class ambit2.structure2name.components.ComponentConnection
 
ConnectionStatisticsProcessor<T> - Class in ambit2.db.processors
 
ConnectionStatisticsProcessor() - Constructor for class ambit2.db.processors.ConnectionStatisticsProcessor
 
ConnectionStatusProcessor<T> - Class in ambit2.db.processors
 
ConnectionStatusProcessor() - Constructor for class ambit2.db.processors.ConnectionStatusProcessor
 
connectStructures(IAtomContainer, int, IAtomContainer, int, IBond.Order) - Method in class ambit2.smarts.ChemObjectFactory
 
connectStructures(String, int, String, int, IBond.Order) - Method in class ambit2.smarts.ChemObjectFactory
 
connectStructures_Spiro(IAtomContainer, int, IAtomContainer, int, IBond.Order) - Method in class ambit2.smarts.ChemObjectFactory
 
consensusFingerprint - Variable in class ambit2.model.structure.DataCoverageFingerprints
 
ConsensusLabel - Class in ambit2.base.data
 
ConsensusLabel() - Constructor for class ambit2.base.data.ConsensusLabel
 
ConsensusLabel(ConsensusLabel.CONSENSUS_LABELS) - Constructor for class ambit2.base.data.ConsensusLabel
 
ConsensusLabel.CONSENSUS_LABELS - Enum in ambit2.base.data
 
Constituent - Class in ambit2.base.relation.composition
 
Constituent(SubstanceRecord, IStructureRecord, Proportion) - Constructor for class ambit2.base.relation.composition.Constituent
 
Constituent - Class in ambit2.export.isa.v1_0.objects
Constituent Definition of a constituent of a material or another constituent
Constituent() - Constructor for class ambit2.export.isa.v1_0.objects.Constituent
 
constituent - Variable in class ambit2.export.isa.v1_0.objects.Linkage
 
constituents - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
container - Variable in class ambit2.base.data.Profile
 
ContainerGroup - Class in ambit2.core.groups
 
ContainerGroup(String, int) - Constructor for class ambit2.core.groups.ContainerGroup
 
ContainerGroup(String, int, ContainerGroup.SGROUP_MIXTURE) - Constructor for class ambit2.core.groups.ContainerGroup
 
ContainerGroup.SGROUP_MIXTURE - Enum in ambit2.core.groups
 
containers - Variable in class ambit2.sln.SLNCompositeObject
 
contains(Object) - Method in class ambit2.core.groups.FilteredList
 
contains(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
contains(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
contains(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer
 
contains(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer
 
contains(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer
 
contains(IStereoElement, IAtom) - Static method in class ambit2.smarts.StereoChemUtils
Checks whether the stereo element contains the atom This function works with invalidated stereo elements.
containsAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList
 
containsKey(Object) - Method in class ambit2.base.data.study.Params
 
containsObject(String) - Method in class ambit2.sln.dictionary.SLNDictionary
 
containsObject(String, ISLNDictionaryObject.Type) - Method in class ambit2.sln.dictionary.SLNDictionary
 
containsValue(Object) - Method in class ambit2.base.data.study.Params
 
content - Variable in class ambit2.base.data.StructureRecord
 
content - Variable in class ambit2.core.data.model.Algorithm
 
content - Variable in class ambit2.core.data.model.ModelWrapper
 
content - Variable in class ambit2.db.results.MemoryRowsModel
 
content - Variable in class ambit2.db.search.StoredQuery
 
content - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
content - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
content_SNLAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
contentMediaType - Variable in class ambit2.core.data.model.ModelWrapper
 
contentsChanged(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel
 
context - Variable in class ambit2.rest.DBConnection
 
context - Variable in class ambit2.rest.task.CallableQueryProcessor
 
contractedBonds - Variable in class ambit2.core.groups.SuperAtom
 
contribution - Variable in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
contribution - Variable in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
conversion - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
ConversionFlags() - Constructor for class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
convert(String, String, Set<AmbitML.out_formats>, int, int) - Method in class ambit2.ml.io.app.AmbitML
 
convertExplicitHAtomsToImplicit(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
 
convertFile(String) - Static method in class ambit2.core.io.SDFBrokenLineTerminationConverter
In Java, a line is considered terminated by any one of the following: a line feed \n, a carriage return \r, or a carriage return followed immediately by a line feed.
ConvertImageUnits() - Constructor for class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens.
convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class ambit2.core.processors.structure.HydrogenAdderProcessor
Deprecated.
convertKekuleSmartsToAromatic(IQueryAtomContainer, IRingSet) - Method in class ambit2.smarts.SmartsToChemObject
 
convertKekuleSmartsToAromatic(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsToChemObject
 
convertToCarbonSkelleton(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
convertToQueryAtomContainer(SuppleAtomContainer) - Static method in class ambit2.markush.Markush2Smarts
 
convertToString - Variable in class ambit2.descriptors.processors.DescriptorResultFormatter
 
convertToSuppleAtomContainer(QueryAtomContainer) - Static method in class ambit2.markush.Markush2Smarts
 
convolution(double[], int, double[], int) - Method in class ambit2.domain.stats.transforms.FFT
Convolution
coord2d - Variable in class ambit2.sln.SLNContainerAttributes
 
coord2dToString(ArrayList<double[]>) - Static method in class ambit2.sln.SLNContainerAttributes
 
coord3d - Variable in class ambit2.sln.SLNContainerAttributes
 
coord3dToString(ArrayList<double[]>) - Static method in class ambit2.sln.SLNContainerAttributes
 
copied - Variable in class ambit2.base.data.study.ValueAnnotated
 
copy - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
copy() - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Copies the dataset and returns URI to a new dataset
copy() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
copyAtoms(Node) - Method in class ambit2.smarts.Node
 
copyChangeBuilders(IAtomContainer, IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
Just copy atoms and bonds, discard all the flags, they will be recalculated later
copyColumnFrom(int, MatrixDouble, int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
copyEffectRecordValues(ProtocolEffectRecord, ProtocolEffectRecord<String, IParams, String>) - Static method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
copyRowFrom(int, MatrixDouble, int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
copyValues(TableColumn) - Method in class ambit2.ui.EditableHeaderTableColumn
 
corFactors - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
corFactorsString - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
CORRECT - Static variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
correctionFactors - Variable in class ambit2.groupcontribution.fragmentation.Fragmentation
 
CorrectionFactorsDesignation - Static variable in class ambit2.groupcontribution.GCMParser
 
correctionName - Variable in class ambit2.tautomers.rules.EnergyCorrection
 
corrleationCoefficient(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
corrleationCoefficient(List<Double>, List<Double>) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
count - Variable in class ambit2.base.data.PropertyStats
 
count - Variable in class ambit2.base.facet.AbstractFacet
 
count() - Method in class ambit2.domain.stats.datastructures.Histogram
 
count() - Method in class ambit2.similarity.stats.Histogram
 
counter - Variable in class ambit2.core.io.SimpleIOListener
 
counter - Static variable in class ambit2.tautomers.TautomerIncrementStep
 
counter - Variable in class ambit2.ui.AmbitSettingsListener
 
country - Variable in class ambit2.base.data.AmbitUser
 
country - Variable in class ambit2.ui.editors.AmbitUserEditor
 
coupling - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule2J
 
coupling - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
couplingIntervalLeftVal - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule2J
 
couplingIntervalLeftVal - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
couplingIntervalRightVal - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule2J
 
couplingIntervalRightVal - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
CoverageModelBuilder - Class in ambit2.rest.model.builder
applicability domain
CoverageModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String[], String[], String, String) - Constructor for class ambit2.rest.model.builder.CoverageModelBuilder
 
CoveragePredictor<Input,T> - Class in ambit2.rest.model.predictor
 
CoveragePredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.CoveragePredictor
 
coverageQueryAttributeToSLNString(int) - Static method in class ambit2.sln.SLNConst
 
CoveredAtomProperty - Static variable in class ambit2.sln.SLNConst
 
cPERCENTILE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cputime - Variable in class ambit2.rest.task.TaskStorage
 
cpuutilisation - Variable in class ambit2.rest.task.TaskStorage
 
create(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
create(Group) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
create(StringBean) - Method in class ambit2.db.processors.DbCreateDatabase
 
create(IStructureRecord) - Method in class ambit2.db.processors.quality.FPStructureWriter
 
create(IStructureRecord) - Method in class ambit2.db.processors.quality.QualityLabelWriter
 
create(IStructureRecord) - Method in class ambit2.db.processors.quality.QualityValueWriter
 
create(IStructureRecord) - Method in class ambit2.db.processors.RepositoryWriter
 
create(IStructureRecord) - Method in class ambit2.db.update.fpae.AtomEnvironmentMatrixWriter
 
create(IStructureRecord) - Method in class ambit2.db.update.fpae.AtomEnvironmentWriter
Deprecated.
 
create(IStructureRecord) - Method in class ambit2.db.update.qlabel.smarts.SMARTSAcceleratorWriter
 
create() - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
create() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
create_bundle_copy - Static variable in class ambit2.db.update.bundle.CreateBundleCopy
 
create_bundle_version - Static variable in class ambit2.db.update.bundle.CreateBundleVersion
 
create_sql - Static variable in class ambit2.db.chemrelation.UpdateStructureRelation
 
create_sql - Static variable in class ambit2.db.substance.CreateSubstance
 
create_sql - Static variable in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
create_sql - Static variable in class ambit2.db.update.bookmark.CreateBookmark
 
create_sql - Static variable in class ambit2.db.update.bundle.CreateBundle
 
create_sql - Static variable in class ambit2.db.update.chemical.CreateChemical
 
create_sql - Static variable in class ambit2.db.update.dataset.CreateDataset
 
create_sql - Static variable in class ambit2.db.update.dictionary.CreateDictionary
 
create_sql - Static variable in class ambit2.db.update.dictionary.TemplateAddProperty
 
create_sql - Static variable in class ambit2.db.update.model.CreateModel
 
create_sql - Static variable in class ambit2.db.update.property.CreateProperty
 
create_sql - Static variable in class ambit2.db.update.property.CreatePropertyReferenceID
 
create_sql - Static variable in class ambit2.db.update.reference.CreateReference
 
create_sql - Static variable in class ambit2.db.update.structure.CreateStructure
 
create_sql - Static variable in class ambit2.db.update.structure.UpdateStructure
 
create_sql_byid - Static variable in class ambit2.db.update.dataset.DatasetAddStructure
 
create_sql_byname - Static variable in class ambit2.db.update.dataset.DatasetAddStructure
 
create_sql_uuid - Static variable in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
CreateAtomEnvironment - Class in ambit2.db.update.fpae
 
CreateAtomEnvironment() - Constructor for class ambit2.db.update.fpae.CreateAtomEnvironment
 
createAtomEnvironmentDescriptor() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
CreateAtomEnvironmentMatrix - Class in ambit2.db.update.fpae
 
CreateAtomEnvironmentMatrix(FPTable) - Constructor for class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
CreateAtomEnvironmentMatrix() - Constructor for class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
createBatch() - Method in class ambit2.base.processors.batch.BatchReporter
 
createBatch() - Method in class ambit2.base.processors.batch.ListReporter
 
createBatch(Q) - Method in class ambit2.db.reporters.QueryProperyReporter
 
createBatch(Q) - Method in class ambit2.db.reporters.QueryStructureReporter
 
createBatch(Q) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
createBatch(Q) - Method in class ambit2.rest.structure.CompoundURIReporter
 
createBatch(Object) - Method in class ambit2.rest.task.CallableNumericalModelCreator
 
createBatch(Target) - Method in class ambit2.rest.task.CallableQueryProcessor
 
createBatch(Object) - Method in class ambit2.rest.task.weka.CallableWekaModelCreator
 
createBatch(Object) - Method in class ambit2.rest.task.weka.CallableWekaPredictor
 
createBin(Double) - Method in class ambit2.similarity.stats.DoubleValuesHistogram
 
createBin(T) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
createBin(String) - Method in class ambit2.similarity.stats.StringValuesHistogram
 
CreateBookmark - Class in ambit2.db.update.bookmark
 
CreateBookmark(Bookmark) - Constructor for class ambit2.db.update.bookmark.CreateBookmark
 
CreateBookmark() - Constructor for class ambit2.db.update.bookmark.CreateBookmark
 
createBrowseModeControls(JComponent) - Method in class ambit2.ui.QueryBrowser
 
createBuffer() - Method in class ambit2.rendering.CompoundImageTools
 
CreateBundle - Class in ambit2.db.update.bundle
 
CreateBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.CreateBundle
 
CreateBundle() - Constructor for class ambit2.db.update.bundle.CreateBundle
 
CreateBundleCopy - Class in ambit2.db.update.bundle
 
CreateBundleCopy() - Constructor for class ambit2.db.update.bundle.CreateBundleCopy
 
CreateBundleCopy(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.CreateBundleCopy
 
CreateBundleVersion - Class in ambit2.db.update.bundle
 
CreateBundleVersion() - Constructor for class ambit2.db.update.bundle.CreateBundleVersion
 
CreateBundleVersion(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.CreateBundleVersion
 
createCalculator() - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
createCallable(Form) - Method in class ambit2.rest.task.LauncherResource
 
CreateChemical - Class in ambit2.db.update.chemical
 
CreateChemical(IChemical) - Constructor for class ambit2.db.update.chemical.CreateChemical
 
CreateChemical() - Constructor for class ambit2.db.update.chemical.CreateChemical
 
createComponents() - Method in class ambit2.ui.editors.ListEditor
 
createConditionComponent() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
createConditionComponent() - Method in class ambit2.dbui.QueryChemicalEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryDatasetEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryFieldEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryFunctionalGroupsEditor
 
createConditionComponent() - Method in class ambit2.dbui.QuerySimilarityEditor
 
createConditionComponent() - Method in class ambit2.dbui.QuerySmartsEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryStoredResultsEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryStructureByQualityEditor
 
createConditionComponent() - Method in class ambit2.dbui.QueryStructureByValueQualityEditor
 
createConvertor(Variant) - Method in class ambit2.rest.AbstractResource
 
createConvertor(Variant) - Method in class ambit2.rest.SimpleTaskResource
 
createCopy() - Method in class ambit2.db.results.AmbitRows
 
createCopyNoConstraints() - Method in class ambit2.db.results.AmbitRows
 
createCopySchema() - Method in class ambit2.db.results.AmbitRows
 
created - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
createDatabase(String) - Method in class ambit2.db.processors.DbCreateDatabase
 
createDataCoverageObject() - Method in enum ambit2.model.numeric.ADomainMethodType
 
CreateDataset - Class in ambit2.db.update.dataset
 
CreateDataset(SourceDataset) - Constructor for class ambit2.db.update.dataset.CreateDataset
 
CreateDataset() - Constructor for class ambit2.db.update.dataset.CreateDataset
 
createDataset - Variable in class ambit2.db.update.dataset.DatasetAddStructure
 
createDataset(Representation, String) - Static method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
createDataset(File, String, String) - Static method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
createDatasetURI(int) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
createDefaultHeaderEditor() - Method in class ambit2.ui.EditableHeaderTableColumn
 
createDefaultImage() - Method in class ambit2.rendering.CompoundImageTools
 
createDefaultImage(String) - Method in class ambit2.rendering.CompoundImageTools
 
createDescriptor(String) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
createDescriptor(String, String[]) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
createDescriptor2Properties(String) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
createDescriptor2Property(String) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
createDescriptor2Property(String, String[]) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
CreateDictionary - Class in ambit2.db.update.dictionary
 
CreateDictionary(Dictionary) - Constructor for class ambit2.db.update.dictionary.CreateDictionary
 
CreateDictionary() - Constructor for class ambit2.db.update.dictionary.CreateDictionary
 
createDictionary - Variable in class ambit2.db.update.dictionary.TemplateAddProperty
 
createDictionary - Variable in class ambit2.db.update.model.CreateModel
 
createDownloadHTTPRequest(List<IStructureRecord>) - Method in class ambit2.pubchem.PUGProcessor
 
createDownloadRequest(List<IStructureRecord>, Writer) - Method in class ambit2.pubchem.PUGProcessor
 
createDragonShell() - Method in class ambit2.dragon.DescriptorDragonShell
 
createEffectRecord(Protocol) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
createEffectRecord() - Method in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
createEffectRecord() - Method in class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
createEffectRecord() - Method in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
createEffectRecordUpdateQuery(ProtocolApplication, EffectRecord) - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
createEffectRecordUpdateQuery(ProtocolApplication, EffectRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
createExactStructure(QueryInfo) - Method in class ambit2.db.processors.QueryInfo2Query
 
createExecutorService(String, int) - Method in class ambit2.rest.task.TaskStorage
 
createFacet(String) - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
createFacet(String) - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
createFacet(String) - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
createFacet(String) - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
createFacet(String) - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
createFacet(String) - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
createFacet(String) - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
createFacet(String) - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
createFacet(String) - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
createFacet(String) - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
createFacet(String) - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
createFacet(String) - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
createFacet(String) - Method in class ambit2.db.substance.QueryCountEndpoints
 
createFacet(String) - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
createFacet(String) - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
createFacet(String) - Method in class ambit2.db.substance.QueryCountSubstanceTypes
 
createFacet(String) - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
createFacet(String) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
createFacet(String) - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
createFacet(String) - Method in class ambit2.db.update.dataset.QueryCount
 
createFeature(RDFNode) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
createFeature(RDFNode) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
createFeature(RDFNode) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
createFieldnameComponent() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryChemicalEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryDatasetEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryFieldEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryFunctionalGroupsEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QuerySimilarityEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QuerySmartsEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryStoredResultsEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryStructureByQualityEditor
 
createFieldnameComponent() - Method in class ambit2.dbui.QueryStructureByValueQualityEditor
 
createFile() - Method in class ambit2.core.io.FileState
 
createFilterReference(String, String, String[]) - Static method in class ambit2.rest.task.CallableDatasetCreator
 
createFindControls(JComponent) - Method in class ambit2.ui.QueryBrowser
 
CreateFingerprintChemical - Class in ambit2.db.update.fp
To replace FP1024Writer
CreateFingerprintChemical(FPTable) - Constructor for class ambit2.db.update.fp.CreateFingerprintChemical
 
CreateFingerprintChemical() - Constructor for class ambit2.db.update.fp.CreateFingerprintChemical
 
CreateFingerprintStructure - Class in ambit2.db.update.fp
To replace FP1024Writer
CreateFingerprintStructure() - Constructor for class ambit2.db.update.fp.CreateFingerprintStructure
 
createFromName(String, String) - Static method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
createGroup(int, SGroupMDL2000Helper.SGROUP_TYPE) - Static method in class ambit2.core.io.SGroupMDL2000Helper
 
createHashedIdentifier(IParams) - Method in class ambit2.base.data.substance.SubstanceProperty
 
createHeader() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
createHeader() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
createHeader() - Method in class ambit2.core.io.IteratingXLSReader
 
createImage(IStructureRecord) - Method in class ambit2.db.reporters.AbstractImageReporter
 
createImageIcon(String) - Static method in class ambit2.ui.Utils
 
createImageWrapper(BufferedImage) - Method in class ambit2.db.reporters.AbstractImageReporter
 
createImageWrapper(BufferedImage) - Method in class ambit2.db.reporters.ImageAreaReporter
 
createImageWrapper(BufferedImage) - Method in class ambit2.db.reporters.ImageReporter
 
createItem(Reference) - Method in class ambit2.rest.legacy.OTAlgorithms
Deprecated.
 
createItem(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
createItem(Reference) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
createItem(Reference) - Method in class ambit2.rest.legacy.OTDatasets
Deprecated.
 
createItem(Reference) - Method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
createListCellRenderer() - Static method in class ambit2.ui.editors.ClassHolderEditor
 
createListCellRenderer(int) - Static method in class ambit2.ui.editors.ClassHolderEditor
 
createMatrix(String, boolean, float) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
createMatrix(String, boolean, float, int, int) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
CreateMatrixFromBundle - Class in ambit2.db.update.bundle.matrix
 
CreateMatrixFromBundle(SubstanceEndpointsBundle, ReadEffectRecordByBundleMatrix._matrix) - Constructor for class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
CreateMatrixFromBundle(SubstanceEndpointsBundle, boolean, ReadEffectRecordByBundleMatrix._matrix) - Constructor for class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
createMaxValueComponent() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
CreateModel - Class in ambit2.db.update.model
 
CreateModel(ModelQueryResults) - Constructor for class ambit2.db.update.model.CreateModel
 
CreateModel() - Constructor for class ambit2.db.update.model.CreateModel
 
createModel(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
createModel(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
createModel() - Method in class ambit2.rest.model.task.CallableModelCreator
 
createModel() - Static method in class ambit2.rest.rdf.Annotea
 
createModel(OntModelSpec) - Static method in class ambit2.rest.rdf.Annotea
 
createModel() - Static method in class ambit2.rest.rdf.BibTex
 
createModel(OntModelSpec) - Static method in class ambit2.rest.rdf.BibTex
 
createModel() - Method in class ambit2.rest.task.CallableNumericalModelCreator
 
createModel() - Method in class ambit2.rest.task.weka.CallableWekaModelCreator
 
createMouseInputListener() - Method in class ambit2.ui.EditableHeaderUI
 
createNavigator(JComponent, List<Dictionary>) - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
createNewQuery(T) - Method in class ambit2.db.results.AmbitRows
 
createObject(String, LiteratureEntry, String) - Method in class ambit2.db.update.bundle.ReadBundle
 
createObject(String, LiteratureEntry, String) - Method in class ambit2.db.update.dataset.AbstractReadDataset
 
createObject() - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
createObjectIterator(Reference, MediaType) - Method in class ambit2.rest.dataset.RDFInstancesParser
 
createObjectIterator(Reference, MediaType) - Method in class ambit2.rest.dataset.RDFStructuresReader
 
createObjectIterator(Reference, MediaType) - Method in class ambit2.rest.RDFBatchParser
 
createOntClass(OntModel) - Method in enum ambit2.rest.rdf.Annotea.Bookmark
 
createOntClass(OntModel) - Method in enum ambit2.rest.rdf.BibTex.BTClass
 
createOntClass(OntModel) - Method in enum ambit2.rest.rdf.OTA.OTAClass
 
createOntClass(OntModel) - Method in enum ambit2.rest.rdf.OTEE.OTEEClass
 
createOptions() - Static method in class ambit2.groupcontribution.cli.GCMPredictCli
 
createOptions() - Static method in class ambit2.groupcontribution.cli.GroupContributionCli
 
createOptions() - Static method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
createOptions() - Static method in class ambit2.pubchem.SearchApplication
 
createOptions() - Static method in class ambit2.reactions.cli.AmbitSmirksCli
 
createOptions() - Static method in class ambit2.reactions.cli.ReactorCli
 
createOptions() - Static method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
createOutWriter() - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
createPageControls(JComponent) - Method in class ambit2.ui.QueryBrowser
 
createPollRequest(List<IStructureRecord>) - Method in class ambit2.pubchem.PUGProcessor
 
createPollRequest(IStructureRecord, Writer) - Static method in class ambit2.pubchem.PUGProcessor
 
createPredictedTemplate(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
createPredictedTemplate(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
createPredictor(ModelQueryResults) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
createPredictor(ModelQueryResults) - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
createPredictor(ModelQueryResults) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
createPredictor(ModelQueryResults) - Method in class ambit2.rest.model.predictor.Structure2DProcessor
 
createPredictor(ModelQueryResults) - Method in class ambit2.rest.model.predictor.StructureProcessor
 
createPresentationModel() - Method in class ambit2.dbui.QueryEditor
 
createPresentationModel() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
createPresentationModel() - Method in class ambit2.ui.editors.BeanEditor
 
createProcessors() - Method in class ambit2.rest.model.task.CallableModelCreator
 
createProcessors() - Method in class ambit2.rest.model.task.CallableModelPredictor
 
createProcessors() - Method in class ambit2.rest.task.CallableQueryProcessor
 
createProperties() - Method in class ambit2.base.data.StructureRecord
 
createProperties(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
createProperties(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
createProperties() - Method in class ambit2.vega.VegaShell
 
createProperty(Property, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
createProperty - Variable in class ambit2.db.update.dictionary.TemplateAddProperty
 
CreateProperty - Class in ambit2.db.update.property
 
CreateProperty(Property) - Constructor for class ambit2.db.update.property.CreateProperty
 
CreateProperty() - Constructor for class ambit2.db.update.property.CreateProperty
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.Annotea.AnnoteaProperty
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.Annotea.Bookmark
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.Annotea.BookmarkProperty
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.BibTex.BTClass
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.OTA.OTAProperty
 
createProperty(OntModel) - Method in enum ambit2.rest.rdf.OTEE.OTAProperty
 
CreatePropertyAnnotation - Class in ambit2.db.update.propertyannotations
 
CreatePropertyAnnotation() - Constructor for class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
CreatePropertyAnnotations - Class in ambit2.db.update.propertyannotations
 
CreatePropertyAnnotations() - Constructor for class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
createPropertyByColumnName(String) - Method in class ambit2.core.io.IteratingDelimitedFileReader
 
createPropertyByColumnName(String) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
createPropertyByColumnName(String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
createPropertyByColumnName(String) - Method in class ambit2.core.io.IteratingXLSReader
 
createPropertyFromReference(Reference, LiteratureEntry, String) - Method in class ambit2.rest.model.builder.ModelBuilder
 
createPropertyFromReference(Reference, LiteratureEntry, Reference, String) - Static method in class ambit2.rest.model.builder.ModelBuilder
 
CreatePropertyReferenceID - Class in ambit2.db.update.property
 
CreatePropertyReferenceID(Property) - Constructor for class ambit2.db.update.property.CreatePropertyReferenceID
 
CreatePropertyReferenceID() - Constructor for class ambit2.db.update.property.CreatePropertyReferenceID
 
CreateQLabelCAS - Class in ambit2.db.update.qlabel
 
CreateQLabelCAS() - Constructor for class ambit2.db.update.qlabel.CreateQLabelCAS
 
CreateQLabelEINECS - Class in ambit2.db.update.qlabel
 
CreateQLabelEINECS() - Constructor for class ambit2.db.update.qlabel.CreateQLabelEINECS
 
CreateQLabelFingerprints - Class in ambit2.db.update.qlabel
 
CreateQLabelFingerprints() - Constructor for class ambit2.db.update.qlabel.CreateQLabelFingerprints
 
CreateQLabelPair - Class in ambit2.db.update.qlabel
Find minority per source SELECT idchemical,idstructure,if(q.label!="Majority","",if(num_sources=(rel+1),"Majority","Minority")), rel,num_sources,label,q.text,p.text FROM quality_chemicals q join quality_pair p using(idchemical) order by idchemical
CreateQLabelPair() - Constructor for class ambit2.db.update.qlabel.CreateQLabelPair
 
createQuery() - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
createQuery() - Method in enum ambit2.db.search.structure.SCOPE
 
createQuery(Context, Request, Response) - Method in class ambit2.rest.AbstractResource
 
createQuery(Context, Request, Response) - Method in class ambit2.rest.SimpleTaskResource
 
createQueryField(Property, String, String) - Method in class ambit2.db.processors.QueryInfo2Query
 
CreateQueryFolder - Class in ambit2.db.update.queryfolder
 
CreateQueryFolder(AmbitUser, SessionID) - Constructor for class ambit2.db.update.queryfolder.CreateQueryFolder
 
CreateQueryFolder(AmbitUser) - Constructor for class ambit2.db.update.queryfolder.CreateQueryFolder
 
CreateQueryFolder() - Constructor for class ambit2.db.update.queryfolder.CreateQueryFolder
 
createQuerySimilarity(QueryInfo) - Method in class ambit2.db.processors.QueryInfo2Query
 
createQueryStructure(ExactStructureSearchMode, String) - Method in class ambit2.db.processors.QueryInfo2Query
 
createQuerySubstructure(QueryInfo) - Method in class ambit2.db.processors.QueryInfo2Query
 
createReader(File) - Static method in class ambit2.reactions.io.ReactionWriteUtils
 
createRecord(int) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
createRecord(String) - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
createRecord(String) - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
createRecord() - Method in class ambit2.rest.rdf.RDFAlgorithmIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFBookmarkIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFMetaDatasetIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFReferenceIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFResourceIterator
 
createRecord() - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
createRecordControls(JComponent) - Method in class ambit2.ui.QueryBrowser
 
createRecordWriter(Request, ResourceDoc) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
createRecordWriter(Request, ResourceDoc) - Method in class ambit2.rest.QueryStaXReporter
 
createRecordWriter(Request, ResourceDoc) - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
createReference - Variable in class ambit2.db.update.property.CreateProperty
 
CreateReference - Class in ambit2.db.update.reference
 
CreateReference(ILiteratureEntry) - Constructor for class ambit2.db.update.reference.CreateReference
 
CreateReference() - Constructor for class ambit2.db.update.reference.CreateReference
 
createReference(Connection) - Method in class ambit2.rest.model.task.CallableModelCreator
Writes the model into database and returns a reference
createReference(Connection) - Method in class ambit2.rest.model.task.CallableModelPredictor
Returns reference to the same dataset, with additional features, predicted by the model
createReference(Connection) - Method in class ambit2.rest.task.CallableQueryProcessor
 
createReference(Connection) - Method in class ambit2.rest.task.weka.CallableWekaModelCreator
 
createResource(String) - Method in class ambit2.rest.rdf.RDFBookmarkIterator
 
createResource(String) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
createResource(String) - Method in class ambit2.rest.rdf.RDFReferenceIterator
 
createResult(IStructureRecord) - Method in class ambit2.db.readers.ValuesByTemplateReader
 
createResult(IStructureRecord) - Method in class ambit2.db.search.property.ValuesReader
 
createResult() - Method in class ambit2.descriptors.processors.AbstractDescriptorFactory
 
createResult() - Method in class ambit2.descriptors.processors.DescriptorsFactory
 
createResultReference() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
createRichTextString(String, Font) - Method in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
createRulePairsWriters() - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
createSearchValueParam() - Method in class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
createSearchValueParam() - Method in class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
createSearchValueParam() - Method in class ambit2.db.update.dataset.DatasetQueryFieldString
 
createShared() - Method in class ambit2.db.results.AmbitRows
 
CreateSMARTSData - Class in ambit2.db.update.qlabel.smarts
 
CreateSMARTSData() - Constructor for class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
createSmartsPattern(String, boolean) - Method in interface ambit2.smarts.query.ISmartsPatternFactory
 
createSmartsPattern(String, boolean) - Method in class ambit2.smarts.query.SmartsPatternFactory
 
createSmartsPattern(SmartsPatternFactory.SmartsParser, String, boolean) - Static method in class ambit2.smarts.query.SmartsPatternFactory
 
createStartingMaterialsFile(File, File, Map<String, Integer>, StartingMaterialsDataBase.StartMaterialStandartization) - Static method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
createStats() - Method in class ambit2.similarity.stats.AbstractModelStatistics
 
createStats() - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
createStats() - Method in class ambit2.similarity.stats.PredictionModelStatistics
 
createStatsButton() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
createStatsFields() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
CreateStoredQuery - Class in ambit2.db.update.storedquery
 
CreateStoredQuery() - Constructor for class ambit2.db.update.storedquery.CreateStoredQuery
 
createStructure - Variable in class ambit2.db.processors.DbStructureWriter
 
CreateStructure - Class in ambit2.db.update.structure
 
CreateStructure(IStructureRecord) - Constructor for class ambit2.db.update.structure.CreateStructure
 
CreateStructure() - Constructor for class ambit2.db.update.structure.CreateStructure
 
createStructureComponent() - Method in class ambit2.dbui.QuerySimilarityEditor
 
CreateStructureQLabel - Class in ambit2.db.update.qlabel
Adds a quality label per structure
CreateStructureQLabel(IStructureRecord, QLabel) - Constructor for class ambit2.db.update.qlabel.CreateStructureQLabel
 
CreateStructureQLabel() - Constructor for class ambit2.db.update.qlabel.CreateStructureQLabel
 
createStructureRecord() - Method in class ambit2.core.io.RawIteratingWrapper
 
CreateStrucType - Class in ambit2.db.update.structure
Writes structure type value into table structure
CreateStrucType() - Constructor for class ambit2.db.update.structure.CreateStrucType
 
createSubLevels - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
CreateSubstance - Class in ambit2.db.substance
 
CreateSubstance(SubstanceRecord) - Constructor for class ambit2.db.substance.CreateSubstance
 
CreateSubstance() - Constructor for class ambit2.db.substance.CreateSubstance
 
createSubstanceStudyUpdateQuery(ProtocolApplication) - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
createSubstanceStudyUpdateQuery(ProtocolApplication) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
createTables(String) - Method in class ambit2.db.processors.DbCreateDatabase
 
createTarget(Reference) - Method in class ambit2.rest.model.task.CallableModelPredictor
 
createTarget(Reference) - Method in class ambit2.rest.task.CallableNumericalModelCreator
 
createTarget(Reference) - Method in class ambit2.rest.task.CallableQueryProcessor
 
createTarget(Reference) - Method in class ambit2.rest.task.weka.CallableWekaModelCreator
 
createTarget(Reference) - Method in class ambit2.rest.task.weka.CallableWekaPredictor
 
createTask(USERID, ICallableTask) - Method in class ambit2.rest.task.TaskStorage
 
createTaskConvertor(Variant, Request, ResourceDoc, DisplayMode) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskReporter(Variant, Request, ResourceDoc, DisplayMode) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskReporterHTML(Request, ResourceDoc, DisplayMode) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskReporterJSON(Variant, Request, ResourceDoc) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskReporterRDF(Variant, Request, ResourceDoc) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskReporterURI(Request, ResourceDoc) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskRepresentation(UUID, Variant, Request, Response, ResourceDoc) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskRepresentation(Iterator<UUID>, Variant, Request, Response, ResourceDoc) - Method in class ambit2.rest.task.FactoryTaskConvertor
 
createTaskStorage() - Method in class ambit2.rest.TaskApplication
 
createTemplate(Dictionary, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
createTemplate() - Method in class ambit2.rest.rdf.RDFAlgorithmIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFBookmarkIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFMetaDatasetIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFModelIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFReferenceIterator
 
createTemplate() - Method in class ambit2.rest.rdf.RDFResourceIterator
 
createTempWriter() - Method in class ambit2.db.reporters.ARFFReporter
 
createThresholdComponent() - Method in class ambit2.dbui.QuerySimilarityEditor
 
createURIReporter(Request, ResourceDoc) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
createURIReporter(Request, ResourceDoc) - Method in class ambit2.rest.QueryStaXReporter
 
createURIReporter(Request, ResourceDoc) - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
createURIReporter(Request, ResourceDoc) - Method in class ambit2.rest.substance.SubstanceRDFReporter
 
createValueComponent() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
createValueComponent() - Method in class ambit2.dbui.QueryDatasetEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryFieldEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryStoredResultsEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryStructureByQualityEditor
 
createValueComponent() - Method in class ambit2.dbui.QueryStructureByValueQualityEditor
 
CreateValueQLabel - Class in ambit2.db.update.qlabel
 
CreateValueQLabel(Integer, QLabel) - Constructor for class ambit2.db.update.qlabel.CreateValueQLabel
 
CreateValueQLabel() - Constructor for class ambit2.db.update.qlabel.CreateValueQLabel
 
createWriter(File) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
createWriter(String) - Static method in class ambit2.reactions.io.ReactionWriteUtils
 
createWriter(String) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
createWriters() - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
creator - Variable in class ambit2.core.data.model.ModelWrapper
 
creator - Variable in class ambit2.db.facets.bookmarks.BookmarksByTopicFacet
 
creator - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
credentials - Variable in class ambit2.rest.wrapper.WrappedService
 
cReference - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cReversibility - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CriticalEffectsObserved - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CrossSectionalDiameterDescriptor - Class in ambit2.descriptors
Cross sectional diameter.
CrossSectionalDiameterDescriptor() - Constructor for class ambit2.descriptors.CrossSectionalDiameterDescriptor
 
crossValidation - Variable in class ambit2.groupcontribution.GCMTestConfig
 
CrossValidation - Class in ambit2.groupcontribution.utils.math
 
CrossValidation() - Constructor for class ambit2.groupcontribution.utils.math.CrossValidation
 
CrossValidation(int) - Constructor for class ambit2.groupcontribution.utils.math.CrossValidation
 
CrossValidation(int, int, CrossValidation.ObjectSelection) - Constructor for class ambit2.groupcontribution.utils.math.CrossValidation
 
crossValidation - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
CrossValidation.ObjectSelection - Enum in ambit2.groupcontribution.utils.math
 
crossValidationFold - Variable in class ambit2.groupcontribution.GCMTestConfig
 
cRoute - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cRouteAdm - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSalinity - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSEQ_NUM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSex - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CSLS_URL - Static variable in class ambit2.search.csls.CSLSRequest
 
CSLSImageRequest - Class in ambit2.search.csls
http://cactus.nci.nih.gov/chemical/structure/c1ccccc1/image
CSLSImageRequest() - Constructor for class ambit2.search.csls.CSLSImageRequest
 
CSLSRequest<R> - Class in ambit2.search.csls
 
CSLSRequest() - Constructor for class ambit2.search.csls.CSLSRequest
 
CSLSStringRequest - Class in ambit2.search.csls
 
CSLSStringRequest() - Constructor for class ambit2.search.csls.CSLSStringRequest
 
CSLSStringRequest(NCISearchProcessor.METHODS) - Constructor for class ambit2.search.csls.CSLSStringRequest
 
cSoilNo - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSoilType - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSolvent - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cSpecies - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CSVFeatureValuesIterator<PROPERTY> - Class in ambit2.rest.legacy
Deprecated.
CSVFeatureValuesIterator(String) - Constructor for class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
CSVFORMAT_SPACE - Variable in class ambit2.core.io.fp.MultiFingerprintsWriter
 
CSVReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
CSVReporter() - Constructor for class ambit2.db.reporters.CSVReporter
 
CSVReporter(String, Template) - Constructor for class ambit2.db.reporters.CSVReporter
 
CSVReporter(String, Template, Profile, String) - Constructor for class ambit2.db.reporters.CSVReporter
 
CSVReporter(String, Template, Profile, String[], SubstanceEndpointsBundle[], String, boolean) - Constructor for class ambit2.db.reporters.CSVReporter
 
cTargetGene - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTemperature - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTestMedium - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTestOrganism - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTestType - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CTIDescriptor - Class in ambit2.descriptors.topological
Charge-related Topological Index (CTI) TODO: reference
CTIDescriptor() - Constructor for class ambit2.descriptors.topological.CTIDescriptor
 
cTimePoint - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cToxicity - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTypeCoverage - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTypeGenotoxicity - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTypeMethod - Static variable in class ambit2.base.ro.I5CONSTANTS
 
cTypeStudy - Static variable in class ambit2.base.ro.I5CONSTANTS
 
CubicRootMolecularWeightDescriptor - Class in ambit2.descriptors.constitutional
Cubic root molecular weight.
CubicRootMolecularWeightDescriptor() - Constructor for class ambit2.descriptors.constitutional.CubicRootMolecularWeightDescriptor
 
curCSVRecord - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
curLayerAtoms - Variable in class ambit2.smarts.AtomEquivalenceInfo
 
curLocalProperties - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
curMaxLevel - Variable in class ambit2.reactions.reactor.ReactorResult
 
curMolId - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
currentIcon - Variable in class ambit2.ui.table.BrowsableTableModel
 
currentPage - Variable in class ambit2.ui.table.PageNavigator
 
currentPage - Variable in class ambit2.ui.table.RecordNavigator
 
currentRecord - Variable in class ambit2.core.io.FileState
 
currentRecord - Variable in class ambit2.core.processors.batch.DefaultIOState
 
currentRecord - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
currentRecordNum - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
currentSide - Variable in class ambit2.db.processors.ProcessorOntology
 
curState - Variable in class ambit2.tautomers.RuleInstance
 
custom_description - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_license - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_logo - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_query - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_search - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_structurequery - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
custom_title - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
customizeJob() - Method in class ambit2.core.io.MDLReader
 
customizeVariants(MediaType[]) - Method in class ambit2.rest.AbstractResource
 
CustomTautomerFilters - Class in ambit2.tautomers.tools
 
CustomTautomerFilters() - Constructor for class ambit2.tautomers.tools.CustomTautomerFilters
 
CustomTautomerRegion - Class in ambit2.tautomers.rules
 
CustomTautomerRegion() - Constructor for class ambit2.tautomers.rules.CustomTautomerRegion
 
cycles - Variable in class ambit2.structure2name.IUPACNameGenerator
 
cyclicAtoms - Variable in class ambit2.structure2name.IUPACNameGenerator
 
CyclicComponent - Class in ambit2.structure2name.components
 
CyclicComponent() - Constructor for class ambit2.structure2name.components.CyclicComponent
 
cyclicComponents - Variable in class ambit2.structure2name.IUPACNameGenerator
 
cyclomaticNum - Variable in class ambit2.structure2name.IUPACNameGenerator
 
cyclomaticNumber(IAtomContainer) - Static method in class ambit2.reactions.rules.scores.RingComplexity
 
cYear - Static variable in class ambit2.base.ro.I5CONSTANTS
 

D

d - Variable in class ambit2.db.processors.DescriptorsCalculator
 
d - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
d - Variable in class ambit2.db.simiparity.space.QMapSpace
 
D_t(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
dash - Static variable in class ambit2.base.processors.CASProcessor
 
Data - Class in ambit2.export.isa.v1_0.objects
ISA data schema JSON-schema representing a data file in the ISA model
Data() - Constructor for class ambit2.export.isa.v1_0.objects.Data
 
Data.Type - Enum in ambit2.export.isa.v1_0.objects
 
DATABASE - Static variable in class ambit2.base.config.Preferences
 
database - Variable in class ambit2.db.LoginInfo
 
database_create - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
DataCoverage<DATA> - Class in ambit2.model.numeric
A parent class to all classess that estimate and assess applicability domain
DataCoverage() - Constructor for class ambit2.model.numeric.DataCoverage
 
DataCoverage(ADomainMethodType) - Constructor for class ambit2.model.numeric.DataCoverage
 
DataCoverageDensity - Class in ambit2.model.numeric
A class to estimate applicability domain by nonparametric probability density estimation
DataCoverageDensity() - Constructor for class ambit2.model.numeric.DataCoverageDensity
 
DataCoverageDescriptors - Class in ambit2.model.numeric
A parent class for all classes that estimate applicability domain in descriptor space This clas estimates descriptor ranges in PCA space
DataCoverageDescriptors() - Constructor for class ambit2.model.numeric.DataCoverageDescriptors
DataCoverage constructor Default mode modeRANGE
DataCoverageDescriptors(ADomainMethodType) - Constructor for class ambit2.model.numeric.DataCoverageDescriptors
DataCoverage constructor
DataCoverageDistance - Class in ambit2.model.numeric
A parent class for all classes that estimate applicability domain by distance in the descriptor space
DataCoverageDistance() - Constructor for class ambit2.model.numeric.DataCoverageDistance
 
DataCoverageDistance(ADomainMethodType) - Constructor for class ambit2.model.numeric.DataCoverageDistance
 
DataCoverageDistanceCityBlock - Class in ambit2.model.numeric.distance
 
DataCoverageDistanceCityBlock() - Constructor for class ambit2.model.numeric.distance.DataCoverageDistanceCityBlock
 
DataCoverageDistanceEuclidean - Class in ambit2.model.numeric.distance
 
DataCoverageDistanceEuclidean() - Constructor for class ambit2.model.numeric.distance.DataCoverageDistanceEuclidean
 
DataCoverageDistanceMahalanobis - Class in ambit2.model.numeric.distance
 
DataCoverageDistanceMahalanobis() - Constructor for class ambit2.model.numeric.distance.DataCoverageDistanceMahalanobis
 
DataCoverageFingeprintsMissingFragments - Class in ambit2.model.structure
 
DataCoverageFingeprintsMissingFragments() - Constructor for class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
DataCoverageFingerprints - Class in ambit2.model.structure
A class to estimate applicability domain by fingerprints
DataCoverageFingerprints() - Constructor for class ambit2.model.structure.DataCoverageFingerprints
 
DataCoverageFingerprintsTanimoto - Class in ambit2.model.structure
 
DataCoverageFingerprintsTanimoto() - Constructor for class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
DataCoverageLeverage - Class in ambit2.model.numeric
 
DataCoverageLeverage() - Constructor for class ambit2.model.numeric.DataCoverageLeverage
 
DataCoverageLeverageHatMatrix - Class in ambit2.model.numeric
Leverage
DataCoverageLeverageHatMatrix() - Constructor for class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
dataEntryID - Variable in class ambit2.base.data.StructureRecord
 
DataFile - Class in ambit2.export.isa.v1_0.objects
 
DataFile() - Constructor for class ambit2.export.isa.v1_0.objects.DataFile
 
dataFileFormat - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
dataFileFormat - Variable in class ambit2.export.isa.ISAExportConfig
 
dataFiles - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
dataFiles - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
dataformat - Variable in class ambit2.core.io.XLSFileWriter
 
dataformat - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
DataGroup - Class in ambit2.core.groups
Corresponds to DAT group found in MOL files
DataGroup(String, int) - Constructor for class ambit2.core.groups.DataGroup
 
DataGroup.DGROUP_DISPLAY - Enum in ambit2.core.groups
 
DataGroup.SGROUP_FIELD - Enum in ambit2.core.groups
 
dataModel - Variable in class ambit2.ui.table.BrowsableTableModel
 
dataObjects - Variable in class ambit2.groupcontribution.dataset.DataSet
 
DataResources - Class in ambit2.rest
 
DATASET - Static variable in class ambit2.core.config.AmbitCONSTANTS
Dataset source (table struc_dataset)
dataset - Variable in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
dataset - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
dataset - Variable in class ambit2.db.processors.DbStructureWriter
 
dataset - Variable in class ambit2.db.processors.ValueWriterNew
 
dataset - Variable in class ambit2.db.search.QueryInfo
 
dataset - Variable in class ambit2.dbui.QueryInfoEditor
 
DataSet - Class in ambit2.groupcontribution.dataset
 
DataSet() - Constructor for class ambit2.groupcontribution.dataset.DataSet
 
DataSet(File) - Constructor for class ambit2.groupcontribution.dataset.DataSet
 
dataset(Reference) - Static method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
dataset(String) - Static method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
dataset - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
dataset - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
dataset_members_prefix - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
dataset_prefixed_compound_uri() - Method in class ambit2.rest.DBConnection
 
dataset_service - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
dataset_service - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
dataset_service - Variable in class ambit2.rest.task.LauncherResource
 
dataset_uri - Variable in class ambit2.rest.task.LauncherResource
 
datasetAddStruc - Variable in class ambit2.db.processors.DbStructureWriter
 
datasetAddStruc - Variable in class ambit2.db.processors.PropertyImporter
 
DatasetAddStructure - Class in ambit2.db.update.dataset
 
DatasetAddStructure(SourceDataset, IStructureRecord) - Constructor for class ambit2.db.update.dataset.DatasetAddStructure
 
DatasetAddStructure() - Constructor for class ambit2.db.update.dataset.DatasetAddStructure
 
DatasetByPrefixNameFacetQuery - Class in ambit2.db.facets.datasets
getFieldname - prefix length getValue - first letters of the prefix (could be null)
DatasetByPrefixNameFacetQuery(String) - Constructor for class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
datasetCenterPoint - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
DatasetCenterPoint - Enum in ambit2.model.numeric
A center point for the distance applicability domain methods
DatasetChemicalsQualityStats - Class in ambit2.db.facets.qlabel
 
DatasetChemicalsQualityStats(String) - Constructor for class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
DatasetConsensusLabelFacet - Class in ambit2.db.facets.qlabel
'CHRIP-www.safe.nite.go.jp', 46, 'Consensus', '2' 'CHRIP-www.safe.nite.go.jp', 799, 'Consensus', '3' 'CHRIP-www.safe.nite.go.jp', 1, 'Majority', '1:1:2' 'CHRIP-www.safe.nite.go.jp', 69, 'Majority', '1:2' 'CHRIP-www.safe.nite.go.jp', 12, 'Unconfirmed', '1' 'CHRIP-www.safe.nite.go.jp', 21, 'Ambiguous', '1:1' 'CHRIP-www.safe.nite.go.jp', 7, 'Ambiguous', '1:1:1'
DatasetConsensusLabelFacet(String) - Constructor for class ambit2.db.facets.qlabel.DatasetConsensusLabelFacet
 
DatasetDeleteStructure - Class in ambit2.db.update.dataset
 
DatasetDeleteStructure(SourceDataset, IStructureRecord) - Constructor for class ambit2.db.update.dataset.DatasetDeleteStructure
 
DatasetDeleteStructure() - Constructor for class ambit2.db.update.dataset.DatasetDeleteStructure
 
datasetIndividual - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
datasetMeta() - Static method in class ambit2.db.substance.processor.DBSubstanceWriter
 
DataSetObject - Class in ambit2.groupcontribution.dataset
 
DataSetObject() - Constructor for class ambit2.groupcontribution.dataset.DataSetObject
 
DataSetObject(IAtomContainer) - Constructor for class ambit2.groupcontribution.dataset.DataSetObject
 
DataSetObjectIterator - Class in ambit2.groupcontribution.dataset
 
DataSetObjectIterator(File, File, int) - Constructor for class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
DataSetObjectIterator(File, File) - Constructor for class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
DatasetPrefixFacet - Class in ambit2.db.facets.datasets
 
DatasetPrefixFacet(String) - Constructor for class ambit2.db.facets.datasets.DatasetPrefixFacet
 
DatasetQueryFieldGeneric<T,C extends net.idea.modbcum.i.IQueryCondition> - Class in ambit2.db.update.dataset
 
DatasetQueryFieldGeneric() - Constructor for class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
DatasetQueryFieldNumeric - Class in ambit2.db.update.dataset
 
DatasetQueryFieldNumeric() - Constructor for class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
DatasetQueryFieldString - Class in ambit2.db.update.dataset
 
DatasetQueryFieldString() - Constructor for class ambit2.db.update.dataset.DatasetQueryFieldString
 
DatasetRDFStaxReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.rest.dataset
DatasetRDFStaxReporter(String, Request, Template, Profile) - Constructor for class ambit2.rest.dataset.DatasetRDFStaxReporter
 
DatasetRDFWriter - Class in ambit2.rest.dataset
 
DatasetRDFWriter(Reference, ResourceDoc) - Constructor for class ambit2.rest.dataset.DatasetRDFWriter
 
DatasetRDFWriter(Request, ResourceDoc) - Constructor for class ambit2.rest.dataset.DatasetRDFWriter
 
DatasetRDFWriter(CompoundURIReporter<IQueryRetrieval<IStructureRecord>>, PropertyURIReporter) - Constructor for class ambit2.rest.dataset.DatasetRDFWriter
 
DatasetRDFWriter(CompoundURIReporter<IQueryRetrieval<IStructureRecord>>, PropertyURIReporter, QueryURIReporter<IStructureRecord, IQueryRetrieval<IStructureRecord>>) - Constructor for class ambit2.rest.dataset.DatasetRDFWriter
 
DataSetReader - Class in ambit2.groupcontribution.io
 
DataSetReader() - Constructor for class ambit2.groupcontribution.io.DataSetReader
 
datasetReportRef - Variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
datasets - Static variable in class ambit2.db.search.QueryInfo
 
datasets - Variable in class ambit2.dbui.QueryDatasetEditor
 
datasets(String, String) - Static method in class ambit2.rest.legacy.OTDatasets
Deprecated.
 
datasets1 - Variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
datasets2 - Variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
datasetService - Variable in class ambit2.rest.task.CallableDatasetCreator
 
DatasetStructureQLabelFacet - Class in ambit2.db.facets.qlabel
 
DatasetStructureQLabelFacet(String) - Constructor for class ambit2.db.facets.qlabel.DatasetStructureQLabelFacet
 
DatasetStructureQualityStats - Class in ambit2.db.facets.qlabel
 
DatasetStructureQualityStats(String) - Constructor for class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
DatasetStrucTypeFacet - Class in ambit2.db.facets.qlabel
 
DatasetStrucTypeFacet(String) - Constructor for class ambit2.db.facets.qlabel.DatasetStrucTypeFacet
 
DatasetStrucTypeStats - Class in ambit2.db.facets.qlabel
 
DatasetStrucTypeStats(String) - Constructor for class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
DatasetTemplateAddProperty - Class in ambit2.db.update.dictionary
 
DatasetTemplateAddProperty(SourceDataset, Property) - Constructor for class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
DatasetTemplateAddProperty() - Constructor for class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
datasetURI - Variable in class ambit2.rest.model.builder.ExpertModelBuilder
 
datasetURI - Variable in class ambit2.rest.task.CallableDatasetCreator
 
DatasetURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<M>,M extends ISourceDataset> - Class in ambit2.rest.dataset
 
DatasetURIReporter(Request) - Constructor for class ambit2.rest.dataset.DatasetURIReporter
 
DatasetURIReporter(Reference) - Constructor for class ambit2.rest.dataset.DatasetURIReporter
 
DatasetURIReporter() - Constructor for class ambit2.rest.dataset.DatasetURIReporter
 
date - Variable in class ambit2.export.isa.v1_0.objects.Process
 
dateformatter - Static variable in class ambit2.base.data.study.ProtocolApplication
 
DB_AA_ENABLED - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
DBBundleStudyWriter - Class in ambit2.db.substance.processor
 
DBBundleStudyWriter(SubstanceEndpointsBundle, SourceDataset, SubstanceRecord) - Constructor for class ambit2.db.substance.processor.DBBundleStudyWriter
 
DbCompoundImageTools - Class in ambit2.db.readers
 
DbCompoundImageTools() - Constructor for class ambit2.db.readers.DbCompoundImageTools
 
DbCompoundImageTools(Dimension) - Constructor for class ambit2.db.readers.DbCompoundImageTools
 
DBConnection - Class in ambit2.rest
 
DBConnection(Context) - Constructor for class ambit2.rest.DBConnection
 
DbCreateDatabase - Class in ambit2.db.processors
 
DbCreateDatabase() - Constructor for class ambit2.db.processors.DbCreateDatabase
 
DbCreateDatabase(String, String) - Constructor for class ambit2.db.processors.DbCreateDatabase
 
DbCreateDatabase(String, String, String, String) - Constructor for class ambit2.db.processors.DbCreateDatabase
 
DbDescriptorValuesWriter - Class in ambit2.db.processors
Writes descriptor values into properties/property_values tables
DbDescriptorValuesWriter() - Constructor for class ambit2.db.processors.DbDescriptorValuesWriter
 
DbDescriptorWriter - Class in ambit2.db.processors
 
DbDescriptorWriter() - Constructor for class ambit2.db.processors.DbDescriptorWriter
 
dbExists(Connection, String) - Static method in class ambit2.db.processors.DbCreateDatabase
 
DBMatrixValueMarker - Class in ambit2.db.substance.processor
 
DBMatrixValueMarker(SubstanceEndpointsBundle) - Constructor for class ambit2.db.substance.processor.DBMatrixValueMarker
 
dbname - Variable in class ambit2.db.version.AmbitDBVersion
 
DBProcessorsChain<Target,Result,P extends net.idea.modbcum.i.IDBProcessor<Target,Result>> - Class in ambit2.db.processors
 
DBProcessorsChain() - Constructor for class ambit2.db.processors.DBProcessorsChain
 
DbReader<ResultType> - Class in ambit2.db
 
DbReader() - Constructor for class ambit2.db.DbReader
 
DbReader.cached_results - Enum in ambit2.db
 
DbReaderStructure - Class in ambit2.db
Reads structures given a query.
DbReaderStructure() - Constructor for class ambit2.db.DbReaderStructure
 
DbReaderStructure(boolean) - Constructor for class ambit2.db.DbReaderStructure
 
DbStructureWriter - Class in ambit2.db.processors
 
DbStructureWriter(SourceDataset) - Constructor for class ambit2.db.processors.DbStructureWriter
 
DBSubstanceWriter - Class in ambit2.db.substance.processor
Writes IUCLID5 substances
DBSubstanceWriter(SourceDataset, SubstanceRecord, boolean, boolean) - Constructor for class ambit2.db.substance.processor.DBSubstanceWriter
 
DBSubstanceWriter(SourceDataset, SubstanceRecord, boolean, boolean, IStructureKey) - Constructor for class ambit2.db.substance.processor.DBSubstanceWriter
 
DBVersion - Interface in ambit2.db
 
DBVersionQuery - Class in ambit2.db.version
 
DBVersionQuery() - Constructor for class ambit2.db.version.DBVersionQuery
 
dc - Static variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
dcPrefix - Static variable in class ambit2.base.data.ChEMBLProperties
 
dcterms - Static variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
debug(String) - Method in class ambit2.dragon.DescriptorDragonShell
 
debug(String) - Method in class ambit2.mopac.DescriptorMopacShell
 
debug(String) - Method in class ambit2.some.DescriptorSOMEShell
 
debugInfo(IAtomContainer) - Method in class ambit2.tautomers.RuleInstance
 
debugInfo() - Method in class ambit2.tautomers.TautomerIncrementStep
 
debugStack() - Method in class ambit2.tautomers.RuleManager
 
DecimalAdjVector_A1(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
DecimalAdjVector_A10(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
DecimalAdjVector_A2(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
DecimalAdjVector_A3(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
decode(String) - Static method in class ambit2.descriptors.fingerprints.PubChemFingerprinter
Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
decode(String) - Static method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
decrement() - Method in class ambit2.similarity.stats.MutableInt
 
DEFAULT_DIR - Static variable in class ambit2.base.config.Preferences
 
DEFAULT_DIR - Static variable in class ambit2.core.config.Resources
default dir
default_mopac_commands - Variable in class ambit2.mopac.Mopac7Writer
 
Default_name - Static variable in class ambit2.base.data.LiteratureEntry
 
DEFAULT_TXT_FILE_COLUMN_NAMES - Static variable in class ambit2.reactions.ReactionDataBase
 
default_values - Static variable in class ambit2.base.config.Preferences
 
default_values - Static variable in class ambit2.ui.EditorPreferences
 
DefaultFragmentationRules - Class in ambit2.reactions.fragmentation
 
DefaultFragmentationRules() - Constructor for class ambit2.reactions.fragmentation.DefaultFragmentationRules
 
defaultImage - Variable in class ambit2.rendering.CompoundImageTools
 
DefaultInputState - Class in ambit2.core.processors.batch
 
DefaultInputState(IIteratingChemObjectReader) - Constructor for class ambit2.core.processors.batch.DefaultInputState
 
DefaultIOState - Class in ambit2.core.processors.batch
 
DefaultIOState() - Constructor for class ambit2.core.processors.batch.DefaultIOState
 
defaultparams - Static variable in class ambit2.mopac.AbstractMopacShell
 
defaultSMILESHeader - Static variable in class ambit2.core.io.FilesWithHeaderWriter
 
defaultSMILESHeader - Static variable in class ambit2.core.io.FileWithHeaderWriter
 
defaultSMILESHeader - Static variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
delay - Variable in class ambit2.rest.task.CallableMockup
 
delete(T) - Method in class ambit2.core.groups.FilteredList
 
delete(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
delete(Group) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
delete - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
delete(OTAlgorithm) - Method in class ambit2.rest.legacy.OTAlgorithms
Deprecated.
 
delete(T) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
delete(OTDataset) - Method in class ambit2.rest.legacy.OTDatasets
Deprecated.
 
delete(OTFeature) - Method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
delete() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
delete_composition - Static variable in class ambit2.db.substance.relation.DeleteSubstanceRelation
 
delete_sql - Static variable in class ambit2.db.chemrelation.DeleteStructureRelation
 
delete_sql - Static variable in class ambit2.db.substance.DeleteSubstance
 
delete_sql - Static variable in class ambit2.db.substance.relation.DeleteSubstanceRelation
 
delete_sql - Static variable in class ambit2.db.substance.study.DeleteEffectRecords
 
delete_sql - Static variable in class ambit2.db.substance.study.DeleteStudy
 
delete_sql - Static variable in class ambit2.db.update.bookmark.DeleteBookmark
 
delete_sql - Static variable in class ambit2.db.update.chemical.DeleteChemical
 
delete_sql - Static variable in class ambit2.db.update.dataset.DatasetDeleteStructure
 
delete_sql - Static variable in class ambit2.db.update.dictionary.DeleteDictionary
 
delete_sql - Static variable in class ambit2.db.update.dictionary.TemplateDeleteProperty
 
delete_sql - Static variable in class ambit2.db.update.model.DeleteModel
 
delete_sql - Static variable in class ambit2.db.update.property.DeleteProperty
 
delete_sql - Static variable in class ambit2.db.update.reference.DeleteReference
 
delete_sql - Static variable in class ambit2.db.update.storedquery.DeleteStoredQuery
 
delete_sql - Static variable in class ambit2.db.update.storedquery.QueryDeleteStructure
 
delete_sql - Static variable in class ambit2.db.update.structure.DeleteStructure
 
delete_sql_by_id - Static variable in class ambit2.db.update.bundle.DeleteBundle
 
delete_sql_by_id - Static variable in class ambit2.db.update.dataset.DeleteDataset
 
delete_sql_chemical - Static variable in class ambit2.db.update.dataset.DatasetDeleteStructure
 
delete_sql_chemical - Static variable in class ambit2.db.update.storedquery.QueryDeleteStructure
 
deleteAtom(IAtom, TetrahedralChirality, StereoChange) - Static method in class ambit2.smarts.smirks.StereoTransformation
 
deleteAtom(IAtom, DoubleBondStereochemistry, StereoChange) - Static method in class ambit2.smarts.smirks.StereoTransformation
 
deleteAtom(IAtom, TetrahedralChirality) - Static method in class ambit2.smarts.StereoChemUtils
 
deleteAtom(IAtom, ExtendedTetrahedral) - Static method in class ambit2.smarts.StereoChemUtils
 
deleteAtom(IAtom, DoubleBondStereochemistry, StereoChange) - Static method in class ambit2.smarts.StereoChemUtils
 
DeleteAtomEnvironment - Class in ambit2.db.update.fpae
 
DeleteAtomEnvironment() - Constructor for class ambit2.db.update.fpae.DeleteAtomEnvironment
 
DeleteBookmark - Class in ambit2.db.update.bookmark
deletes bookmark
DeleteBookmark(Bookmark) - Constructor for class ambit2.db.update.bookmark.DeleteBookmark
 
DeleteBookmark() - Constructor for class ambit2.db.update.bookmark.DeleteBookmark
 
DeleteBundle - Class in ambit2.db.update.bundle
 
DeleteBundle(SubstanceEndpointsBundle, int) - Constructor for class ambit2.db.update.bundle.DeleteBundle
 
DeleteBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.DeleteBundle
 
DeleteBundle() - Constructor for class ambit2.db.update.bundle.DeleteBundle
 
DeleteChemical - Class in ambit2.db.update.chemical
 
DeleteChemical(IChemical) - Constructor for class ambit2.db.update.chemical.DeleteChemical
 
DeleteChemical() - Constructor for class ambit2.db.update.chemical.DeleteChemical
 
DeleteChemicalsFromBundle - Class in ambit2.db.update.bundle.chemicals
 
DeleteChemicalsFromBundle(SubstanceEndpointsBundle, IStructureRecord) - Constructor for class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
DeleteChemicalsFromBundle(IStructureRecord) - Constructor for class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
DeleteChemicalsFromBundle() - Constructor for class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
deleted - Variable in class ambit2.base.data.study.ValueAnnotated
 
DELETED_ATOM - Static variable in class ambit2.smarts.smirks.StereoTransformation
 
DeleteDataset - Class in ambit2.db.update.dataset
 
DeleteDataset(SourceDataset, int) - Constructor for class ambit2.db.update.dataset.DeleteDataset
 
DeleteDataset(SourceDataset) - Constructor for class ambit2.db.update.dataset.DeleteDataset
 
DeleteDataset() - Constructor for class ambit2.db.update.dataset.DeleteDataset
 
DeleteDictionary - Class in ambit2.db.update.dictionary
 
DeleteDictionary(Dictionary) - Constructor for class ambit2.db.update.dictionary.DeleteDictionary
 
DeleteDictionary() - Constructor for class ambit2.db.update.dictionary.DeleteDictionary
 
DeleteEffectRecords - Class in ambit2.db.substance.study
deletes effects records given document uuid
DeleteEffectRecords(ProtocolApplication<Protocol, Params, String, Params, String>) - Constructor for class ambit2.db.substance.study.DeleteEffectRecords
 
DeleteEffectRecords() - Constructor for class ambit2.db.substance.study.DeleteEffectRecords
 
DeleteEndpointFromBundle - Class in ambit2.db.update.bundle.endpoints
 
DeleteEndpointFromBundle(SubstanceEndpointsBundle, SubstanceProperty) - Constructor for class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
DeleteEndpointFromBundle(SubstanceProperty) - Constructor for class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
DeleteEndpointFromBundle() - Constructor for class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
deleteMatrix - Variable in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
DeleteMatrixFromBundle - Class in ambit2.db.update.bundle.matrix
 
DeleteMatrixFromBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.matrix.DeleteMatrixFromBundle
 
DeleteMatrixProtocolApplicationValue<VALUE> - Class in ambit2.db.update.bundle.matrix
Mark a value in the buncle_substance_experiments table (values copied from substance_experiment) as deleted (along with a comment why)
DeleteMatrixProtocolApplicationValue() - Constructor for class ambit2.db.update.bundle.matrix.DeleteMatrixProtocolApplicationValue
 
DeleteMatrixProtocolApplicationValue(SubstanceEndpointsBundle, ValueAnnotated<VALUE, String>) - Constructor for class ambit2.db.update.bundle.matrix.DeleteMatrixProtocolApplicationValue
 
DeleteMatrixValue<VALUE> - Class in ambit2.db.update.bundle.matrix
Mark a value in the buncle_substance_experiments table (values copied from substance_experiment) as deleted (along with a comment why)
DeleteMatrixValue() - Constructor for class ambit2.db.update.bundle.matrix.DeleteMatrixValue
 
DeleteMatrixValue(SubstanceEndpointsBundle, ValueAnnotated<VALUE, Integer>) - Constructor for class ambit2.db.update.bundle.matrix.DeleteMatrixValue
 
DeleteModel - Class in ambit2.db.update.model
 
DeleteModel(ModelQueryResults) - Constructor for class ambit2.db.update.model.DeleteModel
 
DeleteModel() - Constructor for class ambit2.db.update.model.DeleteModel
 
deleteOnClose - Variable in class ambit2.db.SessionID
 
deleteProperty(Property, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
DeleteProperty - Class in ambit2.db.update.property
 
DeleteProperty(Property) - Constructor for class ambit2.db.update.property.DeleteProperty
 
DeleteProperty() - Constructor for class ambit2.db.update.property.DeleteProperty
 
DeletePropertyAnnotation - Class in ambit2.db.update.propertyannotations
 
DeletePropertyAnnotation() - Constructor for class ambit2.db.update.propertyannotations.DeletePropertyAnnotation
 
DeleteQueryFolder - Class in ambit2.db.update.queryfolder
Delete an entire query folder
DeleteQueryFolder(AmbitUser, SessionID) - Constructor for class ambit2.db.update.queryfolder.DeleteQueryFolder
 
DeleteReference - Class in ambit2.db.update.reference
 
DeleteReference(ILiteratureEntry) - Constructor for class ambit2.db.update.reference.DeleteReference
 
DeleteReference() - Constructor for class ambit2.db.update.reference.DeleteReference
 
deleteRow() - Method in class ambit2.db.results.AmbitRows
 
DeleteStoredQuery - Class in ambit2.db.update.storedquery
 
DeleteStoredQuery(IStoredQuery) - Constructor for class ambit2.db.update.storedquery.DeleteStoredQuery
 
DeleteStoredQuery() - Constructor for class ambit2.db.update.storedquery.DeleteStoredQuery
 
DeleteStructure - Class in ambit2.db.update.structure
 
DeleteStructure(IStructureRecord) - Constructor for class ambit2.db.update.structure.DeleteStructure
 
DeleteStructure() - Constructor for class ambit2.db.update.structure.DeleteStructure
 
DeleteStructureQLabel - Class in ambit2.db.update.qlabel
Deletes quality label given a structure
DeleteStructureQLabel(IStructureRecord, QLabel) - Constructor for class ambit2.db.update.qlabel.DeleteStructureQLabel
 
DeleteStructureQLabel() - Constructor for class ambit2.db.update.qlabel.DeleteStructureQLabel
 
DeleteStructureRelation - Class in ambit2.db.chemrelation
 
DeleteStructureRelation() - Constructor for class ambit2.db.chemrelation.DeleteStructureRelation
 
DeleteStructureRelation(IStructureRecord, IStructureRecord, String) - Constructor for class ambit2.db.chemrelation.DeleteStructureRelation
 
DeleteStudy - Class in ambit2.db.substance.study
 
DeleteStudy() - Constructor for class ambit2.db.substance.study.DeleteStudy
 
DeleteSubstance - Class in ambit2.db.substance
 
DeleteSubstance(SubstanceRecord) - Constructor for class ambit2.db.substance.DeleteSubstance
 
DeleteSubstance() - Constructor for class ambit2.db.substance.DeleteSubstance
 
DeleteSubstanceFromBundle - Class in ambit2.db.update.bundle.substance
 
DeleteSubstanceFromBundle(SubstanceEndpointsBundle, SubstanceRecord) - Constructor for class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
DeleteSubstanceFromBundle(SubstanceRecord) - Constructor for class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
DeleteSubstanceFromBundle() - Constructor for class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
DeleteSubstanceRelation - Class in ambit2.db.substance.relation
Deletes row from substance_relation table
DeleteSubstanceRelation() - Constructor for class ambit2.db.substance.relation.DeleteSubstanceRelation
 
DeleteSubstanceRelation(SubstanceRecord, IStructureRecord, STRUCTURE_RELATION) - Constructor for class ambit2.db.substance.relation.DeleteSubstanceRelation
 
DeleteValueQLabel - Class in ambit2.db.update.qlabel
 
DeleteValueQLabel(Integer, QLabel) - Constructor for class ambit2.db.update.qlabel.DeleteValueQLabel
 
DeleteValueQLabel() - Constructor for class ambit2.db.update.qlabel.DeleteValueQLabel
 
delim - Static variable in class ambit2.core.data.MoleculeTools
 
DelimitedFileFormat - Class in ambit2.core.io
File format for delimited files
DelimitedFileFormat() - Constructor for class ambit2.core.io.DelimitedFileFormat
Default field delimiter ',' Default text delimiter '"'
DelimitedFileFormat(String, char) - Constructor for class ambit2.core.io.DelimitedFileFormat
 
DelimitedFileReader - Class in ambit2.core.io
 
DelimitedFileReader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileReader
Default delimited file format - CSV
DelimitedFileReader(Reader) - Constructor for class ambit2.core.io.DelimitedFileReader
 
DelimitedFileReader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileReader
 
DelimitedFileReader(InputStream) - Constructor for class ambit2.core.io.DelimitedFileReader
 
DelimitedFileWriter - Class in ambit2.core.io
Writes delimited files
DelimitedFileWriter(Writer, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileWriter
 
DelimitedFileWriter(Writer) - Constructor for class ambit2.core.io.DelimitedFileWriter
 
DelimitedFileWriter(OutputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileWriter
 
DelimitedFileWriter(OutputStream) - Constructor for class ambit2.core.io.DelimitedFileWriter
 
delimiter - Static variable in class ambit2.core.io.RawIteratingSDFReader
 
delimiter - Variable in class ambit2.db.reporters.ARFFReporter
 
delimiter - Variable in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
delimiter - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
delimiter - Variable in class ambit2.ui.DelimitersPanel
 
delimiters - Static variable in class ambit2.ui.DelimitersPanel
 
DelimitersPanel - Class in ambit2.ui
FileOpen dialog accessory
DelimitersPanel() - Constructor for class ambit2.ui.DelimitersPanel
 
DelimitersPanel(boolean) - Constructor for class ambit2.ui.DelimitersPanel
 
dependent - Variable in class ambit2.core.data.model.ModelWrapper
 
dependentVariables - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
depict - Variable in class ambit2.db.reporters.AbstractImageReporter
 
depict - Variable in class ambit2.db.reporters.PDFReporter
 
DepictRequest - Class in ambit2.pubchem
 
DepictRequest() - Constructor for class ambit2.pubchem.DepictRequest
 
deprecated() - Method in enum ambit2.base.data.study.Protocol._categories
 
DerivedMolecularWeightDescriptor - Class in ambit2.descriptors.constitutional
Parent class for molecular weight related descriptors
DerivedMolecularWeightDescriptor(String[]) - Constructor for class ambit2.descriptors.constitutional.DerivedMolecularWeightDescriptor
 
derivesFrom - Variable in class ambit2.export.isa.v1_0.objects.Material
 
derivesFrom - Variable in class ambit2.export.isa.v1_0.objects.Sample
 
descirptors - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
DescrData(double, double) - Constructor for class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager.DescrData
 
descrInstanceIndex - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
description - Variable in class ambit2.base.data.ClassHolder
 
description - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
description - Variable in class ambit2.base.io.AmbitFileFilter
 
description - Variable in class ambit2.base.io.MolFileFilter
 
description - Variable in class ambit2.core.data.model.Algorithm
 
description - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
description - Variable in class ambit2.export.isa.v1_0.objects.DataFile
 
description - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
description - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
description - Variable in class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
description - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
description - Variable in class ambit2.export.isa.v1_0.objects.Study
 
description - Variable in class ambit2.groupcontribution.groups.GroupInfo
 
descriptor - Variable in class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
DescriptorCalculationProcessor - Class in ambit2.descriptors.processors
 
DescriptorCalculationProcessor() - Constructor for class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
DescriptorCalculationProcessor(IMolecularDescriptor) - Constructor for class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
DescriptorCorrectionFactor - Class in ambit2.groupcontribution.correctionfactors
 
DescriptorCorrectionFactor(CDKDescriptorInfo, CDKDescriptorManager) - Constructor for class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
DescriptorDragonShell - Class in ambit2.dragon
Used by DescriptorDragonShell
Invokes dragon6shell (http://talete.it) DRAGON_HOME environment variable should point to Talete Dragon6 directory.
DescriptorDragonShell() - Constructor for class ambit2.dragon.DescriptorDragonShell
 
DescriptorEngineProcessor - Class in ambit2.descriptors.processors
Calculates descriptors found in cdk jars.
DescriptorEngineProcessor() - Constructor for class ambit2.descriptors.processors.DescriptorEngineProcessor
 
descriptorEntry(Target, Property, int, int) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
descriptorEntry(DescriptorValue, Property, int, int) - Method in class ambit2.db.processors.DbDescriptorWriter
 
descriptorEntry(Target, Property, int, int) - Method in class ambit2.db.processors.ValueWriter
 
DescriptorExpression - Class in ambit2.rules.conditions
 
DescriptorExpression() - Constructor for class ambit2.rules.conditions.DescriptorExpression
 
DescriptorExpression.LogicalOperation - Enum in ambit2.rules.conditions
 
DescriptorInfo - Class in ambit2.groupcontribution.correctionfactors
 
DescriptorInfo() - Constructor for class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
descriptorInstances - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
descriptorList - Variable in class ambit2.rules.conditions.AbstractDescriptorSolver
 
DescriptorMopacShell - Class in ambit2.mopac
Used by DescriptorMopacShell
Invokes mopac.exe from Mopac 7.1 http://openmopac.net/Downloads/Downloads.html.
Doesn't work for molecules with number of heavy atoms > 60, number of all atoms > 120.
DescriptorMopacShell() - Constructor for class ambit2.mopac.DescriptorMopacShell
 
descriptorName - Variable in class ambit2.rules.weight.DescriptorWeight
 
descriptorNames - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
descriptorNames - Variable in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
descriptorNames - Variable in class ambit2.dragon.DescriptorDragonShell
 
DescriptorPredictor<C extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord>> - Class in ambit2.rest.model.predictor
 
DescriptorPredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.DescriptorPredictor
 
DescriptorRangeScore - Class in ambit2.reactions.generator.score.components
 
DescriptorRangeScore() - Constructor for class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
DescriptorResultFormatter - Class in ambit2.descriptors.processors
Prints DescriptorValue as a string
DescriptorResultFormatter(boolean) - Constructor for class ambit2.descriptors.processors.DescriptorResultFormatter
 
DescriptorResultFormatter(Locale) - Constructor for class ambit2.descriptors.processors.DescriptorResultFormatter
 
DescriptorResultFormatter(Locale, int) - Constructor for class ambit2.descriptors.processors.DescriptorResultFormatter
 
DescriptorResultFormatter(boolean, int) - Constructor for class ambit2.descriptors.processors.DescriptorResultFormatter
 
descriptors - Variable in class ambit2.db.processors.AbstractDescriptorCalculator
 
descriptors - Variable in class ambit2.dragon.DragonDescriptorDictionary
 
descriptors - Variable in class ambit2.dragon.DragonShell
 
descriptors - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
DescriptorsCalculator - Class in ambit2.db.processors
 
DescriptorsCalculator() - Constructor for class ambit2.db.processors.DescriptorsCalculator
 
DescriptorsFactory - Class in ambit2.descriptors.processors
 
DescriptorsFactory() - Constructor for class ambit2.descriptors.processors.DescriptorsFactory
 
descriptorSolver - Variable in class ambit2.reactions.reactor.Reactor
 
DescriptorSolverSet - Class in ambit2.rules.conditions
 
DescriptorSolverSet() - Constructor for class ambit2.rules.conditions.DescriptorSolverSet
 
DescriptorSolverSet(List<IDescriptorSolver>) - Constructor for class ambit2.rules.conditions.DescriptorSolverSet
 
DescriptorSOMEShell - Class in ambit2.some
Used by DescriptorSOMEShell
Invokes some.exe from Mopac 7.1 http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz.
DescriptorSOMEShell() - Constructor for class ambit2.some.DescriptorSOMEShell
 
DescriptorsRank() - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
DescriptorsRank() - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
Descriptors Rank
descriptorValue2Property(IMolecularDescriptor, String, DescriptorValue) - Static method in class ambit2.descriptors.processors.DescriptorsFactory
 
DescriptorValue2Property - Class in ambit2.descriptors.processors
 
DescriptorValue2Property() - Constructor for class ambit2.descriptors.processors.DescriptorValue2Property
 
DescriptorValue2Property.answer - Enum in ambit2.descriptors.processors
 
DescriptorValueCondition - Class in ambit2.rules.conditions
 
DescriptorValueCondition(IValue, IDescriptorSolver, String) - Constructor for class ambit2.rules.conditions.DescriptorValueCondition
 
DescriptorWeight - Class in ambit2.rules.weight
 
DescriptorWeight() - Constructor for class ambit2.rules.weight.DescriptorWeight
 
designRationale - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
details - Variable in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
detailsCaption - Variable in class ambit2.ui.editors.BeanEditor
 
detailsModel - Variable in class ambit2.dbui.QueryInfoEditor
 
detailsModel - Variable in class ambit2.ui.editors.BeanEditor
 
detailsModel - Variable in class ambit2.ui.editors.FileSelector
 
detectAromaticity(IAtomContainer) - Static method in class ambit2.core.helper.CDKHueckelAromaticityDetector
 
DevelopmentalEffectsObserved - Static variable in class ambit2.base.ro.I5CONSTANTS
 
DGroup - Class in ambit2.groupcontribution.groups
 
DGroup() - Constructor for class ambit2.groupcontribution.groups.DGroup
 
dialog - Variable in class ambit2.ui.WizardPanel
 
dictDependent - Variable in class ambit2.db.update.model.CreateModel
 
Dictionary - Class in ambit2.base.data
encapsulates pseudo ontology , defined in template and dictionary tables
Dictionary() - Constructor for class ambit2.base.data.Dictionary
 
Dictionary(String, String) - Constructor for class ambit2.base.data.Dictionary
 
Dictionary(String, String, String) - Constructor for class ambit2.base.data.Dictionary
 
dictionary - Variable in class ambit2.core.io.ToXMLReaderSimple
 
DictionaryEditor - Class in ambit2.ui.editors
 
DictionaryEditor() - Constructor for class ambit2.ui.editors.DictionaryEditor
 
DictionaryObjectQuery - Class in ambit2.db.search
 
DictionaryObjectQuery(Dictionary) - Constructor for class ambit2.db.search.DictionaryObjectQuery
 
DictionaryObjectQuery() - Constructor for class ambit2.db.search.DictionaryObjectQuery
 
DictionaryObjectQuery(String) - Constructor for class ambit2.db.search.DictionaryObjectQuery
 
DictionaryQuery<T extends Dictionary> - Class in ambit2.db.search
 
DictionaryQuery() - Constructor for class ambit2.db.search.DictionaryQuery
 
DictionaryQuery(String) - Constructor for class ambit2.db.search.DictionaryQuery
 
DictionaryQueryPanel - Class in ambit2.dbui.dictionary
 
DictionaryQueryPanel() - Constructor for class ambit2.dbui.dictionary.DictionaryQueryPanel
 
DictionaryRows - Class in ambit2.db.results
 
DictionaryRows() - Constructor for class ambit2.db.results.DictionaryRows
 
DictionarySubjectQuery - Class in ambit2.db.search
 
DictionarySubjectQuery(Dictionary) - Constructor for class ambit2.db.search.DictionarySubjectQuery
 
DictionarySubjectQuery() - Constructor for class ambit2.db.search.DictionarySubjectQuery
 
DictionarySubjectQuery(String) - Constructor for class ambit2.db.search.DictionarySubjectQuery
 
dictPredicted - Variable in class ambit2.db.update.model.CreateModel
 
dictPredictors - Variable in class ambit2.db.update.model.CreateModel
 
diff(Object, Object, double, double) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
diff_rank(int, double) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
disconectBonds(IAtomContainer, ArrayList<IBond>) - Static method in class ambit2.reactions.fragmentation.FragmentationRule
 
disconectBonds(IAtomContainer, int[]) - Static method in class ambit2.reactions.fragmentation.FragmentationRule
 
display() - Method in enum ambit2.db.processors.ProcessorOntology.SIDE
 
display() - Method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
 
display(Frame, String, boolean) - Method in class ambit2.ui.WizardPanel
 
DisplayMode - Enum in ambit2.rest
 
distance - Variable in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
distance - Variable in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
distance - Variable in class ambit2.similarity.measure.DistanceComparable
 
distance_histogram - Variable in class ambit2.similarity.stats.ModelValuesHistogram
 
DistanceComparable<T> - Class in ambit2.similarity.measure
Encapsulates object and its calculated distance.
DistanceComparable(T, double, boolean) - Constructor for class ambit2.similarity.measure.DistanceComparable
 
DistanceComparable(T, Float, Object, boolean) - Constructor for class ambit2.similarity.measure.DistanceComparable
 
DistanceDegreeVector(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
distanceFunction - Variable in class ambit2.similarity.knn.NearestNeighborsSearch
 
dlu - Variable in class ambit2.ui.WizardPanel
 
doAction() - Method in interface ambit2.rules.actions.IAction
 
doAssessment(double[], int) - Method in class ambit2.model.numeric.DataCoverageDensity
 
doAssessment(Matrix, int, int) - Method in class ambit2.model.numeric.DataCoverageDescriptors
does the actual assessment, to be overrided by inherited class
doAssessment(double[], int) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
doAssessment(double[], int) - Method in class ambit2.model.numeric.DataCoverageDistance
 
doCalculation(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
doCalculation(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
doCalculation(IAtomContainer) - Method in class ambit2.descriptors.SizeDescriptor
Transforms coordinates to PCA space (this making sizes invariant to rotation) Sizes are ordered (max first)
doCall() - Method in class ambit2.rest.task.CallableBuilder
 
doCall() - Method in class ambit2.rest.task.CallableMockup
 
doCall() - Method in class ambit2.rest.task.CallableNumericalModelCreator
 
doCall() - Method in class ambit2.rest.task.CallablePOST
 
doCall() - Method in class ambit2.rest.task.CallableProtectedTask
 
doCall() - Method in class ambit2.rest.task.CallableQueryProcessor
 
documentType - Variable in class ambit2.db.substance.CreateSubstance
 
documentUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
documentUUID - Variable in class ambit2.base.data.study.ProtocolEffectRecord
 
doEstimation(Matrix, int, int) - Method in class ambit2.model.numeric.DataCoverageDensity
 
doEstimation(Matrix, int, int) - Method in class ambit2.model.numeric.DataCoverageDescriptors
does the actual estimation, to be overrided by inherited class
doEstimation(Matrix, int, int) - Method in class ambit2.model.numeric.DataCoverageDistance
 
doi - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
doInit() - Method in class ambit2.rest.AbstractResource
 
doInit() - Method in class ambit2.rest.ProtectedResource
 
doInit() - Method in class ambit2.rest.SimpleTaskResource
 
doInit() - Method in class ambit2.rest.task.LauncherResource
 
done() - Method in class ambit2.rest.task.ExecutableTask
 
doRelease() - Method in class ambit2.rest.ProtectedResource
 
DoseResponseRelationship - Static variable in class ambit2.base.ro.I5CONSTANTS
 
doTask(IAtomContainer) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
doTransformation(IAtomContainer) - Method in class ambit2.reactions.SimilarityManager
 
double_nf - Variable in class ambit2.similarity.stats.AbstractModelStatistics
 
DoubleArrayDataset - Class in ambit2.model.dataset
Fixed length dataset, for testing purposes
DoubleArrayDataset(double[][], double[]) - Constructor for class ambit2.model.dataset.DoubleArrayDataset
 
DoubleBondAromaticityNotSpecified - Class in ambit2.smarts
 
DoubleBondAromaticityNotSpecified(IChemObjectBuilder) - Constructor for class ambit2.smarts.DoubleBondAromaticityNotSpecified
 
doubleBondStereochemistry2String(DoubleBondStereochemistry, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
DoubleBondStereoInfo - Class in ambit2.smarts
 
DoubleBondStereoInfo() - Constructor for class ambit2.smarts.DoubleBondStereoInfo
 
DoubleBondStereoInfo.DBStereo - Enum in ambit2.smarts
 
DoubleHistogramBin - Class in ambit2.similarity.stats
 
DoubleHistogramBin(Double, Double) - Constructor for class ambit2.similarity.stats.DoubleHistogramBin
 
DoubleNonAromaticBond - Class in ambit2.smarts
 
DoubleNonAromaticBond(IChemObjectBuilder) - Constructor for class ambit2.smarts.DoubleNonAromaticBond
 
doubleParam - Variable in class ambit2.sln.SLNExpressionToken
 
DoubleValuesHistogram<U extends Bin> - Class in ambit2.similarity.stats
 
DoubleValuesHistogram(String) - Constructor for class ambit2.similarity.stats.DoubleValuesHistogram
 
download(URL, File) - Static method in class ambit2.base.io.DownloadTool
 
download(InputStream, File) - Static method in class ambit2.base.io.DownloadTool
 
download(InputStream, OutputStream) - Static method in class ambit2.base.io.DownloadTool
 
download(String, OutputStream) - Static method in class ambit2.base.io.DownloadTool
 
download(String, File) - Static method in class ambit2.base.io.DownloadTool
 
download(OutputStream, MediaType) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
DownloadTool - Class in ambit2.base.io
 
DownloadTool() - Constructor for class ambit2.base.io.DownloadTool
 
DRAGON_EXE - Static variable in class ambit2.dragon.DragonShell
 
DRAGON_HOME - Static variable in class ambit2.dragon.DragonShell
 
DragonDescriptorDictionary - Class in ambit2.dragon
 
DragonDescriptorDictionary() - Constructor for class ambit2.dragon.DragonDescriptorDictionary
 
DragonShell - Class in ambit2.dragon
Launches Dragon6 as an external executable and reads the results back.
DragonShell() - Constructor for class ambit2.dragon.DragonShell
DragonShell._options - Enum in ambit2.dragon
 
DrawableDensity - Interface in ambit2.domain.stats.transforms.densityestimation
Drawable Density
dropFilter(int) - Method in interface ambit2.base.data.IFilteredColumns
 
dropFilter(int) - Method in class ambit2.db.results.StoredQueryTableModel
 
dropFilter(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
dropHydrogens - Variable in class ambit2.smi23d.ShellSmi2SDF
 
dropTables(Connection, String, List<String>) - Static method in class ambit2.db.processors.DbCreateDatabase
 
dropTables(Connection, String, String[]) - Static method in class ambit2.db.processors.DbCreateDatabase
 
DSSTox_RID - Static variable in class ambit2.core.io.ToxcastAssayReader
 
DSSTOX_RID_index - Variable in class ambit2.core.io.ToxcastAssayReader
 
DSSToxCID - Class in ambit2.core.processors.structure.key
DSSTox_CID
DSSToxCID() - Constructor for class ambit2.core.processors.structure.key.DSSToxCID
 
DSSToxGenericSID - Class in ambit2.core.processors.structure.key
DSSToxGenericSID
DSSToxGenericSID() - Constructor for class ambit2.core.processors.structure.key.DSSToxGenericSID
 
DSSToxID - Class in ambit2.core.processors.structure.key
 
DSSToxID(Property) - Constructor for class ambit2.core.processors.structure.key.DSSToxID
 
DSSToxRID - Class in ambit2.core.processors.structure.key
 
DSSToxRID() - Constructor for class ambit2.core.processors.structure.key.DSSToxRID
 
dummy() - Static method in class ambit2.smarts.SMIRKSTransform
 
DX - Static variable in class ambit2.base.data.LiteratureEntry
 
dx - Variable in class ambit2.core.io.json.SubstanceStudyParser
 
dx - Variable in class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
dx - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
dx - Variable in class ambit2.rest.substance.SubstanceRDFReporter
 
DXChemicalPerception - Static variable in class ambit2.core.io.dx.DXParser
 
DXParser - Class in ambit2.core.io.dx
 
DXParser() - Constructor for class ambit2.core.io.dx.DXParser
 
dxParser - Variable in class ambit2.core.processors.StructureNormalizer
 
dxRoot - Variable in class ambit2.core.io.dx.DXParser
 
DXStructureProperties - Static variable in class ambit2.core.io.dx.DXParser
 
DXTAG - Static variable in class ambit2.core.io.dx.DXParser
 

E

eAERODYNAMIC_DIAMETER - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eAGGLO_AGGR_DIAM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eAGGLO_AGGR_DISTRIBUTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eAGGLO_AGGR_SIZE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eAGGLO_AGGR_SIZE_DIST - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eAGGLO_AGGREGATION_ID - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eASPECT_RATIO - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eASPECT_RATIO_X - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eASPECT_RATIO_Y - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eASPECT_RATIO_Z - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eATOMIC_COMPOSITION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eBCF - Static variable in class ambit2.base.ro.I5CONSTANTS
 
EC - Static variable in class ambit2.base.data.Property
 
eCATALYTIC_ACTIVITY - Static variable in class ambit2.base.ro.I5CONSTANTS
 
EccentricBasedMadanIndicesDescriptor - Class in ambit2.descriptors.topological
 
EccentricBasedMadanIndicesDescriptor() - Constructor for class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
ECHA_REFERENCE - Static variable in class ambit2.core.io.ECHAPreregistrationListReader
 
ECHA_URL - Static variable in class ambit2.core.io.ECHAPreregistrationListReader
 
ECHAPreregistrationListReader - Class in ambit2.core.io
Reads preregistration list in XML format as in http://apps.echa.europa.eu/preregistered/prsDownload.aspx
ECHAPreregistrationListReader(InputStream) - Constructor for class ambit2.core.io.ECHAPreregistrationListReader
 
ECHAPreregistrationListReader.echa_tags - Enum in ambit2.core.io
 
ecProperty - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
ecProperty - Static variable in class ambit2.core.io.I5ReaderSimple
 
eCRYSTALLINE_PHASE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eCRYSTALLITE_SIZE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
editable - Variable in class ambit2.base.data.LiteratureEntry
 
editable - Variable in class ambit2.dbui.dictionary.AmbitRowsPanel
 
editable - Variable in class ambit2.ui.editors.BeanEditor
 
editable - Variable in class ambit2.ui.editors.FileSelector
 
editable - Variable in class ambit2.ui.editors.ListEditor
 
editable - Variable in class ambit2.ui.Panel2D
 
editable - Variable in class ambit2.ui.QueryBrowser
 
EditableHeader - Class in ambit2.ui
 
EditableHeader(TableColumnModel, boolean) - Constructor for class ambit2.ui.EditableHeader
 
EditableHeaderTableColumn - Class in ambit2.ui
 
EditableHeaderTableColumn() - Constructor for class ambit2.ui.EditableHeaderTableColumn
 
EditableHeaderUI - Class in ambit2.ui
 
EditableHeaderUI() - Constructor for class ambit2.ui.EditableHeaderUI
 
EditableHeaderUI.MouseInputHandler - Class in ambit2.ui
 
editAction - Variable in class ambit2.ui.Panel2D
 
editCellAt(int) - Method in class ambit2.ui.EditableHeader
 
editCellAt(int, EventObject) - Method in class ambit2.ui.EditableHeader
 
editingCanceled(ChangeEvent) - Method in class ambit2.ui.EditableHeader
 
editingColumn - Variable in class ambit2.ui.EditableHeader
 
editingStopped(ChangeEvent) - Method in class ambit2.ui.EditableHeader
 
editMolecule(boolean, Component) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
editor - Variable in class ambit2.dbui.QueryScopeEditor
 
editor - Variable in class ambit2.ui.editors.EditorPanel
 
editor - Variable in class ambit2.ui.editors.ListEditor
 
editorComp - Variable in class ambit2.ui.EditableHeader
 
EditorPanel - Class in ambit2.ui.editors
 
EditorPanel() - Constructor for class ambit2.ui.editors.EditorPanel
 
EditorPanel(IAmbitEditor) - Constructor for class ambit2.ui.editors.EditorPanel
 
EditorPreferences - Class in ambit2.ui
 
EditorPreferences() - Constructor for class ambit2.ui.EditorPreferences
 
eDUSTINEX - Static variable in class ambit2.base.ro.I5CONSTANTS
 
effect_stdev - Static variable in class ambit2.base.ro.I5CONSTANTS
 
effectQuery - Variable in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
EffectRecord<ENDPOINT,CONDITIONS,UNIT> - Class in ambit2.base.data.study
Effect record.
EffectRecord() - Constructor for class ambit2.base.data.study.EffectRecord
 
EffectRecord._fields - Enum in ambit2.base.data.study
 
effectRecordLoc - Variable in class ambit2.export.isa.ISAExportConfig
 
effectRecordLocString - Variable in class ambit2.export.isa.ISAExportConfig
 
effects - Variable in class ambit2.base.data.study.ProtocolApplication
 
eFRACTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eFUNCTIONAL_GROUP - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eGenotoxicity - Static variable in class ambit2.base.ro.I5CONSTANTS
 
EHOMO - Static variable in class ambit2.mopac.DescriptorMopacShell
 
eigenvalues - Static variable in class ambit2.mopac.Mopac7Reader
 
EINECS - Class in ambit2.core.data
 
EINECS() - Constructor for class ambit2.core.data.EINECS
 
einecs - Variable in class ambit2.pubchem.EntrezSearchOptions
 
EINECS_name - Static variable in class ambit2.base.data.LiteratureEntry
 
EINECS_uri - Static variable in class ambit2.base.data.LiteratureEntry
 
EINECSKey - Class in ambit2.core.processors.structure.key
returns einecs rn, given structure and its properties
EINECSKey() - Constructor for class ambit2.core.processors.structure.key.EINECSKey
 
einecsProperty - Variable in class ambit2.core.io.RawIteratingFolderReader
 
eISOELECTRIC_POINT - Static variable in class ambit2.base.ro.I5CONSTANTS
 
el - Variable in class ambit2.groupcontribution.utils.math.MatrixDouble
 
electronContainers() - Method in class ambit2.core.groups.SuppleAtomContainer
 
electronWithdrawingLevelScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
electronWithdrawingLevelWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
elementIndex - Variable in class ambit2.export.isa.base.ExternalDataFileLocation
 
elementIndex - Variable in class ambit2.export.isa.base.ISALocation
 
elementName - Variable in class ambit2.export.isa.base.ISALocation
 
elementType - Variable in class ambit2.smarts.StereoChange
 
elSymbols - Static variable in class ambit2.sln.SLNConst
 
elSymbols - Static variable in class ambit2.smarts.SmartsConst
 
ELUMO - Static variable in class ambit2.mopac.DescriptorMopacShell
 
email - Variable in class ambit2.base.data.AmbitUser
 
email - Variable in class ambit2.export.isa.v1_0.objects.Person
 
email - Variable in class ambit2.ui.editors.AmbitUserEditor
 
eMELTINGPOINT - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eMODAL_PORE_VOLUME - Static variable in class ambit2.base.ro.I5CONSTANTS
 
empty - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
empty - Variable in class ambit2.descriptors.AtomEnvironmentDescriptor
 
EmptyIterator() - Constructor for class ambit2.core.groups.AbstractGroup.EmptyIterator
 
EmptyKey - Class in ambit2.core.processors.structure.key
REturns null key
EmptyKey() - Constructor for class ambit2.core.processors.structure.key.EmptyKey
 
EmptyMoleculeException - Exception in ambit2.base.exceptions
 
EmptyMoleculeException() - Constructor for exception ambit2.base.exceptions.EmptyMoleculeException
 
enabled - Variable in class ambit2.base.data.Property
 
enabled - Variable in class ambit2.base.external.CommandShell
 
enabled - Variable in class ambit2.core.processors.AbstractStructureProcessor
 
enabled - Variable in class ambit2.descriptors.FunctionalGroup
 
enabled - Variable in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
enabled - Variable in class ambit2.ml.io.OutputARFF
 
enabled - Variable in class ambit2.ml.io.OutputVW
 
enabled - Variable in class ambit2.ml.io.OutputVW_LDA
 
enabled - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
enableFeatures - Variable in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
enableFeatures - Variable in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
endLine - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
endLineNum - Variable in class ambit2.tautomers.Tautomer2DescriptorUtils
 
endpoint - Variable in class ambit2.base.data.study.EffectRecord
 
endpoint - Variable in class ambit2.core.data.model.Algorithm
 
endpoint - Variable in class ambit2.core.data.model.ModelQueryResults
 
endpoint - Variable in class ambit2.db.substance.QueryCountEndpoints
 
endpoint - Variable in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
endpoint_type_MEAN - Static variable in class ambit2.base.ro.I5CONSTANTS
 
endpoint_type_MEDIAN - Static variable in class ambit2.base.ro.I5CONSTANTS
 
endpoint_type_MEDIAN_MASS - Static variable in class ambit2.base.ro.I5CONSTANTS
 
endpoint_type_PERCENT - Static variable in class ambit2.base.ro.I5CONSTANTS
 
endpointcategory - Variable in class ambit2.base.data.substance.SubstanceProperty
 
EndpointCompoundFacet - Class in ambit2.db.facets.datasets
 
EndpointCompoundFacet(String) - Constructor for class ambit2.db.facets.datasets.EndpointCompoundFacet
 
EndpointCompoundFacetQuery - Class in ambit2.db.facets.datasets
Lists number of datasets, given endpoint and (optionally) a compound
EndpointCompoundFacetQuery(String) - Constructor for class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
endpointGroup - Variable in class ambit2.base.data.study.EffectRecord
 
endpointName - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
EndpointRoleByBundle - Class in ambit2.db.facets.bundle
 
EndpointRoleByBundle(String) - Constructor for class ambit2.db.facets.bundle.EndpointRoleByBundle
 
Endpoints - Class in ambit2.base.data
 
Endpoints() - Constructor for class ambit2.base.data.Endpoints
 
endpointSynonyms - Variable in class ambit2.base.data.study.EffectRecord
 
endpointType - Variable in class ambit2.base.data.study.EffectRecord
 
endpointURI - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
endRecord(String, Integer, String, String, String) - Method in class ambit2.core.io.ToXMLReaderSimple
 
endRow(int, String, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
energy - Variable in class ambit2.tautomers.rules.EnergyCorrection
 
energyConst - Variable in class ambit2.tautomers.TautomerRanking
 
EnergyCorrection - Class in ambit2.tautomers.rules
 
EnergyCorrection() - Constructor for class ambit2.tautomers.rules.EnergyCorrection
 
energyCorrections - Variable in class ambit2.tautomers.rules.EnergyRule
 
EnergyRanking - Class in ambit2.tautomers.ranking
 
EnergyRanking() - Constructor for class ambit2.tautomers.ranking.EnergyRanking
 
EnergyRanking(String) - Constructor for class ambit2.tautomers.ranking.EnergyRanking
 
EnergyRule - Class in ambit2.tautomers.rules
 
EnergyRule() - Constructor for class ambit2.tautomers.rules.EnergyRule
 
engine - Variable in class ambit2.descriptors.processors.DescriptorEngineProcessor
 
entities - Variable in class ambit2.chebi.ChEBIClient
 
entity - Variable in class ambit2.rest.RemoteStreamConvertor
 
EntrezESearchParser - Class in ambit2.pubchem
Reads Entrez eSearch query result (DTD available at http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd ) and returns List, where StructureRecord.getFormat() is equal to PubChemFormat
EntrezESearchParser() - Constructor for class ambit2.pubchem.EntrezESearchParser
 
EntrezSearchOptions - Class in ambit2.pubchem
 
EntrezSearchOptions() - Constructor for class ambit2.pubchem.EntrezSearchOptions
 
EntrezSearchProcessor - Class in ambit2.pubchem
Searches PubChem for structures given search terms (via Entrez) and returns SDF files.
EntrezSearchProcessor() - Constructor for class ambit2.pubchem.EntrezSearchProcessor
 
entrezURL - Static variable in class ambit2.pubchem.EntrezSearchProcessor
 
entropy() - Method in class ambit2.domain.stats.datastructures.Histogram
Information entropy of a discrete probability distribution pi
entropy() - Method in class ambit2.similarity.stats.Histogram
Information entropy of a discrete probability distribution pi
entry2structurerecord(LiteEntity, IStructureRecord) - Method in class ambit2.chebi.ChEBIClient
 
entrySet() - Method in class ambit2.base.data.study.Params
 
ePercentDegradation - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ePHOTOCATALYTIC_ACTIVITY - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ePOROSITY - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ePOUR_DENSITY - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eps - Static variable in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
eqTester - Variable in class ambit2.smarts.SMIRKSManager
 
equals(Object) - Method in class ambit2.base.data.AbstractLabel
 
equals(Object) - Method in class ambit2.base.data.Dictionary
 
equals(Object) - Method in class ambit2.base.data.LiteratureEntry
 
equals(Object) - Method in class ambit2.base.data.Property
 
equals(Object) - Method in class ambit2.base.data.SourceDataset
 
equals(Object) - Method in class ambit2.base.data.substance.SubstanceProperty
 
equals(Object) - Method in class ambit2.core.data.model.Algorithm
 
equals(Object) - Method in class ambit2.core.groups.AbstractGroup
 
equals(Object) - Method in class ambit2.core.io.FileState
 
equals(Object) - Method in class ambit2.core.processors.structure.key.NameOnlyProperty
 
equals(Object) - Method in class ambit2.descriptors.AtomEnvironment
 
equals(Object) - Method in class ambit2.descriptors.SizeDescriptor
 
equals(Object) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
equals(Object) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
equals(Object) - Method in class ambit2.similarity.measure.DistanceComparable
 
equals(Object) - Method in class ambit2.similarity.stats.Bin
 
equals(Object) - Method in class ambit2.similarity.stats.MutableInt
 
equals(Object) - Method in class ambit2.similarity.stats.ValuePair
 
equals(Object) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
equals(Object) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
EquivalenceTester - Class in ambit2.smarts
 
EquivalenceTester() - Constructor for class ambit2.smarts.EquivalenceTester
 
equivalentAtoms(IAtom, IAtom) - Method in class ambit2.smarts.EquivalenceTester
 
equivalentMaps(List<IAtom>, List<IAtom>) - Method in class ambit2.smarts.EquivalenceTester
 
eRadicalFormation_Observations - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eRadicalFormation_Quantitative - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ERM_NEW - Static variable in class ambit2.tautomers.TautomerConst
 
ERM_OLD - Static variable in class ambit2.tautomers.TautomerConst
 
err_invalidcas - Static variable in class ambit2.core.config.Resources
Invalid CAS
error(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler
 
error - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
error - Variable in class ambit2.rest.AbstractResource
 
error - Variable in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
error - Variable in class ambit2.rest.task.CallableMockup
 
error - Variable in class ambit2.rest.task.Task
 
ERROR - Static variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
ERROR_TAG - Static variable in class ambit2.tautomers.processor.StructureStandardizer
 
errorIfDisconnected - Variable in class ambit2.mopac.AbstractMopacShell
 
errors - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
errors - Variable in class ambit2.groupcontribution.io.GCM2Properties
 
errors - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
errors - Variable in class ambit2.groupcontribution.transformations.TransformationUtils
 
errors - Variable in class ambit2.reactions.ReactionDataBase
 
errors - Variable in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
errors - Variable in class ambit2.tautomers.rules.AtomCondition
 
errors - Variable in class ambit2.tautomers.rules.EnergyCorrection
 
errors - Variable in class ambit2.tautomers.rules.EnergyRule
 
errorsToString() - Method in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
errQualifier - Variable in class ambit2.base.data.study.EffectRecord
 
errValue - Variable in class ambit2.base.data.study.EffectRecord
 
eSHAPE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eSHAPE_DESCRIPTIVE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eShift - Variable in class ambit2.tautomers.TautomerRanking
 
eSOLUBILITY_ORG_SOLVENT - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eSPECIFIC_PORE_VOLUME - Static variable in class ambit2.base.ro.I5CONSTANTS
 
EStateFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
Wrapper for EStateFingerprinter, implementing IMolecularDescriptor
EStateFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.EStateFingerprinterWrapper
 
estimate(Matrix) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
estimateConsensusFP(double[], double) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
estimateDensity(double[], int, Kernel, int, double, double, double, double[]) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
EstimateDensityFromData(Matrix, TransformFilter) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
EstimateDensityFromData Estimates density from set of points If filter is not null, then density in transformed space is estimated
estimateThreshold(double, double[]) - Method in class ambit2.model.numeric.DataCoverageDensity
 
estimateThreshold(double, double[]) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
estimateThreshold(double[], int) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
estimateThresholdValues(double, double[], int) - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
eTURNOVERFREQUENCY - Static variable in class ambit2.base.ro.I5CONSTANTS
 
euclideanDistance(double[], double[], int) - Method in class ambit2.model.numeric.DataCoverageDistance
 
EuclideanDistance - Class in ambit2.similarity.measure
 
EuclideanDistance() - Constructor for class ambit2.similarity.measure.EuclideanDistance
 
EurasBCFReader - Class in ambit2.core.io.bcf
 
EurasBCFReader(InputStream, int) - Constructor for class ambit2.core.io.bcf.EurasBCFReader
 
evaluate(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
evaluate(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
evaluate(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
evaluateAttributes(NearestNeighborsSearch<T>, int) - Method in interface ambit2.featureselection.IAttributeSelection
 
evaluateAttributes(NearestNeighborsSearch<T>, int) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
evaluated - Variable in class ambit2.featureselection.AbstractAttributeSelection
 
evaluations - Variable in class ambit2.core.data.model.ModelWrapper
 
EvaluationStats<Content> - Class in ambit2.model.evaluation
 
EvaluationStats(IEvaluation.EVType, Content) - Constructor for class ambit2.model.evaluation.EvaluationStats
 
eVapourPressure - Static variable in class ambit2.base.ro.I5CONSTANTS
 
eWaterSolubility - Static variable in class ambit2.base.ro.I5CONSTANTS
 
ex - Variable in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
EXACT - Static variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
ExactStructureSearchMode - Enum in ambit2.core.processors.structure.key
 
example - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
EXCEL_COLUMN_WIDTH_FACTOR - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
exception(Exception) - Method in interface ambit2.pubchem.ResultListener
 
excludedGenericReactions - Variable in class ambit2.reactions.ReactionDataBase
 
excludeFilters - Variable in class ambit2.tautomers.FilterTautomers
 
excludeFilters - Variable in class ambit2.tautomers.KnowledgeBase
 
excludeFiltersOriginalPos - Variable in class ambit2.tautomers.FilterTautomers
 
excludeFragments - Static variable in class ambit2.tautomers.PredefinedKnowledgeBase
 
excludeHidden - Variable in class ambit2.db.substance.relation.ReadSubstanceComposition
 
excludeReactionsWithConfigErrors() - Method in class ambit2.reactions.ReactionDataBase
 
exec - Variable in class ambit2.db.processors.AbstractRepositoryWriter
 
exec - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
exec - Variable in class ambit2.db.processors.ProcessorStructureRetrieval
 
exec - Variable in class ambit2.db.reporters.QueryPacketReporter
 
exec - Variable in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
exec - Variable in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
executables - Variable in class ambit2.base.external.CommandShell
 
ExecutableTask<USERID> - Class in ambit2.rest.task
 
ExecutableTask(Callable<ITaskResult>, ITask<ITaskResult, USERID>) - Constructor for class ambit2.rest.task.ExecutableTask
 
execute(Connection, Q) - Method in class ambit2.db.PreparedStatementBatchExecutor
 
execute(Group, IQueryUpdate<Group, Target>) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
execute(Connection) - Method in class ambit2.db.results.AmbitRows
 
execute() - Method in class ambit2.db.results.AmbitRows
 
execute(Connection, Q) - Method in class ambit2.db.search.QueryExecutor
 
execute(Connection, Q) - Method in class ambit2.db.StatementExecutor
 
execute(Connection, Q) - Method in class ambit2.db.UpdateExecutor
 
executeCmd(String) - Method in class ambit2.ui.jmol.ImageTools3D
 
executesProtocol - Variable in class ambit2.export.isa.v1_0.objects.Process
 
executor - Variable in class ambit2.db.DbReader
 
executor - Variable in class ambit2.db.processors.ProcessorOntology
 
executor - Variable in class ambit2.db.results.AmbitRows
 
executorn - Variable in class ambit2.db.readers.ValuesByTemplateReader
 
executort - Variable in class ambit2.db.readers.ValuesByTemplateReader
 
exitCode - Variable in class ambit2.base.external.CommandShell
 
exitCodeOK(int) - Method in class ambit2.base.external.CommandShell
 
exitCodeOK(int) - Method in class ambit2.smi23d.ShellSmi2SDF
 
EXPAND_COLUMN - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage
 
EXPAND_ROW - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage
 
EXPAND_ROW_AND_COLUMN - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage
 
expandedString() - Method in class ambit2.core.data.HashIntDescriptorResult
Used for db storage
EXPERIMENT - Static variable in class ambit2.core.config.AmbitCONSTANTS
Experimental data record
EXPERIMENT_LIST - Static variable in class ambit2.core.config.AmbitCONSTANTS
List of experiments
experimentalConditionsInfo - Variable in class ambit2.reactions.GenericReaction
 
experimentalConditionsScore - Variable in class ambit2.reactions.GenericReaction
 
experimentalConditionsScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
experimentalConditionsScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
ExpertModelBuilder - Class in ambit2.rest.model.builder
 
ExpertModelBuilder(String, String, Reference, ModelURIReporter, AlgorithmURIReporter, String) - Constructor for class ambit2.rest.model.builder.ExpertModelBuilder
 
ExpertModelBuilder(String, String, Reference, ModelURIReporter, AlgorithmURIReporter, boolean, String) - Constructor for class ambit2.rest.model.builder.ExpertModelBuilder
 
ExpertModelpredictor<Predictor> - Class in ambit2.rest.model.predictor
 
ExpertModelpredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.ExpertModelpredictor
 
explain(QueryDatasetByFeatures) - Method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
 
explanationInfo - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
ExplicitH - Static variable in class ambit2.smarts.CMLUtilities
 
explicitH - Variable in class ambit2.tautomers.RuleInstance
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
explicitHAtoms() - Method in interface ambit2.tautomers.zwitterion.ICenter
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
explicitHAtoms() - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
export() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
export(SubstanceEndpointsBundle, Iterator<SubstanceRecord>) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
exportConfiguration - Variable in class ambit2.export.isa.json.ISAJsonExporter
 
extChirInfo - Variable in class ambit2.smarts.SmartsAtomExpression
 
extDataFileType - Variable in class ambit2.export.isa.ISAExportConfig
 
ExtendedChiralityInfo - Class in ambit2.smarts
 
ExtendedChiralityInfo() - Constructor for class ambit2.smarts.ExtendedChiralityInfo
 
ExtendedFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
 
ExtendedFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.ExtendedFingerprinterWrapper
 
ExtendedInterval(double[], int, double[]) - Static method in class ambit2.domain.stats.Tools
 
extendedTetrahedral2String(ExtendedTetrahedral, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
extendedURI - Variable in class ambit2.base.data.substance.SubstanceProperty
 
extension - Variable in class ambit2.base.io.AmbitFileFilter
 
extension - Variable in class ambit2.base.io.MolFileFilter
 
extensionDescription - Static variable in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
extensionDescriptions - Variable in class ambit2.core.io.FileState
 
extensions - Static variable in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
ExternalDataFileHeader - Class in ambit2.export.isa.base
 
ExternalDataFileHeader() - Constructor for class ambit2.export.isa.base.ExternalDataFileHeader
 
ExternalDataFileLocation - Class in ambit2.export.isa.base
 
ExternalDataFileLocation() - Constructor for class ambit2.export.isa.base.ExternalDataFileLocation
 
ExternalDataFileManager - Class in ambit2.export.isa.base
 
ExternalDataFileManager(File, ISAConst.DataFileFormat) - Constructor for class ambit2.export.isa.base.ExternalDataFileManager
 
ExternalDataFileManager(File, ISAConst.DataFileFormat, ExternalDataFileHeader) - Constructor for class ambit2.export.isa.base.ExternalDataFileManager
 
ExternalDataFileManager.StorageMode - Enum in ambit2.export.isa.base
 
ExternalIdentifier - Class in ambit2.base.data.substance
 
ExternalIdentifier(String, String) - Constructor for class ambit2.base.data.substance.ExternalIdentifier
 
ExternalIdentifier() - Constructor for class ambit2.base.data.substance.ExternalIdentifier
 
externalids - Variable in class ambit2.base.data.SubstanceRecord
 
externalLocalProperties - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
ExternalModel<M,OUTPUT> - Class in ambit2.rest.model.predictor
 
ExternalModel() - Constructor for class ambit2.rest.model.predictor.ExternalModel
 
ExternalModelPredictor<C extends ExternalModel> - Class in ambit2.rest.model.predictor
 
ExternalModelPredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.ExternalModelPredictor
 
ExternalModelVega - Class in ambit2.vega
 
ExternalModelVega() - Constructor for class ambit2.vega.ExternalModelVega
 
externalSetFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
externalSetFile - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
externalSetTest - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
externalTestSet - Variable in class ambit2.groupcontribution.GCMTestConfig
 
externId - Variable in class ambit2.reactions.GenericReaction
 
extractArrayKeyword(JsonNode, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractArrayKeyword(JsonNode, String, boolean, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractAtomContainer(IQueryAtomContainer, IRingSet) - Method in class ambit2.smarts.SmartsToChemObject
Maximal possible atom container from this query is generated.
extractAtomContainer(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsToChemObject
Version of the function when the Ring data is not supplied outside
extractAtomContainerFullyConnected(IQueryAtomContainer, IRingSet) - Method in class ambit2.smarts.SmartsToChemObject
Maximal possible atom container from this query is generated BUT this container is always fully connected as the original query.
extractAtomContainerFullyConnected(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsToChemObject
 
extractBooleanKeyword(JsonNode, String, boolean) - Method in class ambit2.core.json.JSONParserUtils
 
extractBooleanKeyword(JsonNode, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractCMLAtomProperties(IAtom, String) - Method in class ambit2.smarts.CMLUtilities
Converts per-atom string property into internal structure
extractConfigFromJson(JsonNode, List<String>) - Static method in class ambit2.sln.io.SLN2SubstanceConfig
 
extractDoubleKeyword(JsonNode, String, boolean) - Method in class ambit2.core.json.JSONParserUtils
 
extractDoubleKeyword(JsonNode, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractDoubleKeyword(JsonNode, String, boolean) - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
extractDoubleKeyword(JsonNode, String, boolean) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
extractIntKeyword(JsonNode, String, boolean) - Method in class ambit2.core.json.JSONParserUtils
 
extractIntKeyword(JsonNode, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractIntKeyword(JsonNode, String, boolean) - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
extractIntKeyword(JsonNode, String, boolean) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
extractObject(JsonNode) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractObject(JsonNode, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractRecordID(IStructureRecord, String, IStructureRecord) - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
extractRecordID(IStructureRecord, String, IStructureRecord) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
extractRecordID(NativeTypeItem, String, IStructureRecord) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
extractRecordID(IStructureRecord, String, IStructureRecord) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
extractRowKeyAndData(String) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
Extract values from a line
extractRowKeyAndData(String) - Method in class ambit2.core.io.ToxcastAssayReader
 
extractRowKeyAndData(String, int, List<String>) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
extractSMARTSProperties(IAtomContainer) - Method in class ambit2.smarts.CMLUtilities
Retrieves properties (set by setCMLSmartsProperties Expects SMARTSProp to be set for each atom !
extractStringKeyword(JsonNode, String, boolean) - Method in class ambit2.core.json.JSONParserUtils
 
extractStringKeyword(JsonNode, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
extractStringKeyword(JsonNode, String, boolean) - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
extractStringKeyword(JsonNode, String, boolean) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
eZETA_POTENTIAL - Static variable in class ambit2.base.ro.I5CONSTANTS
 

F

facet - Variable in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
facet - Variable in class ambit2.db.update.dataset.QueryCount
 
FacetAnnotator - Class in ambit2.db.substance.study.facet
 
FacetAnnotator(File) - Constructor for class ambit2.db.substance.study.facet.FacetAnnotator
 
FacetedSearchSubstance - Class in ambit2.db.substance
 
FacetedSearchSubstance() - Constructor for class ambit2.db.substance.FacetedSearchSubstance
 
facets - Variable in class ambit2.base.data.StructureRecord
 
facets - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
facets - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
facetURL - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
Factor - Class in ambit2.export.isa.v1_0.objects
ISA factor schema JSON-schema representing a factor value in the ISA model
Factor() - Constructor for class ambit2.export.isa.v1_0.objects.Factor
 
factor - Variable in class ambit2.smarts.StructureSetAnalyzer
 
factorName - Variable in class ambit2.export.isa.v1_0.objects.Factor
 
factors - Variable in class ambit2.export.isa.v1_0.objects.Study
 
factorType - Variable in class ambit2.export.isa.v1_0.objects.Factor
 
FactorValue - Class in ambit2.export.isa.v1_0.objects
ISA factor value schema JSON-schema representing a factor value in the ISA model
FactorValue() - Constructor for class ambit2.export.isa.v1_0.objects.FactorValue
 
factorValues - Variable in class ambit2.export.isa.v1_0.objects.Sample
 
factory - Variable in class ambit2.core.data.HashIntDescriptorResult
 
factory - Variable in class ambit2.core.processors.structure.InchiProcessor
 
factoryResource - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
FactoryTaskConvertor<USERID> - Class in ambit2.rest.task
 
FactoryTaskConvertor(ITaskStorage<USERID>) - Constructor for class ambit2.rest.task.FactoryTaskConvertor
 
failedNodes - Variable in class ambit2.reactions.reactor.ReactorResult
 
FASTSMARTS - Static variable in class ambit2.base.config.Preferences
 
FastSmartsMatcher - Class in ambit2.smarts.query
 
FastSmartsMatcher() - Constructor for class ambit2.smarts.query.FastSmartsMatcher
 
FastSmartsMatcher(String, boolean) - Constructor for class ambit2.smarts.query.FastSmartsMatcher
 
fatalError(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler
 
fax - Variable in class ambit2.export.isa.v1_0.objects.Person
 
fclassifier - Variable in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
fclusterer - Variable in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
FDescriptorsImportance - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
FDescriptorsRankThreshold - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
feature(String, String) - Static method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
featureAAEnabled - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
features - Variable in class ambit2.db.processors.ValueWriterNew
Looks for all Property, assigned to this structure and retrieves IDs from properties table.
features(String, String) - Static method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
features - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
featuresQuery - Variable in class ambit2.rest.task.CallableDatasetCreator
 
featureTemplate - Variable in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
featureTemplate - Variable in class ambit2.rest.rdf.RDFDataEntryIterator
 
featureTemplate - Variable in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
FEnabled - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
FFT - Class in ambit2.domain.stats.transforms
Fast Fourie Transform class
FFT() - Constructor for class ambit2.domain.stats.transforms.FFT
Creates a new instance of FFT class
FFT1(int, double[], double[], double[], double[]) - Method in class ambit2.domain.stats.transforms.FFT
FFT transform
fftshift(double[], int) - Method in class ambit2.domain.stats.transforms.Misc
 
field - Variable in class ambit2.db.processors.quality.QualityValueWriter
 
field - Variable in class ambit2.ui.DelimitersPanel
 
fieldDelimiter - Variable in class ambit2.core.io.DelimitedFileFormat
 
fieldname - Variable in class ambit2.db.search.AbstractQuery
 
fieldname - Variable in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
fieldname1 - Variable in class ambit2.db.search.QueryInfo
 
fieldname2 - Variable in class ambit2.db.search.QueryInfo
 
fieldname3 - Variable in class ambit2.db.search.QueryInfo
 
fieldname_dataset - Variable in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
fieldnames - Static variable in class ambit2.db.search.QueryInfo
 
fieldNames - Variable in class ambit2.export.isa.base.ExternalDataFileHeader
 
fieldnames1 - Variable in class ambit2.dbui.QueryInfoEditor
 
fieldnames2 - Variable in class ambit2.dbui.QueryInfoEditor
 
fieldnames3 - Variable in class ambit2.dbui.QueryInfoEditor
 
fields - Variable in class ambit2.base.data.ProfileListModel
 
fields - Variable in class ambit2.db.results.StoredQueryTableModel
 
fields - Variable in class ambit2.ui.editors.BeanEditor
 
fields - Variable in class ambit2.ui.editors.SelectFieldsPanel
 
fields - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
fieldSeparator - Static variable in class ambit2.export.isa.tab.ISATABConst
 
fieldsModel - Variable in class ambit2.ui.editors.SelectFieldsPanel
 
file - Variable in class ambit2.core.io.FileState
 
file - Variable in class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
file - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
file - Variable in class ambit2.ml.io.OutputVW
 
file - Variable in class ambit2.ml.io.OutputVW_LDA
 
file_arff - Variable in class ambit2.ml.io.OutputARFF
 
fileExtension - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
fileExtension - Variable in class ambit2.rest.RemoteStreamConvertor
 
fileFormat - Variable in class ambit2.core.io.FileState
 
fileFormat - Variable in class ambit2.core.processors.batch.DefaultInputState
 
fileHeader - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
FileInputState - Class in ambit2.core.io
Use FileInputState.getReader(InputStream, String) to get a reader of the right type.
FileInputState() - Constructor for class ambit2.core.io.FileInputState
 
FileInputState(String) - Constructor for class ambit2.core.io.FileInputState
 
FileInputState(File) - Constructor for class ambit2.core.io.FileInputState
 
filename - Static variable in class ambit2.base.config.Preferences
 
filename - Variable in class ambit2.base.data.study.StructureRecordValidator
 
filename - Variable in class ambit2.core.io.FileState
 
filename - Variable in class ambit2.core.io.IteratingFileReader
 
fileName - Variable in class ambit2.export.isa.base.ExternalDataFileLocation
 
filename - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
filename - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
filename - Variable in class ambit2.export.isa.v1_0.objects.Study
 
filename - Static variable in class ambit2.ui.EditorPreferences
 
filename - Variable in class ambit2.ui.editors.FileSelector
 
fileNamePrefix - Variable in class ambit2.rest.RemoteStreamConvertor
 
FileNotFoundException - Exception in ambit2.pubchem
 
FileNotFoundException(IProcessor, Exception) - Constructor for exception ambit2.pubchem.FileNotFoundException
 
FileOutputState - Class in ambit2.core.io
Use FileOutputState.getWriter(OutputStream, String) to get a writer of the right type.
FileOutputState() - Constructor for class ambit2.core.io.FileOutputState
 
FileOutputState(String) - Constructor for class ambit2.core.io.FileOutputState
 
FileOutputState(File) - Constructor for class ambit2.core.io.FileOutputState
 
filePath - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
fileRuleNames - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
files - Variable in class ambit2.core.io.IteratingFolderReader
 
FileSelector - Class in ambit2.ui.editors
 
FileSelector() - Constructor for class ambit2.ui.editors.FileSelector
 
FileState - Class in ambit2.core.io
This is to be able to verify if a file has changed since it has been last processed by FileBatchProcessing
FileState() - Constructor for class ambit2.core.io.FileState
 
FileState(String) - Constructor for class ambit2.core.io.FileState
 
FileState(File) - Constructor for class ambit2.core.io.FileState
 
filestate - Variable in class ambit2.ui.editors.FileSelector
 
FileState._FILE_TYPE - Enum in ambit2.core.io
 
FilesWithHeaderWriter - Class in ambit2.core.io
 
FilesWithHeaderWriter() - Constructor for class ambit2.core.io.FilesWithHeaderWriter
 
FileWithHeaderWriter - Class in ambit2.core.io
 
FileWithHeaderWriter() - Constructor for class ambit2.core.io.FileWithHeaderWriter
 
fileWriter - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
fill(int) - Static method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
fillArrayWith(int, int[]) - Static method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
fillArrayWith(double, double[]) - Static method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
fillArrayWithRandomIntegers(int[], int) - Method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
fillDefaultISAConfig(ISAExportConfig) - Static method in class ambit2.export.isa.ISAExportConfig
 
fillDiagonal(int[][], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillDiagonal(double[][], double) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillDiagonalWith(double) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
filledLevels - Static variable in class ambit2.mopac.Mopac7Reader
 
fillMatrix(int[][], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillMatrix(double[][], double) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillVector(int, int[], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillVector(GraphMatrices.DMAtomState, GraphMatrices.DMAtomState[], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
fillWith(double) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
filter - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
Filter - Class in ambit2.tautomers
 
Filter() - Constructor for class ambit2.tautomers.Filter
 
filter(List<IAtomContainer>) - Method in class ambit2.tautomers.FilterTautomers
 
filterByFeature(OTFeature, boolean) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
filterByFeatures(OTFeatures, boolean) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
filterConfig - Variable in class ambit2.rest.wrapper.WrappedService
 
FilteredCount<T extends Comparable<T>> - Class in ambit2.db.search.property
 
FilteredCount() - Constructor for class ambit2.db.search.property.FilteredCount
 
FilteredCountNominal - Class in ambit2.db.search.property
 
FilteredCountNominal() - Constructor for class ambit2.db.search.property.FilteredCountNominal
 
FilteredCountNumeric - Class in ambit2.db.search.property
 
FilteredCountNumeric() - Constructor for class ambit2.db.search.property.FilteredCountNumeric
 
FilteredList<T> - Class in ambit2.core.groups
A list that can be filtered by setting a filter elements.
FilteredList() - Constructor for class ambit2.core.groups.FilteredList
 
FilteredMDLReader - Class in ambit2.core.io
 
FilteredMDLReader() - Constructor for class ambit2.core.io.FilteredMDLReader
 
FilteredMDLReader(InputStream) - Constructor for class ambit2.core.io.FilteredMDLReader
 
FilteredMDLReader(Reader) - Constructor for class ambit2.core.io.FilteredMDLReader
 
FilteredSelectStoredQuery - Class in ambit2.db.update.storedquery
 
FilteredSelectStoredQuery() - Constructor for class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
filteredSubsetWithFeatures(OTFeatures) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Return dataset entries (compounds), having values for specified features
filteredSubsetWithFeatures(OTFeatures) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
filteredSubsetWithoutFeatures(OTFeatures) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Return dataset entries (comnpounds),not having values for specified features
filteredSubsetWithoutFeatures(OTFeatures) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
FilteredTasksIterator<USERID> - Class in ambit2.rest.task
 
FilteredTasksIterator(ITaskStorage<USERID>) - Constructor for class ambit2.rest.task.FilteredTasksIterator
 
FilteredWekaModelBuilder - Class in ambit2.rest.task.weka
Builds WEKA model from ModelQueryResults.
FilteredWekaModelBuilder(Reference, ModelURIReporter, AlgorithmURIReporter, String[], String[], String) - Constructor for class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
FilteredWekaPredictor<T> - Class in ambit2.rest.task.weka
Wrapper for weka models
FilteredWekaPredictor(Reference, ModelQueryResults, ModelURIReporter) - Constructor for class ambit2.rest.task.weka.FilteredWekaPredictor
 
FilteredWekaPredictor(Reference, ModelQueryResults, ModelURIReporter, String[]) - Constructor for class ambit2.rest.task.weka.FilteredWekaPredictor
 
filterEquivalentMappings(List<List<IAtom>>) - Method in class ambit2.smarts.EquivalenceTester
 
FilterIsEnabled() - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
filterTask(ITask<ITaskResult, USERID>, int) - Method in class ambit2.rest.SimpleTaskResource
 
filterTasks() - Method in class ambit2.rest.task.TaskStorage
 
FilterTautomers - Class in ambit2.tautomers
 
FilterTautomers(TautomerManager) - Constructor for class ambit2.tautomers.FilterTautomers
 
FImportantFactors - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
finalize() - Method in class ambit2.core.smiles.SmilesParserWrapper
 
finalize() - Method in class ambit2.db.results.AmbitRows
 
finalize() - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
finalize() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
finalize() - Method in class ambit2.rest.task.CallableDatasetCreator
 
finalize() - Method in class ambit2.rest.TaskApplication
 
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.AbstractGroup
does nothing
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.ComponentGroup
 
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.ContainerGroup
 
finalizeAtomList(IAtomContainer) - Method in interface ambit2.core.groups.ISGroup
 
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.MonomerGroup
 
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.MultipleGroup
 
finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.SuperAtom
 
finalizedProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
finalizeParentAtomList(IAtomContainer) - Method in class ambit2.core.groups.MultipleGroup
 
finalizeRecord() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
finalizeRecord(boolean) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
finalizeRecordInFile() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
find(IAtomContainer) - Method in class ambit2.descriptors.PKANode
 
find() - Method in class ambit2.ui.table.BrowsableTableModel
 
find() - Method in interface ambit2.ui.table.IFindNavigator
 
findAllCenters(IAtomContainer) - Static method in class ambit2.tautomers.zwitterion.AminoGroup
 
findAllCenters(IAtomContainer) - Static method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
findAllCenters(IAtomContainer) - Static method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
findAllCenters(IAtomContainer) - Static method in class ambit2.tautomers.zwitterion.SulfGroup
 
findAllGroupMappings() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
findAllSubstituents() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
findAtomClasses() - Method in class ambit2.smarts.EquivalenceTester
 
findChemical(IStructureRecord) - Method in class ambit2.db.processors.RepositoryWriter
 
findColumn(String) - Method in class ambit2.db.results.AmbitRows
 
findCyclicAndAcyclicComponets() - Method in class ambit2.structure2name.IUPACNameGenerator
 
findDBStereoElementByStereoBond(IBond, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
findExtendedTetrahedralByChiralCenter(IAtom, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
FindNavigator - Class in ambit2.ui.table
 
FindNavigator(IFindNavigator) - Constructor for class ambit2.ui.table.FindNavigator
 
findNext() - Method in class ambit2.ui.table.BrowsableTableModel
 
findNext() - Method in interface ambit2.ui.table.IFindNavigator
 
findPrevious() - Method in class ambit2.ui.table.BrowsableTableModel
 
findPrevious() - Method in interface ambit2.ui.table.IFindNavigator
 
findReactionInstances(IAtomContainer, SMIRKSManager) - Method in class ambit2.reactions.GenericReaction
 
findReactionInstances(IAtomContainer, SMIRKSManager, SmartsConst.SSM_MODE) - Method in class ambit2.reactions.GenericReaction
 
findSimilar(SessionID, int, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
findSpiroAtoms() - Method in class ambit2.structure2name.IUPACNameGenerator
 
findSubstituents(HAtomEnvironmentInstance) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
findTask(String) - Method in class ambit2.rest.task.TaskStorage
 
findTask(UUID) - Method in class ambit2.rest.task.TaskStorage
 
findTask(String) - Method in class ambit2.rest.TaskApplication
 
findTetrahedralChiralityByChiralCenter(IAtom, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
findValue - Variable in class ambit2.ui.table.FindNavigator
 
Fingerprint - Static variable in class ambit2.core.config.AmbitCONSTANTS
Daylight - like hashed fingerprint
Fingerprint<Type,Content> - Class in ambit2.db.update.fp
 
Fingerprint() - Constructor for class ambit2.db.update.fp.Fingerprint
 
Fingerprint(Type, Content) - Constructor for class ambit2.db.update.fp.Fingerprint
 
fingerprint - Variable in class ambit2.smarts.ScreeningData
 
Fingerprint2DescriptorWrapper - Class in ambit2.descriptors.fingerprints
 
Fingerprint2DescriptorWrapper(IFingerprinter) - Constructor for class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
FingerprintDistance - Class in ambit2.similarity.measure
Tanimoto similarity index between fingerprints.
FingerprintDistance() - Constructor for class ambit2.similarity.measure.FingerprintDistance
 
fingerprinter - Static variable in class ambit2.core.data.MoleculeTools
 
fingerprinter - Variable in class ambit2.core.processors.structure.FingerprintGenerator
 
FingerprintGenerator<FGenerator extends org.openscience.cdk.fingerprint.IFingerprinter> - Class in ambit2.core.processors.structure
** Fingerprint generator processor.
FingerprintGenerator(FGenerator) - Constructor for class ambit2.core.processors.structure.FingerprintGenerator
 
FingerprintHistogramDataset - Class in ambit2.db.chart
 
FingerprintHistogramDataset() - Constructor for class ambit2.db.chart.FingerprintHistogramDataset
 
fingerPrintLength - Variable in class ambit2.model.structure.DataCoverageFingerprints
 
FingerprintsByStatus - Class in ambit2.db.search.structure
 
FingerprintsByStatus(FPTable) - Constructor for class ambit2.db.search.structure.FingerprintsByStatus
 
FingerprintsByStatus() - Constructor for class ambit2.db.search.structure.FingerprintsByStatus
 
fingerprintsCalculated - Variable in class ambit2.model.structure.DataCoverageFingerprints
 
FingerprintsModelBuilder - Class in ambit2.rest.model.builder
DataCoverageFingerprints
FingerprintsModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String[], String[], String, String) - Constructor for class ambit2.rest.model.builder.FingerprintsModelBuilder
 
FingerprintsPredictor - Class in ambit2.rest.model.predictor
 
FingerprintsPredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.FingerprintsPredictor
 
FingerprintSTATUS - Static variable in class ambit2.core.config.AmbitCONSTANTS
fingerprint status invalid=1; valid=2; error = 3
FingerprintTIME - Static variable in class ambit2.core.config.AmbitCONSTANTS
Time to generate hashed fingerprint
finish(ActionEvent) - Method in class ambit2.ui.WizardPanel
 
FInputDescriptorNumber - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
FInterpolate - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
firePropertyChange(String, Object, Object) - Method in class ambit2.rest.task.CallableDatasetCreator
 
first() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader
 
first - Variable in class ambit2.db.reporters.SDFReporter
 
first() - Method in class ambit2.db.results.AmbitRows
 
first() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
first() - Method in interface ambit2.model.IDataset
 
firstElementInCombination(int, int[]) - Method in class ambit2.smarts.ComponentMapping
 
firstIndexOf(int, int[]) - Static method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
firstIndexOf(double, double[]) - Static method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
firstLayer(IAtomContainer) - Method in class ambit2.smarts.AtomEquivalenceInfo
 
firstLine - Variable in class ambit2.some.SOMERawReader
 
firstName - Variable in class ambit2.base.data.AmbitUser
 
firstName - Variable in class ambit2.export.isa.v1_0.objects.Person
 
firstName - Variable in class ambit2.ui.editors.AmbitUserEditor
 
firstState() - Method in class ambit2.tautomers.CombinedRuleInstance
 
firstState() - Method in interface ambit2.tautomers.IRuleInstance
 
firstState() - Method in class ambit2.tautomers.RuleInstance
 
FIsEnabled - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
fisher - Variable in class ambit2.db.simiparity.space.QMapSpace
 
fixErrors - Variable in class ambit2.base.data.study.StructureRecordValidator
 
fixSHValence7Atoms(IAtomContainer) - Static method in class ambit2.smarts.smirks.Transformations
 
flag - Variable in class ambit2.similarity.stats.MutableInt
 
FlagAddImplicitHAtomsOnResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagAddImplicitHAtomsOnSLNAtomConversion - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
FlagAddImplicitHAtomsOnTautomerProcess - Variable in class ambit2.tautomers.TautomerManager
 
FlagAddNonStereoSmiles - Variable in class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialStandartization
 
FlagAgentMatch - Variable in class ambit2.smarts.smirks.ReactionSearch
 
FlagAllCompositionInOneProcess - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagApplyDuplicationCheckInChI - Variable in class ambit2.tautomers.FilterTautomers
 
FlagApplyDuplicationCheckIsomorphism - Variable in class ambit2.tautomers.FilterTautomers
 
FlagApplyDuplicationFilter - Variable in class ambit2.tautomers.FilterTautomers
 
FlagApplyExcludeFilter - Variable in class ambit2.tautomers.FilterTautomers
 
FlagApplySimpleAromaticityRankCorrection - Variable in class ambit2.tautomers.FilterTautomers
 
FlagApplySimpleAromaticityRankCorrection - Variable in class ambit2.tautomers.TautomerManager
 
FlagApplyStereoTransformation - Variable in class ambit2.smarts.SMIRKSManager
 
FlagApplyWarningFilter - Variable in class ambit2.tautomers.FilterTautomers
 
FlagAromaticityTransformation - Variable in class ambit2.smarts.SMIRKSManager
 
FlagBufferOutput - Variable in class ambit2.groupcontribution.GCMReportConfig
 
FlagCalcProductInchiKey - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagCalculateCACTVSEnergyRank - Variable in class ambit2.tautomers.TautomerManager
 
FlagCheckAromaticityOnResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagCheckDuplicationOnRegistering - Variable in class ambit2.tautomers.TautomerManager
 
FlagCheckNodeDuplicationOnPush - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagCheckNumOfRegistrationsForIncrementalAlgorithm - Variable in class ambit2.tautomers.TautomerManager
 
FlagCheckReactionConditions - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagCheckReactionMapping - Variable in class ambit2.smarts.smirks.ReactionSearch
 
FlagCheckResultStereo - Variable in class ambit2.smarts.SMIRKSManager
 
FlagCheckStereoElements - Variable in class ambit2.smarts.IsomorphismTester
 
FlagCheckStereoElements - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
FlagCheckValencyOnRegistering - Variable in class ambit2.tautomers.TautomerManager
 
FlagClearAromaticityBeforeResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagClearExcplicitHAtomsBeforeResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagClearHybridizationBeforeResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagClearImplicitHAtomsBeforeResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagClearStereo - Variable in class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialStandartization
 
FlagConsoleOutput - Variable in class ambit2.groupcontribution.GCMReportConfig
 
FlagConvertAddedImplicitHToExplicitOnResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagConvertExplicitHToImplicitOnResultProcess - Variable in class ambit2.smarts.SMIRKSManager
 
FlagDescriptionAdditiveContent - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagEnergyRankingMethod - Variable in class ambit2.tautomers.TautomerManager
 
FlagExcludeWarnFiltersOnRegistering - Variable in class ambit2.tautomers.TautomerManager
 
FlagExcludeWarningTautomers - Variable in class ambit2.tautomers.FilterTautomers
 
FlagExportContentAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportFormulaAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportInchiAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportInchiKeyAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportRelationAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportSmilesAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagExportStrucTypeAsConstituentCharacteristics - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagFailedNodeOnOneForbiddenProduct - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagFilter - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
FlagFilterDuplicates - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
FlagFilterEquivalentMappings - Variable in class ambit2.smarts.SMIRKSManager
 
FlagFilterIncorrectHAtomsStructures - Variable in class ambit2.tautomers.FilterTautomers
 
FlagFilterIncorrectValencySumStructures - Variable in class ambit2.tautomers.FilterTautomers
 
FlagFragmenationOnly - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
FlagGenerateStereoBasedOn2D - Variable in class ambit2.tautomers.TautomerManager
 
FlagGenerateTautomerRelationGraph - Variable in class ambit2.tautomers.TautomerManager
 
FlagGoToStateSpecialOK - Variable in class ambit2.tautomers.RuleInstance
 
FlagHAtomsTransformation - Variable in class ambit2.smarts.SMIRKSManager
 
FlagHAtomsTransformationMode - Variable in class ambit2.smarts.SMIRKSManager
 
FlagImplicitH - Variable in class ambit2.tautomers.RuleInstance
 
FlagLogExplicitHToImplicit - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagLogMainReactionFlow - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagLogNameInReactionPath - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagLogNumberOfProcessedNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagLogReactionPath - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagNewRuleInstanceSearchOnEnergyRanking - Variable in class ambit2.tautomers.TautomerManager
 
FlagOmitEmptyTokens - Variable in class ambit2.groupcontribution.GCMParser
 
FlagOverlapMode - Variable in class ambit2.tautomers.RuleInstance
 
FlagPreserveOriginalAtomID - Variable in class ambit2.sln.SLNHelper
 
FlagPrintExtendedRuleInstances - Variable in class ambit2.tautomers.TautomerManager
 
FlagPrintIcrementalStepDebugInfo - Variable in class ambit2.tautomers.TautomerManager
 
FlagPrintTargetMoleculeInfo - Variable in class ambit2.tautomers.TautomerManager
 
FlagProcessRemainingStackIncSteps - Variable in class ambit2.tautomers.TautomerManager
 
FlagProcessRemainingStackNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagProcessResultStructures - Variable in class ambit2.smarts.SMIRKSManager
 
FlagProcessSingleReagentInNode - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagReactOneReagentOnly - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagReactRecursively - Variable in class ambit2.reactions.reactor.Reactor
 
FlagRecurseBackResultTautomers - Variable in class ambit2.tautomers.TautomerManager
 
FlagRegisterOnlyBestRankTautomers - Variable in class ambit2.tautomers.TautomerManager
 
FlagRemoveReagentIfAllowedProduct - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagRemoveReagentIfForbiddenProduct - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
flags - Variable in class ambit2.tautomers.rules.CustomTautomerRegion
 
FlagSaveCompositionAsExtensionMaterial - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagSaveCompositionAsStudy - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagSetStereoElementsOnTautomerProcess - Variable in class ambit2.tautomers.TautomerManager
 
FlagSkipRuleParsingErrors - Variable in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
FlagSSMode - Variable in class ambit2.smarts.SMIRKSManager
 
FlagStopGenerationOnReachingRuleSelectorLimit - Variable in class ambit2.tautomers.TautomerManager
 
FlagStopOnMaxLevel - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagStoreCACTVSRank - Variable in class ambit2.tautomers.ranking.CanonicTautomer
 
FlagStoreFailedNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagStoreIsomorphismNode - Variable in class ambit2.smarts.IsomorphismTester
 
FlagStoreIsomorphismNode - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
FlagStoreProducts - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagStoreRemovedByFilterTautomers - Variable in class ambit2.tautomers.FilterTautomers
 
FlagStoreSuccessNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagSuccessNodeOnReachingAllowedProducts - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagSuccessNodeOnZeroForbiddenProducts - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagSwitchToCombinatorialOnReachingRuleLimit - Variable in class ambit2.tautomers.TautomerManager
 
FlagTraceParentNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagTraceReactionPath - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
FlagTreatAromaticBondsAsEquivalentFilter - Variable in class ambit2.tautomers.FilterTautomers
 
FlagTrimTokens - Variable in class ambit2.groupcontribution.GCMParser
 
flagUse - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
FlagUse - Variable in class ambit2.reactions.GenericReaction
 
FlagUse - Variable in class ambit2.reactions.Reaction
 
FlagUse13Shifts - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUse15Shifts - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUse17Shifts - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUse19Shifts - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUseAbsolutePathForExternalDataFileLocation - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagUseAbsolutePathForFileLocation - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
FlagUseCarboxylicGroups - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
FlagUseChlorineRules - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUseDeafultExtDataFileHeader - Variable in class ambit2.export.isa.ISAExportConfig
 
FlagUsePhosphoricGroups - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
FlagUsePrimaryAmines - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
FlagUseRingChainRules - Variable in class ambit2.tautomers.KnowledgeBase
 
FlagUseSecondaryAmines - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
flagUseString - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
FlagUseSulfonicAndSulfinicGroups - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
FlagUseTertiaryAmines - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
flagVerbose - Variable in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
flatQuery - Variable in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
FMaxVector - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
FMinVector - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
fmSupport - Variable in class ambit2.rest.freemarker.FreeMarkerResource
 
Fn - Variable in class ambit2.rest.legacy.OTFibonacciSequence
Deprecated.
 
FNumberOfFactors - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
FNumberOfImportantFactors - Variable in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
folder - Variable in class ambit2.ml.io.OutputVW
 
folderIcon - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
folders - Variable in class ambit2.db.reporters.CSVReporter
 
font - Variable in class ambit2.db.reporters.PDFReporter
 
footer(Output, ItemList) - Method in class ambit2.base.processors.batch.BatchReporter
 
footer(Result, IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
footer(Writer, Q) - Method in class ambit2.db.reporters.ARFFReporter
 
footer(Writer, Q) - Method in class ambit2.db.reporters.CMLReporter
 
footer(Writer, Q) - Method in class ambit2.db.reporters.CSVReporter
 
footer(StringWriter, Q) - Method in class ambit2.db.reporters.ImageAreaReporter
 
footer(BufferedImage, Q) - Method in class ambit2.db.reporters.ImageReporter
 
footer(Document, Q) - Method in class ambit2.db.reporters.PDFReporter
 
footer(Output, Q) - Method in class ambit2.db.reporters.QueryPacketReporter
 
footer(Output, Q) - Method in class ambit2.db.reporters.QueryProperyReporter
 
footer(Document, Q) - Method in class ambit2.db.reporters.RTFReporter
 
footer(Writer, Q) - Method in class ambit2.db.reporters.SDFReporter
 
footer(Writer, Q) - Method in class ambit2.db.reporters.SmilesReporter
 
footer(OutputStream, Q) - Method in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
footer(OutputStream, Q) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
footer(OutputStream, Q) - Method in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
footer(XMLStreamWriter) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
footer(XMLStreamWriter) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
footer(Writer, Q) - Method in class ambit2.rest.dataset.DatasetURIReporter
 
footer(ResultSet) - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
footer(XMLStreamWriter, Q) - Method in class ambit2.rest.QueryStaXReporter
 
footer(Writer, Iterator<T>) - Method in class ambit2.rest.reporters.CatalogRDFReporter
 
footer(Writer, Iterator<T>) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
footer() - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
footer() - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
footer() - Method in class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
footer() - Method in class ambit2.rest.task.dsl.OTDatasetTableReport
 
footer(Writer, Iterator<UUID>) - Method in class ambit2.rest.task.TaskJSONReporter
 
forbidden - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
forbiddenProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
forbiddenProducts - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
force_field - Variable in class ambit2.mopac.DescriptorMopacShell
 
forceAromaticBondsAlways - Variable in class ambit2.smarts.SmartsToChemObject
 
forceAromaticBondsForNonRingAtoms - Variable in class ambit2.smarts.SmartsToChemObject
 
forcedelete_sql_ - Static variable in class ambit2.db.update.chemical.DeleteChemical
 
forceOrdering - Variable in class ambit2.db.search.structure.QuerySimilarity
 
forceReadRDFLocalObjects - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
forceStructureDelete - Variable in class ambit2.db.update.chemical.DeleteChemical
 
foreignInputDataset - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
Form - Static variable in class ambit2.base.ro.I5CONSTANTS
 
form - Variable in class ambit2.pubchem.DepictRequest
 
form - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
format - Variable in class ambit2.base.data.StructureRecord
 
format - Variable in class ambit2.core.data.model.Algorithm
 
format - Variable in class ambit2.core.io.DelimitedFileReader
 
format - Variable in class ambit2.core.io.DelimitedFileWriter
 
format - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
format - Variable in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
format - Variable in class ambit2.core.io.RawIteratingCSVReader
 
format(SubstanceProperty, Object) - Method in class ambit2.core.io.study.StudyFormatter
 
format(SubstanceProperty, String) - Method in class ambit2.core.io.study.StudyFormatter
 
format(SubstanceProperty, IValue) - Method in class ambit2.core.io.study.StudyFormatter
 
format(SubstanceProperty, MultiValue<IValue>) - Method in class ambit2.core.io.study.StudyFormatter
 
format(ProtocolApplication<Protocol, String, String, Object, String>, IStudyPrinter) - Method in class ambit2.core.io.study.StudyFormatter
 
format - Variable in class ambit2.descriptors.processors.DescriptorResultFormatter
 
format - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
format - Variable in class ambit2.model.numeric.DataCoverageLeverage
 
format - Variable in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
format(IStructureRecord, String, String) - Method in class ambit2.pubchem.EntrezSearchProcessor
 
format_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
formatCAS(String) - Method in class ambit2.search.chemidplus.ChemIdPlusRequest
 
formatCategoryHeader(String, IStudyPrinter) - Method in class ambit2.core.io.study.StudyFormatter
 
formatParams(StringBuilder, ObjectNode, PropertyAnnotations) - Method in class ambit2.core.io.study.StudyFormatter
 
formatSynonyms(boolean) - Method in class ambit2.base.data.study.EffectRecord
 
formatter - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
formatter - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
formatValue(Value) - Method in class ambit2.core.io.study.StudyFormatter
 
formatValue(EffectRecord<String, Object, String>) - Method in class ambit2.core.io.study.StudyFormatter
 
formula - Variable in class ambit2.base.data.StructureRecord
 
FORMULA - Static variable in class ambit2.core.config.AmbitCONSTANTS
Chemical Formula
formula - Variable in class ambit2.db.search.QueryInfo
 
formula_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
foundState - Variable in class ambit2.tautomers.RuleInstance
 
FOutputDescriptorNumber - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
fp1024_screening - Variable in class ambit2.db.search.structure.QuerySMARTS
 
FP1024Writer - Class in ambit2.db.processors
Writes fingerprints, taken from IStructureRecord.getProperty(AmbitCONSTANTS.Fingerprint).
FP1024Writer() - Constructor for class ambit2.db.processors.FP1024Writer
 
FP1024Writer(FPTable) - Constructor for class ambit2.db.processors.FP1024Writer
 
FP1024Writer.FP1024_status - Enum in ambit2.db.processors
 
fp2string(IAtomContainer, CircularFingerprinter.FP, int) - Static method in class ambit2.descriptors.fingerprints.CircularFingerprintInterpretable
 
fp_prescreen - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
FP_SIZE - Static variable in class ambit2.descriptors.fingerprints.PubChemFingerprinter
Number of bits in this fingerprint.
FP_SIZE - Static variable in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
fpgen - Variable in class ambit2.rest.model.predictor.FingerprintsPredictor
 
fpGenerator - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
fpGenerator - Variable in class ambit2.db.search.structure.QuerySMARTS
 
FPLength - Variable in class ambit2.core.processors.structure.FingerprintGenerator
 
fpmode - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
fpmode - Variable in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
fpmode - Variable in class ambit2.descriptors.processors.BitSetGenerator
 
fpProfile - Variable in class ambit2.model.structure.DataCoverageFingerprints
 
FPStructureWriter - Class in ambit2.db.processors.quality
 
FPStructureWriter() - Constructor for class ambit2.db.processors.quality.FPStructureWriter
 
fpTable - Variable in class ambit2.db.processors.FP1024Writer
 
fptable - Variable in class ambit2.db.update.fp.CreateFingerprintChemical
 
fptable - Variable in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
FPTable - Enum in ambit2.descriptors.processors
 
fractionDigits - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
fractionDigits - Variable in class ambit2.groupcontribution.GCMReportConfig
 
fractionDigits - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
fragMaps - Variable in class ambit2.smarts.ComponentMapping
 
fragmentation - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
Fragmentation - Class in ambit2.groupcontribution.fragmentation
 
Fragmentation() - Constructor for class ambit2.groupcontribution.fragmentation.Fragmentation
 
Fragmentation - Class in ambit2.reactions.fragmentation
 
Fragmentation() - Constructor for class ambit2.reactions.fragmentation.Fragmentation
 
Fragmentation(ArrayList<FragmentationRule>) - Constructor for class ambit2.reactions.fragmentation.Fragmentation
 
FragmentationRule - Class in ambit2.reactions.fragmentation
 
FragmentationRule() - Constructor for class ambit2.reactions.fragmentation.FragmentationRule
 
FragmentationRule(String, IQueryAtomContainer, IsomorphismTester) - Constructor for class ambit2.reactions.fragmentation.FragmentationRule
 
fragmentComponents - Variable in class ambit2.smarts.SmartsParser
 
FragmentProcessor - Class in ambit2.core.processors
Keeps the largest fragment
FragmentProcessor(Logger) - Constructor for class ambit2.core.processors.FragmentProcessor
 
fragmentQuery - Variable in class ambit2.tautomers.Filter
 
fragments - Variable in class ambit2.smarts.SmartsParser
 
fragments - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
fragmentSmarts - Variable in class ambit2.tautomers.Filter
 
frameRead(ReaderEvent) - Method in class ambit2.core.io.SimpleIOListener
 
frameRead(ReaderEvent) - Method in class ambit2.ui.AmbitSettingsListener
 
FreeMarkerApplication<USERID> - Class in ambit2.rest.freemarker
 
FreeMarkerApplication() - Constructor for class ambit2.rest.freemarker.FreeMarkerApplication
 
FreeMarkerResource - Class in ambit2.rest.freemarker
Renders HTML by freemarker template, if htmlByTemplate is true.
FreeMarkerResource() - Constructor for class ambit2.rest.freemarker.FreeMarkerResource
 
FreeMarkerStatusService - Class in ambit2.rest.freemarker
 
FreeMarkerStatusService(FreeMarkerApplication, FreeMarkerStatusService.REPORT_LEVEL) - Constructor for class ambit2.rest.freemarker.FreeMarkerStatusService
 
FreeMarkerStatusService.REPORT_LEVEL - Enum in ambit2.rest.freemarker
 
freeMarkerSupport - Variable in class ambit2.rest.freemarker.FreeMarkerStatusService
 
FreeMarkerSupport - Class in ambit2.rest.freemarker
 
FreeMarkerSupport() - Constructor for class ambit2.rest.freemarker.FreeMarkerSupport
 
FreeMarkerSupport(String) - Constructor for class ambit2.rest.freemarker.FreeMarkerSupport
 
FreeTextPropertyQuery - Class in ambit2.db.search.property
Same as FreeTextQuery , but retrieves properties
FreeTextPropertyQuery() - Constructor for class ambit2.db.search.property.FreeTextPropertyQuery
 
FreeTextQuery - Class in ambit2.db.search.structure
select idchemical,metric from ( (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where name like "MA%" and value like "Reaction%" ) union (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%" and name like "Reaction%" ) union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "MA%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%") union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "Reaction%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "Reaction%") ) a
FreeTextQuery() - Constructor for class ambit2.db.search.structure.FreeTextQuery
 
frequency - Variable in class ambit2.descriptors.AtomEnvironment
 
frequency() - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
frequency - Variable in class ambit2.reactions.SimilarityManager.TransformedStartMaterialData
 
frequency - Variable in class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
fromIndex - Variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
 
fromString(String) - Static method in enum ambit2.export.isa.base.ISALocation.Layer
 
fromString(String) - Static method in enum ambit2.groupcontribution.correctionfactors.ICorrectionFactor.Type
 
fromString(String) - Static method in enum ambit2.groupcontribution.groups.IGroup.Type
 
fromValue(String) - Static method in enum ambit2.export.isa.v1_0.objects.Data.Type
 
fromValue(String) - Static method in enum ambit2.export.isa.v1_0.objects.Material.Type
 
FT_EXCLUDE - Static variable in class ambit2.tautomers.Filter
 
FT_WARNING - Static variable in class ambit2.tautomers.Filter
 
fulllinks - Variable in class ambit2.base.ro.AbstractAnnotator
 
fullString - Variable in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
fullString - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
FuncGroupsChartGenerator - Class in ambit2.db.chart
chart number of chemicals with functional groups
FuncGroupsChartGenerator() - Constructor for class ambit2.db.chart.FuncGroupsChartGenerator
 
FuncGroupsDescriptorFactory - Class in ambit2.descriptors
 
FuncGroupsDescriptorFactory() - Constructor for class ambit2.descriptors.FuncGroupsDescriptorFactory
 
funcs(double, double[], double[], int) - Method in interface ambit2.domain.stats.IFunc
 
function - Variable in class ambit2.base.relation.composition.Proportion
 
FunctionalGroup - Class in ambit2.descriptors
 
FunctionalGroup() - Constructor for class ambit2.descriptors.FunctionalGroup
 
FunctionalGroup(String, String, String, String) - Constructor for class ambit2.descriptors.FunctionalGroup
 
FunctionalGroup(String, String, String, String, String) - Constructor for class ambit2.descriptors.FunctionalGroup
 
FunctionalGroup(String, String, String) - Constructor for class ambit2.descriptors.FunctionalGroup
 
FunctionalGroup - Class in ambit2.structure2name.components
 
FunctionalGroup() - Constructor for class ambit2.structure2name.components.FunctionalGroup
 
FunctionalGroupData - Class in ambit2.structure2name.rules
 
FunctionalGroupData() - Constructor for class ambit2.structure2name.rules.FunctionalGroupData
 
FunctionalGroupDescriptor - Class in ambit2.descriptors
Functional groups (by SMARTS)
FunctionalGroupDescriptor() - Constructor for class ambit2.descriptors.FunctionalGroupDescriptor
 
functionalGroups - Variable in class ambit2.structure2name.rules.IUPACRuleDataBase
 
functions - Variable in class ambit2.rules.functions.NestedFunctions
 
fusedBond - Variable in class ambit2.structure2name.components.ComponentConnection
 

G

g - Variable in class ambit2.db.processors.quality.FPStructureWriter
 
g - Variable in class ambit2.db.processors.quality.QualityLabelWriter
 
g - Variable in class ambit2.db.search.structure.QuerySimilarityStructure
 
g - Variable in class ambit2.db.update.fpae.AtomEnvironmentWriter
Deprecated.
 
g - Variable in class ambit2.db.update.qlabel.smarts.SMARTSAcceleratorWriter
 
g2 - Variable in class ambit2.db.simiparity.space.QMapSpace
 
gaCode - Variable in class ambit2.rest.freemarker.FreeMarkerApplication
 
GaussianClusters(double[][], int, int, double[], int) - Static method in class ambit2.domain.stats.Tools
 
GCM2Json - Class in ambit2.groupcontribution.io
 
GCM2Json() - Constructor for class ambit2.groupcontribution.io.GCM2Json
 
GCM2Json(IsomorphismTester, SmartsParser) - Constructor for class ambit2.groupcontribution.io.GCM2Json
 
GCM2Properties - Class in ambit2.groupcontribution.io
 
GCM2Properties() - Constructor for class ambit2.groupcontribution.io.GCM2Properties
 
gcmConfigFile - Variable in class ambit2.groupcontribution.cli.GCMPredictCli
 
gcmConfigFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
GCMConfigInfo() - Constructor for class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
GCMParser - Class in ambit2.groupcontribution
 
GCMParser() - Constructor for class ambit2.groupcontribution.GCMParser
 
GCMParser(SmartsParser, IsomorphismTester) - Constructor for class ambit2.groupcontribution.GCMParser
 
GCMPredictCli - Class in ambit2.groupcontribution.cli
 
GCMPredictCli() - Constructor for class ambit2.groupcontribution.cli.GCMPredictCli
 
GCMReportConfig - Class in ambit2.groupcontribution
 
GCMReportConfig() - Constructor for class ambit2.groupcontribution.GCMReportConfig
 
GCMTestConfig - Class in ambit2.groupcontribution
 
GCMTestConfig() - Constructor for class ambit2.groupcontribution.GCMTestConfig
 
gcmType - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
gcmTypeString - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
gen - Variable in class ambit2.core.processors.structure.key.SmilesKey
 
gen - Variable in class ambit2.smi23d.ShellSmi2SDF
 
generate(IAtomContainer, IAtom, RendererModel) - Method in class ambit2.rendering.AtomAnnotationGenerator
 
generate(IAtomContainer, RendererModel) - Method in class ambit2.rendering.AtomLabelGenerator
 
generate(IAtomContainer, RendererModel) - Method in class ambit2.rendering.ImageMapGenerator
 
GENERATE2D - Static variable in class ambit2.base.config.Preferences
 
GENERATE2D - Static variable in class ambit2.core.config.Resources
generate 2D
generate2d(IAtomContainer) - Method in class ambit2.mopac.Mopac7Writer
 
generate2D(IAtomContainer, boolean, IAtomContainerSet) - Method in class ambit2.rendering.CompoundImageTools
 
generate2D - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generate2d - Variable in class ambit2.ui.Panel2D
 
generate3DStructure(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
generate3DStructure(IAtomContainer) - Method in class ambit2.mopac.MopacShell
 
generate3DStructure(IAtomContainer) - Method in class ambit2.mopac.MopacShellBalloon
 
generate3DStructure(IAtomContainer) - Method in class ambit2.mopac.MopacShellOB
 
generateAcyclicComponent(IAtom) - Method in class ambit2.structure2name.IUPACNameGenerator
 
generateAllReactionInstances(IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
generateAllReactionInstances(IAtomContainer, List<GenericReaction>) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
generateBondMapping(IAtomContainer, List<IAtom>) - Method in class ambit2.smarts.IsomorphismTester
 
generateBondMapping(IQueryAtomContainer, List<IAtom>) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
generateChildrenNodes(RetroSynthNode) - Method in class ambit2.reactions.retrosynth.RetroSynthesis
 
generateComponents() - Method in class ambit2.structure2name.IUPACNameGenerator
 
generateContainerForAtomList(List<IAtom>, IAtomContainer) - Static method in class ambit2.structure2name.components.ComponentUtils
 
generateCorrectionFactorMatrix(DataSet, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
generateDescriptorExpression(List<Object>) - Static method in class ambit2.rules.conditions.DescriptorExpression
 
generateDocumentUUID(ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
generateFragmentationMatrix(DataSet, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
generateFullAtomMapping(List, IAtomContainer, IAtomContainer) - Method in class ambit2.smarts.SmartsManager
This function generates full Atom Mapping from a Bond mapping (result from the CDK isomorphism
generateFullIsomorphismMapping(List, IAtomContainer, IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
generateFulltautomerInfo(String, String) - Method in class ambit2.tautomers.Tautomer2DescriptorUtils
 
generateHShifts() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
generateImage(String) - Method in class ambit2.rendering.CompoundImageTools
 
generateImage(String, IAtomContainerHighlights, boolean, boolean) - Method in class ambit2.rendering.CompoundImageTools
 
generateImage(String, IAtomContainerHighlights, boolean, boolean, CompoundImageTools.Mode2D) - Method in class ambit2.rendering.CompoundImageTools
 
generateInChI - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateIUPACName(IAtomContainer) - Method in class ambit2.structure2name.IUPACNameGenerator
 
generateMultiplePropertyMatrix(DataSet, List<String>) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
generateMultiplePropertyMatrix2(DataSet, List<DescriptorInfo>) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
generatePairForEachRuleInstance(TautomerManager, IAtomContainer, boolean) - Static method in class ambit2.tautomers.TautomerUtils
 
generateProducts() - Method in class ambit2.reactions.GenericReactionInstance
 
generateProperty(IAtomContainer) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
generateProperty(IAtomContainer) - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
generateProperty(IAtomContainer) - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
generateProperty(IAtomContainer) - Method in class ambit2.descriptors.processors.BitSetGenerator
 
generateProperty(IAtomContainer) - Method in class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
generatePropertyMatrix(DataSet, String) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
generateRulePairs(IAtomContainer) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
generateSequenceStepForReactionInstance(ReactionSequenceLevel, int, GenericReaction, List<IAtom>) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
generateSequenceStepForReactionInstance(ReactionSequenceLevel, int, GenericReactionInstance) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
generateSMILES - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateSMILES_Aromatic - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateSMILES_Canonical - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateStereofrom2D - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateTautomers - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
generateTautomers() - Method in class ambit2.tautomers.TautomerManager
This is pure combinatorial approach It is the initial approach 00 based on binary combinations.
generateTautomers_ImprovedCombApproach() - Method in class ambit2.tautomers.TautomerManager
 
generateTautomersIncrementaly() - Method in class ambit2.tautomers.TautomerManager
 
generateUUIDfromString(String, String) - Static method in class ambit2.base.data.study.StructureRecordValidator
 
generateZwitterions() - Method in class ambit2.tautomers.zwitterion.ZwitterionManager
 
generator - Variable in class ambit2.similarity.knn.NNAtomEnvironmentSimilarity
 
generator - Variable in class ambit2.similarity.knn.NNFingerprintSimilarity
 
GenericGroup - Class in ambit2.core.groups
 
GenericGroup(String, int) - Constructor for class ambit2.core.groups.GenericGroup
 
GenericParserUtils - Class in ambit2.reactions.rules
 
GenericParserUtils() - Constructor for class ambit2.reactions.rules.GenericParserUtils
 
GenericReaction - Class in ambit2.reactions
 
GenericReaction() - Constructor for class ambit2.reactions.GenericReaction
 
GenericReaction.ReactionConfigStatus - Enum in ambit2.reactions
 
GenericReaction.ReactionType - Enum in ambit2.reactions
 
GenericReaction.TransformType - Enum in ambit2.reactions
 
GenericReactionInstance - Class in ambit2.reactions
 
GenericReactionInstance() - Constructor for class ambit2.reactions.GenericReactionInstance
 
GenericReactionInstance(GenericReaction, IAtomContainer, List<IAtom>) - Constructor for class ambit2.reactions.GenericReactionInstance
 
GenericReactionInstance(GenericReaction, IAtomContainer, List<IAtom>, IAtomContainer) - Constructor for class ambit2.reactions.GenericReactionInstance
 
genericReactions - Variable in class ambit2.reactions.ReactionDataBase
 
GenericRuleMetaInfo - Class in ambit2.reactions.rules
 
GenericRuleMetaInfo() - Constructor for class ambit2.reactions.rules.GenericRuleMetaInfo
 
get(P) - Method in class ambit2.base.data.Profile
 
get(Object) - Method in class ambit2.base.data.study.Params
 
get(int) - Method in class ambit2.core.data.ArrayResult
 
get(int) - Method in class ambit2.core.groups.FilteredList
 
get(int) - Method in class ambit2.db.search.QueryCombined
 
get(Variant) - Method in class ambit2.rest.AbstractResource
 
get(Variant) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
get(String) - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
get(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
get(String) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
get(Variant) - Method in class ambit2.rest.ProtectedResource
 
get(Variant) - Method in class ambit2.rest.task.LauncherResource
 
get(URL) - Method in class ambit2.search.chemidplus.AbstractSearchRequest
 
get2DgridPoints(int[], double[], double[], double[], int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
get2DGridPoints
getA() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getAction() - Method in interface ambit2.rules.IActionRule
 
getActiveRuleNames() - Method in class ambit2.tautomers.KnowledgeBase
 
getActivityThreshold() - Method in class ambit2.db.simiparity.space.QMap
 
getAdditionalAromaticityRank(IAtomContainer) - Static method in class ambit2.tautomers.RuleManager
 
getAdditionalConfig() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getAdditionalFiles() - Method in class ambit2.base.external.Command
 
getAdditiveAdjacencyMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getAddress() - Method in class ambit2.base.data.AmbitUser
 
getAdjacencyMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getAdminPass() - Method in class ambit2.db.processors.DbCreateDatabase
 
getAffiliation() - Method in class ambit2.base.data.AmbitUser
 
getAgent() - Method in class ambit2.rest.ProtectedResource
 
getAgent() - Method in class ambit2.rest.task.CallableQueryProcessor
 
getAjaxTimeout() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
msec
getAjaxTimeoutOption() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getAlgorithm() - Method in class ambit2.core.data.model.ModelWrapper
 
getAlgorithm() - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
getAlgorithm() - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
getAlgorithm() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getAlgorithmReporter() - Method in class ambit2.rest.model.builder.ModelBuilder
 
getAlgorithms(Form, String) - Method in class ambit2.rest.task.CallablePOST
 
getAllErrors() - Method in class ambit2.sln.io.SLN2ChemObject
 
getAllErrors() - Method in class ambit2.sln.io.SLN2SMARTS
 
getAllErrors() - Method in class ambit2.sln.io.SLN2Substance
 
getAllErrors() - Method in class ambit2.sln.search.SLNSearchManager
 
getAllErrors() - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
getAllErrors() - Method in class ambit2.tautomers.KnowledgeBase
 
getAllErrors() - Method in class ambit2.tautomers.rules.JsonRuleParser
 
getAllErrorsAsString() - Method in class ambit2.groupcontribution.GCMParser
 
getAllErrorsAsString() - Method in class ambit2.groupcontribution.io.GCM2Json
 
getAllErrorsAsString() - Method in class ambit2.groupcontribution.io.GCM2Properties
 
getAllErrorsAsString() - Method in class ambit2.groupcontribution.Learner
 
getAllErrorsAsString() - Method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
getAllErrorsAsString() - Method in class ambit2.smarts.smirks.ReactionSearch
 
getAllIsomorphismMappings(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
If no isomorphism is found the result is empty vector
getAllIsomorphismMappings(IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
getAllIsomorphismMappings(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
If no isomorphism is found the result is empty vector
getAllMappings(IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
getAllowedOrigins() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getAllowedOrigins() - Method in class ambit2.rest.OriginFilter
 
getAllowedValues() - Method in class ambit2.base.data.Property
 
getAllRuleNames() - Method in class ambit2.tautomers.KnowledgeBase
 
getAllStereoElementsStatus(IAtomContainer, List<IStereoElement>) - Static method in class ambit2.smarts.StereoChemUtils
 
getAllWarningAsString() - Method in class ambit2.groupcontribution.io.GCM2Json
 
getAllWarningAsString() - Method in class ambit2.groupcontribution.io.GCM2Properties
 
getAmplitude(double) - Method in class ambit2.domain.stats.transforms.densityestimation.KCEpanechnikov
 
getAmplitude(Matrix) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
getAmplitude(double) - Method in class ambit2.domain.stats.transforms.densityestimation.Kernel
 
getAmplitude(double) - Method in class ambit2.domain.stats.transforms.densityestimation.KLaplacian
 
getAmplitude(double) - Method in class ambit2.domain.stats.transforms.densityestimation.KNormal
 
getAnnotation() - Method in interface ambit2.base.data.study.IValue
 
getAnnotation() - Method in class ambit2.base.data.study.Value
 
getAnnotation() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getAnnotations() - Method in class ambit2.base.data.Property
 
getAnswer() - Method in class ambit2.ui.WizardPanel
 
getAppDomainMethodType() - Method in class ambit2.model.numeric.DataCoverage
 
getAppDomainMethodType() - Method in interface ambit2.model.numeric.IDataCoverage
 
getApplicationConditions() - Method in class ambit2.reactions.GenericReaction
 
getApplicationRoot() - Method in class ambit2.rest.task.LauncherResource
 
getApplicationRootReference() - Method in class ambit2.rest.model.builder.ModelBuilder
 
getApplicationStatus() - Method in class ambit2.reactions.GenericReactionInstance
 
getArray(int) - Method in class ambit2.db.results.AmbitRows
 
getArray(String) - Method in class ambit2.db.results.AmbitRows
 
getAsciiStream(int) - Method in class ambit2.db.results.AmbitRows
 
getAsciiStream(String) - Method in class ambit2.db.results.AmbitRows
 
getAsJSONString() - Method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
getAsMatrix(IStructureRecord) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
getAssayUUID() - Method in class ambit2.base.data.study.ProtocolApplication
 
getAtm() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getAtom(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getAtom_environment() - Method in class ambit2.descriptors.AtomEnvironment
 
getAtomCode(IAtom, IBond, int, int) - Static method in class ambit2.smarts.AtomEquivalenceInfo
 
getAtomComplexities() - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
getAtomComplexityCalculator() - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
getAtomContainer(IStructureRecord) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
getAtomContainer(IStructureRecord) - Method in class ambit2.db.results.StoredQueryTableModel
 
getAtomContainer(IStructureRecord) - Method in class ambit2.descriptors.processors.BitSetGenerator
 
getAtomCount() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getAtomDesignation(int[]) - Method in class ambit2.groupcontribution.GroupContributionModel
 
getAtomDesignationVerbose(int[]) - Method in class ambit2.groupcontribution.GroupContributionModel
 
getAtomExpressionTokens(SmartsAtomExpression) - Static method in class ambit2.smarts.SmartsHelper
 
getAtomFingerprintSize() - Method in class ambit2.descriptors.AtomEnvironentMatrix
to hold counts of all atom types defined by factory for maxlevel and one additional entry for undefined atom types
getAtomFingerprintSize() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
to hold counts of all atom types defined by factory for maxlevel and one additional entry for undefined atom types
getAtomIterator(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getAtomListAsString(List<IAtom>, IAtomContainer) - Static method in class ambit2.structure2name.components.ComponentUtils
 
getAtomNeighbourCode(IAtom, IAtom) - Method in class ambit2.smarts.SmartsParser
 
getAtomno() - Method in class ambit2.descriptors.AtomEnvironment
 
getAtomNumber(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getAtomPaths(IAtom, IAtomContainer, int, boolean) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
getAtomPaths1(IAtom, IAtomContainer, boolean) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
getAtomPaths2(IAtom, IAtomContainer, boolean) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
getAtomPathsAsString(IAtom, IAtomContainer) - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
getAtomRadius(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.getAtomRadius()
getAtomRingIndices() - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
getAtoms(boolean) - Method in class ambit2.core.groups.AbstractGroup
 
getAtoms(boolean) - Method in interface ambit2.core.groups.ISGroup
 
getAtoms(boolean) - Method in class ambit2.core.groups.MultipleGroup
 
getAtoms(boolean) - Method in class ambit2.core.groups.SuperAtom
 
getAtoms() - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
getAtoms() - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
getAtoms() - Method in class ambit2.structure2name.components.AbstractComponent
 
getAtoms() - Method in interface ambit2.structure2name.components.IIUPACComponent
 
getAtoms() - Method in class ambit2.tautomers.CombinedRuleInstance
 
getAtoms() - Method in interface ambit2.tautomers.IRuleInstance
 
getAtoms() - Method in class ambit2.tautomers.RuleInstance
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
getAtoms() - Method in interface ambit2.tautomers.zwitterion.ICenter
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
getAtoms() - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
getAtomsAttributes(SLNContainer) - Static method in class ambit2.sln.SLNHelper
 
getAtomsAttributes(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getAtomSelector(IAtomContainer, SOMERawReader.someindex) - Static method in class ambit2.some.SOMERawReader
 
getAtomSetCollectionName(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getAtomSetCount(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getAtomsExpressionTokens(IQueryAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getAtomsString(IQueryAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getAtomsString(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getAtomTopDegrees(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
getAtomTopologicalLayers(IAtomContainer, int) - Static method in class ambit2.descriptors.utils.TopologicalLayers
 
getAtomTopologicalLayers(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalLayers
 
getAtomType(int) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getAtomType(int) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getAtomTypeFactoryStream() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getAtomTypeFactoryStream() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getAtomWeightedDistanceMatrix(IAtomContainer, double[]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getAtomXDInfo(IAtom) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
getAttribute(T, int) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
getAttributes() - Method in class ambit2.sln.SLNContainer
 
getAttributeSelection() - Method in class ambit2.model.AbstractModel
 
getAttributeSelection() - Method in interface ambit2.model.IModelDefinition
 
getAuthor(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getAverageSimilarity() - Method in interface ambit2.similarity.ISimilarityResultType
 
getAvg() - Method in class ambit2.base.data.PropertyStats
 
getAzideGroupPositions(IAtomContainer) - Static method in class ambit2.tautomers.rules.CustomTautomerRegion
 
getB() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getBacisInchiOptions() - Static method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
getBackground() - Method in interface ambit2.core.io.ICompoundImageTools
 
getBackground() - Method in class ambit2.rendering.CompoundImageTools
 
getBackground() - Method in class ambit2.ui.ImageCellRenderer
 
getBalloonHome() - Method in class ambit2.balloon.ShellBalloon
 
getBalloonHome() - Method in class ambit2.balloon.ShellBalloonWeb
 
getBaseReference() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
getBaseReference() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
getBaseReference() - Method in class ambit2.rest.RDFBatchParser
 
getBaseURLDepth() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getBasicScore() - Method in class ambit2.reactions.GenericReaction
 
getBestInstance(List<GenericReactionInstance>) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getBestRankComponent() - Method in class ambit2.structure2name.IUPACNameGenerator
 
getBigDecimal(int) - Method in class ambit2.db.results.AmbitRows
 
getBigDecimal(String) - Method in class ambit2.db.results.AmbitRows
 
getBigDecimal(int, int) - Method in class ambit2.db.results.AmbitRows
 
getBigDecimal(String, int) - Method in class ambit2.db.results.AmbitRows
 
getBinaryStream(int) - Method in class ambit2.db.results.AmbitRows
 
getBinaryStream(String) - Method in class ambit2.db.results.AmbitRows
 
getBinNumber(double) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getBinsSql() - Method in class ambit2.db.search.property.PropertyRange
 
getBinsSql() - Method in class ambit2.db.search.property.QueryMetricRange
 
getBinWidth() - Method in class ambit2.db.chart.XTabChartGenerator
 
getBitFingerprint(IAtomContainer) - Method in class ambit2.core.data.HashIntDescriptorResult
 
getBitFingerprint(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getBitFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
getBits() - Method in class ambit2.db.update.fp.Fingerprint
 
getBits() - Method in interface ambit2.db.update.fp.IFingerprint
 
getBitSetString(BitSet) - Method in class ambit2.smarts.Screening
 
getBlob(int) - Method in class ambit2.db.results.AmbitRows
 
getBlob(String) - Method in class ambit2.db.results.AmbitRows
 
getBlocks() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
getBond(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBond(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBondAttributes(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getBondCharNumber(char) - Static method in class ambit2.smarts.SmartsConst
 
getBondCode(IBond, int, int, int) - Static method in class ambit2.smarts.AtomEquivalenceInfo
 
getBondCount() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBondIndexSequence(IAtomContainer) - Static method in class ambit2.tautomers.ranking.TautomerStringCode
 
getBondIterator(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getBondMappings(IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
getBondNumber(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBondNumber(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBondOrderSum(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getBonds(boolean) - Method in class ambit2.core.groups.AbstractGroup
 
getBonds(boolean) - Method in interface ambit2.core.groups.ISGroup
 
getBonds(boolean) - Method in class ambit2.core.groups.MultipleGroup
 
getBonds(boolean) - Method in class ambit2.core.groups.SuperAtom
 
getBondsAttributes(SLNContainer) - Static method in class ambit2.sln.SLNHelper
 
getBondsString(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getBondsString(IQueryAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
getBoolean(int) - Method in class ambit2.db.results.AmbitRows
 
getBoolean(String) - Method in class ambit2.db.results.AmbitRows
 
getBorderColor() - Method in interface ambit2.core.io.ICompoundImageTools
 
getBorderColor() - Method in class ambit2.rendering.CompoundImageTools
 
getBorderWidth() - Method in class ambit2.rendering.CompoundImageTools
 
getBrowserMode() - Method in class ambit2.ui.table.BrowsableTableModel
 
getBrowserMode() - Method in interface ambit2.ui.table.IBrowserMode
 
getBuilder() - Method in class ambit2.rest.model.task.CallableModelCreator
 
getBuilder() - Method in class ambit2.smarts.ChemObjectFactory
 
getBuilder() - Method in class ambit2.smarts.SmartsToChemObject
 
getBundle() - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
getBundle() - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
getBundle() - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
getBundle() - Method in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
getBundle() - Method in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
getBundle_number() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getBundleReference(SubstanceEndpointsBundle) - Static method in class ambit2.base.data.LiteratureEntry
 
getBundleRole() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getBundles() - Method in class ambit2.db.reporters.CSVReporter
 
getByte(int) - Method in class ambit2.db.results.AmbitRows
 
getByte(String) - Method in class ambit2.db.results.AmbitRows
 
getBytes(int) - Method in class ambit2.db.results.AmbitRows
 
getBytes(String) - Method in class ambit2.db.results.AmbitRows
 
getC() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getCached(String, String, ResultType) - Method in class ambit2.db.DbReader
Returns cached query results or NOTCACHED if not in the cache.
getCached(String, String, IStructureRecord) - Method in class ambit2.db.DbReaderStructure
 
getCached(IStructureRecord) - Method in class ambit2.db.reporters.AbstractImageReporter
 
getCached(IStructureRecord) - Method in class ambit2.db.reporters.ImageAreaReporter
 
getCached(IStructureRecord) - Method in class ambit2.db.reporters.ImageReporter
 
getCachedRowSet() - Static method in class ambit2.db.CachedRowSetFactory
 
getCachedStatement(String) - Method in class ambit2.db.StatementExecutor
 
getCalcLog() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getCalculatedDescrData() - Method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
getCalculationDetailsAsString() - Method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
getCalculationErrors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCallback() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
getCallback() - Method in class ambit2.tautomers.processor.TautomerProcessor
 
getCanonicTautomer(List<IAtomContainer>) - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
getCanonicTautomer(List<IAtomContainer>) - Method in class ambit2.tautomers.TautomerManager
 
getCanonicTautomer0(List<IAtomContainer>) - Method in class ambit2.tautomers.TautomerManager
 
getCanonicTautomerMethod() - Method in class ambit2.tautomers.TautomerManager
 
getCaption() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Class
 
getCarbonSkelleton(List<QuerySequenceElement>) - Method in class ambit2.smarts.ChemObjectFactory
 
getCarbonSkelletonsFromString(String) - Static method in class ambit2.smarts.SmartsHelper
 
getCAS() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getCASInstance() - Static method in class ambit2.base.data.Property
 
getCASReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getCategory() - Method in class ambit2.base.data.study.Protocol
 
getCategory() - Method in class ambit2.db.cache.QueryCachedResults
 
getCategory() - Method in class ambit2.db.search.AbstractQuery
 
getCategory() - Method in class ambit2.db.search.property.FilteredCount
 
getCategory() - Method in class ambit2.db.search.QueryCombined
 
getCategory() - Method in class ambit2.db.search.StoredQuery
 
getCategory() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
getCategory() - Method in class ambit2.db.search.structure.QuerySMARTS
 
getCategory() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
getCategory() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getCategory() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getCategoryConfig(Protocol._categories) - Method in class ambit2.core.io.study.StudyFormatter
 
getCategoryTitle(ISourceDataset) - Method in class ambit2.db.chart.BarChartGeneratorDataset
 
getCategoryTitle(ISourceDataset) - Method in class ambit2.db.chart.HistogramChartGenerator
 
getCategoryType() - Method in interface ambit2.base.interfaces.ICategory
Return one of ICategory.CategoryType
getCdkDescrMan() - Method in class ambit2.groupcontribution.GCMParser
 
getCellColor(int, int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getCellEditor(int) - Method in class ambit2.ui.EditableHeader
 
getCellEditor() - Method in class ambit2.ui.EditableHeader
 
getCellSize(int, int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getCenter(IAtomContainer, IAtom) - Static method in class ambit2.tautomers.zwitterion.AminoGroup
 
getCenter(IAtomContainer, IAtom) - Static method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
getCenter(IAtomContainer, IAtom) - Static method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
getCenter(IAtomContainer, IAtom) - Static method in class ambit2.tautomers.zwitterion.SulfGroup
 
getCentral_atom() - Method in class ambit2.descriptors.AtomEnvironment
 
getCharacterStream(int) - Method in class ambit2.db.results.AmbitRows
 
getCharacterStream(String) - Method in class ambit2.db.results.AmbitRows
 
getChartTitle(ISourceDataset) - Method in class ambit2.db.chart.BarChartGeneratorDataset
 
getChebiProperty(String, String) - Static method in class ambit2.chebi.ChEBIClient
 
getChEMBL_Activity_Instance(String) - Static method in class ambit2.base.data.ChEMBLProperties
 
getChEMBL_CompoundURI_Instance() - Static method in class ambit2.base.data.ChEMBLProperties
 
getChEMBL_Name_Instance() - Static method in class ambit2.base.data.ChEMBLProperties
 
getChEMBL_Smiles_Instance() - Static method in class ambit2.base.data.ChEMBLProperties
 
getChEMBLPropertyInstance(String, ChEMBLProperties.ChEMBL_Class) - Static method in class ambit2.base.data.ChEMBLProperties
 
getChEMBLReference(ChEMBLProperties.ChEMBL_Class) - Static method in class ambit2.base.data.ChEMBLProperties
 
getChemicalAtomEccentricity(double[][]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getChemicalsOnly() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getChunkSize() - Method in class ambit2.db.reporters.QueryPacketReporter
 
getCitation(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getCitationConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getCity() - Method in class ambit2.base.data.AmbitUser
 
getClassifier() - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
getClassifier() - Method in class ambit2.rest.task.weka.WekaPredictor
 
getClassIndex(Form) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getClassName() - Method in enum ambit2.core.processors.structure.key.IStructureKey.Matcher
 
getClazz() - Method in class ambit2.base.data.ClassHolder
 
getClazz() - Method in class ambit2.base.data.Property
 
getClazz() - Method in enum ambit2.db.search.property.AbstractPropertyRetrieval._PROPERTY_TYPE
 
getClientAtomStringProperty(Object, String) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getClob(int) - Method in class ambit2.db.results.AmbitRows
 
getClob(String) - Method in class ambit2.db.results.AmbitRows
 
getClusterer() - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
getClusterer() - Method in class ambit2.rest.task.weka.WekaPredictor
 
getCode() - Method in enum ambit2.base.data.study.ReliabilityParams._r_flags
 
getCode() - Method in exception ambit2.base.exceptions.HttpException
 
getCode(IAtomContainer, boolean, int[]) - Static method in class ambit2.tautomers.ranking.TautomerStringCode
 
getCode0(IAtomContainer, boolean) - Static method in class ambit2.tautomers.ranking.TautomerStringCode
 
getCodeStrBondSequence() - Method in class ambit2.tautomers.TautomerManager
 
getColor(double) - Method in enum ambit2.some.SOMERawReader.someindex
 
getColStatPercentageThreshold() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getColumnClass(int) - Method in class ambit2.db.results.StoredQueryTableModel
 
getColumnClass(int) - Method in class ambit2.dbui.CachedRowSetTableModel
 
getColumnClass(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
getColumnCount() - Method in class ambit2.base.data.PropertiesTableModel
 
getColumnCount() - Method in class ambit2.db.results.StoredQueryTableModel
 
getColumnCount() - Method in class ambit2.dbui.CachedRowSetTableModel
 
getColumnCount() - Method in class ambit2.similarity.stats.ConfusionMatrix
 
getColumnCount() - Method in class ambit2.ui.table.BrowsableTableModel
 
getColumnCount() - Method in class ambit2.ui.table.StructureRecordsTableModel
 
getColumnName(int) - Method in class ambit2.base.data.PropertiesTableModel
 
getColumnName(int) - Method in class ambit2.db.results.StoredQueryTableModel
 
getColumnName(int) - Method in class ambit2.dbui.CachedRowSetTableModel
 
getColumnName(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
getColumnName(int) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
getColumns() - Method in class ambit2.ui.editors.BeanEditor
 
getColumns() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getCombine() - Method in class ambit2.db.search.QueryInfo
 
getCombine_queries() - Method in class ambit2.db.search.QueryCombined
 
getCommand() - Method in interface ambit2.db.processors.ICommand
 
getCommand() - Method in class ambit2.db.results.AmbitRows
 
getCommand() - Method in class ambit2.rendering.StructureEditorProcessor
 
getComment(String, String) - Static method in class ambit2.export.isa.v1_0.ISAJsonUtils1_0
 
getCommentChar() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
getComments(String, Target) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
getComments(String, DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
getComments(String, DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorWriter
 
getComments(String, IStructureRecord) - Method in class ambit2.db.processors.PropertyValuesWriter
 
getComments() - Method in class ambit2.db.version.AmbitDBVersion
 
getCompactShape(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
 
getCompanyName() - Method in class ambit2.base.data.study.ProtocolApplication
 
getCompanyUUID() - Method in class ambit2.base.data.study.ProtocolApplication
 
getCompatibleNotation(SLNContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
getComplementDistanceMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getComponentDataAsString() - Method in class ambit2.structure2name.IUPACNameGenerator
 
getComponents() - Method in class ambit2.core.groups.ContainerGroup
 
getComponentString(List<IAtom>, IAtomContainer) - Static method in class ambit2.structure2name.components.ComponentUtils
 
getCompositionName() - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
getCompositionUUID() - Method in class ambit2.base.relation.composition.CompositionRelation
Composition UUID
getCompositionUUID() - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
getCompoundReporter() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.FingerprintsPredictor
 
getCompoundURL(NativeTypeItem) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getCompoundURL(IStructureRecord) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
getCompoundURL(Instance) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
getCompoundURL(Instance) - Method in class ambit2.rest.task.weka.WekaPredictor
 
getConcordanceCorrelationCoefficient(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getConcordanceCorrelationCoefficient(List<Double>, List<Double>) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getConcurrency() - Method in class ambit2.db.results.AmbitRows
 
getCondition() - Method in class ambit2.db.search.AbstractQuery
 
getCondition() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getCondition() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getCondition() - Method in interface ambit2.rules.IBasicRule
 
getCondition1() - Method in class ambit2.db.search.QueryInfo
 
getCondition2() - Method in class ambit2.db.search.QueryInfo
 
getCondition3() - Method in class ambit2.db.search.QueryInfo
 
getConditionFromString(String) - Static method in class ambit2.core.filter.MoleculeFilter
 
getConditionFromString(String) - Static method in class ambit2.reactions.rules.ReactionParser
 
getConditions() - Method in class ambit2.base.data.study.EffectRecord
 
getConditions() - Method in class ambit2.core.filter.MoleculeFilter
 
getConditions() - Method in class ambit2.reactions.GenericReaction
 
getConditions() - Method in class ambit2.rules.conditions.ConditionExpression
 
getConditionsConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getConditionScores() - Method in class ambit2.reactions.GenericReaction
 
getConditionsScore() - Method in class ambit2.reactions.GenericReactionInstance
 
getConditionType() - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
getConditionValue(String) - Method in class ambit2.core.io.StringArrayHeader
 
getConfig(OpenSSOServicesConfig.CONFIG) - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getConfig() - Method in class ambit2.vega.VegaShell
 
getConfigChangeLineSeparator() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getConfigStatus() - Method in class ambit2.reactions.GenericReaction
 
getConfiguration() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
getConnectedAtomsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedAtomsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedBondsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedBondsCount(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedBondsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedElectronContainersList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedLonePairsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedLonePairsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedSingleElectronsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnectedSingleElectronsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getConnection() - Method in class ambit2.db.processors.DBProcessorsChain
 
getConnection() - Method in class ambit2.db.results.StoredQueryTableModel
 
getConnection(String, String) - Method in class ambit2.rest.DBConnection
 
getConnection() - Method in class ambit2.rest.DBConnection
 
getConnection(int, boolean, int) - Method in class ambit2.rest.DBConnection
 
getConnection(String) - Method in class ambit2.rest.DBConnection
 
getConnectionNamedConfig(String, String, int, boolean, int) - Method in class ambit2.rest.DBConnection
 
getConnections(List<ComponentConnection>, double, ComponentUtils.Comparison) - Static method in class ambit2.structure2name.components.ComponentUtils
 
getConnectionURI() - Method in class ambit2.rest.DBConnection
 
getConnectionURI(String, String) - Method in class ambit2.rest.DBConnection
 
getContainer() - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
getContainer() - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
getContent() - Method in class ambit2.base.data.StructureRecord
 
getContent() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getContent() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getContent() - Method in class ambit2.core.data.model.Algorithm
 
getContent() - Method in interface ambit2.core.data.model.IEvaluation
 
getContent() - Method in class ambit2.core.data.model.ModelWrapper
 
getContent() - Method in interface ambit2.db.search.IStoredQuery
 
getContent() - Method in class ambit2.db.search.StoredQuery
 
getContent() - Method in class ambit2.model.evaluation.EvaluationStats
 
getContent(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
getContent(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
getContentColumn() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getContentMediaType() - Method in class ambit2.core.data.model.ModelWrapper
 
getContext() - Method in class ambit2.rest.DBConnection
 
getContribution() - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
getContribution() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
getContribution() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
getContribution() - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
getContribution() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getContribution() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getContribution() - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
getConversionErrors() - Method in class ambit2.sln.io.SLN2ChemObject
 
getConversionErrors() - Method in class ambit2.sln.io.SLN2SMARTS
 
getConversionErrors() - Method in class ambit2.sln.io.SLN2Substance
 
getConversionWarnings() - Method in class ambit2.sln.io.SLN2ChemObject
 
getConversionWarnings() - Method in class ambit2.sln.io.SLN2SMARTS
 
getConversionWarnings() - Method in class ambit2.sln.io.SLN2Substance
 
getCookies() - Method in class ambit2.rest.task.CallableQueryProcessor
 
getCorrectionFactorFromString(String) - Method in class ambit2.groupcontribution.GCMParser
 
getCorrectionFactors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCorrectionFactorsAsString() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCorrectionFactorsAsString(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCorrectionFactorsCount(IAtomContainer, GroupContributionModel) - Static method in class ambit2.groupcontribution.Calculator
 
getCorrectionFactorsFromString(String, char) - Method in class ambit2.groupcontribution.GCMParser
 
getCorrectionFactorsParametersAsJsonArray(ICorrectionFactor) - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCount() - Method in class ambit2.base.data.PropertyStats
 
getCount() - Method in class ambit2.base.facet.AbstractFacet
 
getCountFingerprint(IAtomContainer) - Method in class ambit2.core.data.HashIntDescriptorResult
 
getCountFingerprint(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getCountFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
getCountry() - Method in class ambit2.base.data.AmbitUser
 
getCoverageValues(Matrix) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
getCoverageValues calculates Highest Density Region of a set of points
getCreated() - Method in class ambit2.base.data.Bookmark
 
getCreated() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getCreated() - Method in class ambit2.db.version.AmbitDBVersion
 
getCreator() - Method in class ambit2.base.data.Bookmark
 
getCreator() - Method in class ambit2.core.data.model.ModelWrapper
 
getCreator() - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacet
 
getCreator() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getCreator(RDFNode) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
getCredentials() - Method in class ambit2.rest.wrapper.WrappedService
 
getCurrentRecord() - Method in interface ambit2.base.interfaces.IInputOutputState
 
getCurrentRecord() - Method in class ambit2.core.io.FileState
 
getCurrentRecord() - Method in class ambit2.core.processors.batch.DefaultIOState
 
getCurrentSide() - Method in class ambit2.db.processors.ProcessorOntology
 
getCurrentState() - Method in class ambit2.tautomers.CombinedRuleInstance
 
getCurrentState() - Method in interface ambit2.tautomers.IRuleInstance
 
getCurrentState() - Method in class ambit2.tautomers.RuleInstance
 
getCursorName() - Method in class ambit2.db.results.AmbitRows
 
getCustomDescription() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCustomExcludeRegionSmarts() - Method in class ambit2.tautomers.rules.TautomerRegion
 
getCustomGroupLocalDescriptors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCustomGroups() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getCustomLicense() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCustomLogo() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCustomQuery() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCustomStructureQuery() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCustomTitle() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getCyclicComponentForAtom(IAtom) - Method in class ambit2.structure2name.IUPACNameGenerator
 
getCyclicComponentFusedToRing(IAtomContainer) - Method in class ambit2.structure2name.IUPACNameGenerator
 
getD() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getDatabase() - Method in class ambit2.db.LoginInfo
 
getDatabase() - Method in class ambit2.dbui.LoginInfoBean
 
getDataEntryID() - Method in class ambit2.base.data.StructureRecord
 
getDataEntryID() - Method in interface ambit2.base.interfaces.IStructureRecord
Data entry (tuples) in a dataset, i.e.
getDataEntryID() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getDataFileFormat() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
getDataModel() - Method in class ambit2.ui.table.BrowsableTableModel
 
getDataModelColumn(int, int) - Method in class ambit2.ui.table.BrowsableTableModel
 
getDataset() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
getDataset() - Method in class ambit2.db.processors.AbstractPropertyWriter
 
getDataset() - Method in class ambit2.db.processors.DbStructureWriter
 
getDataset() - Method in class ambit2.db.processors.PropertyImporter
 
getDataset() - Method in class ambit2.db.processors.RepositoryWriter
 
getDataset() - Method in class ambit2.db.processors.ValueWriterNew
 
getDataset() - Method in class ambit2.db.search.QueryInfo
 
getDataset() - Method in class ambit2.db.search.structure.QueryDataset
 
getDataset() - Method in class ambit2.db.simiparity.space.QMap
 
getDataset() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
getDataset_service() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
getDatasetCenterPoint() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
getDatasetID() - Method in class ambit2.base.data.StructureRecord
 
getDatasetID() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getDatasetID() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getDatasetIndividual() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getDatasetReportRef() - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
getDatasets() - Static method in class ambit2.db.search.QueryInfo
 
getDatasets() - Method in interface ambit2.similarity.stats.IModelHistogram
 
getDatasets() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
getDatasetService(Form) - Method in class ambit2.rest.task.CallablePOST
 
getDatasetService() - Method in class ambit2.rest.task.LauncherResource
 
getDatasetURI(Form) - Method in class ambit2.rest.task.CallablePOST
 
getDataSourceName() - Method in class ambit2.db.results.AmbitRows
 
getDataStringBuffer() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
getDate() - Method in class ambit2.base.data.Bookmark
 
getDate(int) - Method in class ambit2.db.results.AmbitRows
 
getDate(String) - Method in class ambit2.db.results.AmbitRows
 
getDate(int, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getDate(String, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getDbname() - Method in class ambit2.db.version.AmbitDBVersion
 
getDBNameAmbit() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getDBNameUsers() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getDbVersion(Connection, String) - Static method in class ambit2.db.processors.DbCreateDatabase
 
getDeafultExternalDataFileHeader() - Static method in class ambit2.export.isa.base.ExternalDataFileHeader
 
getDecriptor(int, List<DescriptorValue>) - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
getDefault() - Static method in class ambit2.base.config.Preferences
 
getDefault() - Static method in class ambit2.ui.EditorPreferences
 
getDefaultConfig() - Static method in class ambit2.export.isa.json.ISAJsonExportConfig
 
getDefaultGenericReacitonTextFileColumnsIndices() - Static method in class ambit2.reactions.ReactionDataBase
 
getDefaultImage() - Method in interface ambit2.core.io.ICompoundImageTools
 
getDefaultImage() - Method in class ambit2.rendering.CompoundImageTools
 
getDefaultReactionScoreSchema() - Static method in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
getDefaultRole() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getDefaultRuleDataBase() - Static method in class ambit2.structure2name.rules.IUPACRuleDataBase
 
getDefaultSchema() - Static method in class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
getDefaultSecondOrderLocalDescriptors() - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
getDefaultSelectorAll() - Static method in class ambit2.tautomers.RuleSelector
 
getDefaultSelectorRandom() - Static method in class ambit2.tautomers.RuleSelector
 
getDefaultSMIRKSManager() - Static method in class ambit2.smarts.SMIRKSManager
 
getDefaultStrategy() - Static method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
getDefaultSyntheticStrategy() - Static method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
getDefaultValue() - Method in enum ambit2.dragon.DragonShell._options
 
getDefaultValue() - Method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
 
getDegreeMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getDelimiter() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
getDelimiter() - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
getDelimiter() - Method in class ambit2.ui.DelimitersPanel
 
getDensityValues(Matrix) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
points for which density values are to be calculated points for which density values are to be calculated
getDependent() - Method in class ambit2.core.data.model.ModelWrapper
 
getDependentVariables() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getDescrInstanceIndex(String) - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
getDescription() - Method in class ambit2.base.data.Bookmark
 
getDescription() - Method in class ambit2.base.data.ClassHolder
 
getDescription() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getDescription() - Method in class ambit2.base.io.AmbitFileFilter
 
getDescription() - Method in class ambit2.base.io.MolFileFilter
 
getDescription() - Method in enum ambit2.base.processors.search.AbstractFinder.MODE
 
getDescription() - Method in class ambit2.core.data.model.Algorithm
 
getDescription() - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
getDescription() - Method in enum ambit2.core.processors.structure.key.IStructureKey.Matcher
 
getDescription() - Method in enum ambit2.rendering.CompoundImageTools.Mode2D
 
getDescription() - Method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
 
getDescription() - Method in enum ambit2.rest.OpenTox.params
 
getDescriptor() - Method in class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
getDescriptor() - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
getDescriptorDesignation(ILocalDescriptor, int) - Static method in class ambit2.groupcontribution.GroupContributionModel
 
getDescriptorEngine() - Method in class ambit2.descriptors.processors.DescriptorEngineProcessor
 
getDescriptorFromDescrValue(DescriptorValue, int) - Static method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
getDescriptorList() - Method in class ambit2.rules.conditions.AbstractDescriptorSolver
 
getDescriptorList() - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
getDescriptorList() - Method in interface ambit2.rules.conditions.IDescriptorSolver
 
getDescriptorName() - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
getDescriptorName() - Method in interface ambit2.rules.conditions.IDescriptorValueCondition
 
getDescriptorNames() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getDescriptorNames() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getDescriptorNames() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.constitutional.DerivedMolecularWeightDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.CrossSectionalDiameterDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getDescriptorNames() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.InChI
 
getDescriptorNames() - Method in class ambit2.descriptors.MaximumDiameterDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.MolecularWeight
 
getDescriptorNames() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.PlanarityDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.SizeDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.SpherosityDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getDescriptorNames() - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getDescriptorNames() - Method in class ambit2.dragon.DescriptorDragonShell
 
getDescriptorNames() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
getDescriptorNames() - Method in class ambit2.dragon.DragonShell
 
getDescriptorNames() - Method in class ambit2.mopac.DescriptorMopacShell
 
getDescriptorNames() - Method in class ambit2.some.DescriptorSOMEShell
 
getDescriptorNamesAsString() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
getDescriptorNamesAsString() - Method in class ambit2.dragon.DragonShell
 
getDescriptorResultType() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getDescriptorResultType() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.constitutional.AtomCountHybridizationDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
Returning results of different size is not very convenient
getDescriptorResultType() - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getDescriptorResultType() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.InChI
 
getDescriptorResultType() - Method in class ambit2.descriptors.MolecularWeight
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.SizeDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.SpherosityDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getDescriptorResultType() - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getDescriptorResultType() - Method in class ambit2.dragon.DescriptorDragonShell
 
getDescriptorResultType() - Method in class ambit2.mopac.DescriptorMopacShell
 
getDescriptorResultType() - Method in class ambit2.some.DescriptorSOMEShell
 
getDescriptors() - Method in class ambit2.db.processors.AbstractDescriptorCalculator
 
getDescriptors() - Method in class ambit2.dragon.DragonShell
 
getDescriptors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getDescriptorsAsString(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
getDescriptorSolver() - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
getDescriptorSolver() - Method in interface ambit2.rules.conditions.IDescriptorValueCondition
 
getDescriptorSolver() - Method in interface ambit2.rules.conditions.INeedsDescriptorSolver
 
getDescriptorsRankThreshold() - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
getDescriptorValueCondition(JsonNode) - Static method in class ambit2.rules.conditions.parser.ConditionJsonParser
 
getDescriptorValueConditionFromToken(String) - Static method in class ambit2.rules.conditions.parser.ConditionParsingUtils
Parses token in the format:
getDescriptoSolver() - Method in class ambit2.reactions.reactor.Reactor
 
getDesignation() - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
getDesignation() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
getDesignation() - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
getDesignation() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getDesignation(int) - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
getDesignation(int) - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
getDesignation() - Method in class ambit2.groupcontribution.groups.AtomGroup
 
getDesignation() - Method in class ambit2.groupcontribution.groups.BondGroup
 
getDesignation() - Method in class ambit2.groupcontribution.groups.DGroup
 
getDesignation() - Method in class ambit2.groupcontribution.groups.GGroup
 
getDesignation() - Method in class ambit2.groupcontribution.groups.GroupInfo
 
getDesignation() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getDetails() - Method in exception ambit2.rest.exception.ImportSubstanceException
 
getDetailsCaption() - Method in class ambit2.ui.editors.BeanEditor
 
getDictionary() - Method in class ambit2.core.io.ToXMLReaderSimple
 
getDictionary() - Static method in class ambit2.sln.dictionary.PredefinedSLNDictionary
 
getDictionaryObject(String) - Method in class ambit2.sln.dictionary.SLNDictionary
 
getDistance() - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
getDistance() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
getDistance(AtomEnvironmentList, AtomEnvironmentList) - Method in class ambit2.similarity.measure.AtomEnvironmentsDistance
Calls AtomEnvironmentList.hellinger(AtomEnvironmentList) and divides on 2 to get it in (0,1) range.
getDistance(BitSet, BitSet) - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
getDistance() - Method in class ambit2.similarity.measure.DistanceComparable
 
getDistance(double[], double[]) - Method in class ambit2.similarity.measure.EuclideanDistance
 
getDistance(BitSet, BitSet) - Method in class ambit2.similarity.measure.FingerprintDistance
 
getDistance(int[], int[]) - Method in class ambit2.similarity.measure.HammingDistance
 
getDistance(T, T) - Method in interface ambit2.similarity.measure.IDistanceFunction
Distance should be large if objects are "far away" from each other, i.e.
getDistance(String, String) - Method in class ambit2.similarity.measure.LevensteinDistance
 
getDistance(IAtomContainer, IAtomContainer) - Method in class ambit2.similarity.measure.MCSSDistance
 
getDistanceFunction() - Method in interface ambit2.similarity.knn.INearestNeighborsSearch
 
getDistanceFunction() - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
getDistanceFunction() - Method in interface ambit2.similarity.stats.INearestNeighborsSearch
 
getDocument(String) - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
getDocument(File) - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
getDocument(InputStream) - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
getDocument() - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
getDocument(InputSource) - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
getDocumentType() - Method in class ambit2.db.substance.CreateSubstance
 
getDocumentUUID() - Method in class ambit2.base.data.study.ProtocolApplication
in ProtocolApplication JSON:
getDocumentUUID() - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
getDomain() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
 
getDomain(double) - Method in class ambit2.model.numeric.DataCoverage
 
getDomain(double[]) - Method in class ambit2.model.numeric.DataCoverage
 
getDomain(double) - Method in class ambit2.model.numeric.DataCoverageDensity
 
getDomain(double[]) - Method in class ambit2.model.numeric.DataCoverageDensity
 
getDomain(double) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
getDomain(double[]) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
getDomain(double) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
getDomain(double[]) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
getDomain(double) - Method in interface ambit2.model.numeric.IDataCoverage
 
getDomain(double[]) - Method in interface ambit2.model.numeric.IDataCoverage
 
getDomain(double) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
getDomain(double[]) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
getDomain(double) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
getDomain(double[]) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
getDomainName() - Method in class ambit2.model.numeric.DataCoverage
 
getDomainName() - Method in interface ambit2.model.numeric.IDataCoverage
 
getDomainName() - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
getDomainName() - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
getDomainTitle(ISourceDataset) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
getDotPath() - Method in class ambit2.core.io.ToXMLReaderSimple
 
getDouble(int) - Method in class ambit2.db.results.AmbitRows
 
getDouble(String) - Method in class ambit2.db.results.AmbitRows
 
getDouble(String) - Static method in class ambit2.reactions.GenericReaction
 
getDXReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getDXReference(String) - Static method in class ambit2.base.data.LiteratureEntry
 
getEditingColumn() - Method in class ambit2.ui.EditableHeader
 
getEditor(Class) - Static method in class ambit2.ui.EditorPreferences
 
getEditor(Object) - Static method in class ambit2.ui.EditorPreferences
 
getEditor(String) - Static method in class ambit2.ui.EditorPreferences
 
getEditor() - Method in class ambit2.ui.editors.ListEditor
 
getEditor(Object) - Method in class ambit2.ui.editors.ListEditor
 
getEditorComponent() - Method in class ambit2.ui.EditableHeader
 
getEffects() - Method in class ambit2.base.data.study.ProtocolApplication
"effects": []
getEffectsConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getEINECS() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getEinecs(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getEINECSInstance() - Static method in class ambit2.base.data.Property
 
getEINECSReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getElectronContainer(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getElectronContainerCount() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getElement(String) - Method in class ambit2.descriptors.IsotopeFactory
Returns an Element with a given element symbol.
getElement(int) - Method in class ambit2.descriptors.IsotopeFactory
Returns an element according to a given atomic number.
getElementAt(int) - Method in class ambit2.base.data.ProfileListModel
 
getElementAt(int) - Method in interface ambit2.base.data.TypedListModel
 
getElementAt(int) - Method in class ambit2.db.results.MemoryRowsModel
 
getElementAt(int) - Method in class ambit2.db.results.RowsModel
 
getElementAt(int) - Method in class ambit2.ui.HeaderComboBoxModel
 
getElementNumber(String) - Static method in class ambit2.smarts.SmartsConst
 
getElementNumberFromChar(char) - Static method in class ambit2.smarts.SmartsConst
 
getElementSymbol(int) - Method in class ambit2.descriptors.IsotopeFactory
Returns the symbol matching the element with the given atomic number.
getEmail() - Method in class ambit2.base.data.AmbitUser
 
getEnableEmailVerificationOption() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getEndChainID() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getEndInsertionCode() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getEndpoint() - Method in class ambit2.base.data.study.EffectRecord
 
getEndpoint() - Method in class ambit2.base.data.study.Protocol
 
getEndpoint() - Method in class ambit2.core.data.model.Algorithm
 
getEndpoint() - Method in class ambit2.core.data.model.ModelQueryResults
 
getEndpoint() - Method in class ambit2.db.substance.QueryCountEndpoints
 
getEndpoint() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getEndpointBundle() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getEndpointcategory() - Method in class ambit2.base.data.substance.SubstanceProperty
 
getEndpointConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getEndpointGroup() - Method in class ambit2.base.data.study.EffectRecord
 
getEndpointName() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getEndpointSynonyms() - Method in class ambit2.base.data.study.EffectRecord
 
getEndpointType() - Method in class ambit2.base.data.study.EffectRecord
 
getEndpointURI() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getEndSequenceNumber() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getEnergyRank(IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
getEnergyRanking() - Method in class ambit2.tautomers.TautomerManager
 
getError() - Method in class ambit2.core.json.JSONParserUtils
 
getError() - Method in class ambit2.db.readers.PropertyValue
 
getError() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getError() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
getError() - Method in class ambit2.rest.task.Task
 
getError() - Method in class ambit2.sln.SLNParserError
 
getError() - Method in class ambit2.smarts.groups.GroupMatch
 
getError() - Method in class ambit2.smarts.SmartsParserError
 
getError() - Method in class ambit2.tautomers.rules.JsonRuleParser
 
getErrorMessages() - Method in class ambit2.sln.SLNParser
 
getErrorMessages() - Method in class ambit2.smarts.SmartsParser
 
getErrors() - Method in class ambit2.groupcontribution.GCMParser
 
getErrors() - Method in class ambit2.groupcontribution.Learner
 
getErrors() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getErrors() - Method in class ambit2.reactions.rules.GenericParserUtils
 
getErrors() - Method in class ambit2.reactions.rules.ReactionParser
 
getErrors() - Method in class ambit2.sln.SLNParser
 
getErrors() - Method in class ambit2.smarts.SmartsManager
 
getErrors() - Method in class ambit2.smarts.SmartsParser
 
getErrors() - Method in class ambit2.smarts.smirks.ReactionSearch
 
getErrors() - Method in class ambit2.smarts.SMIRKSManager
 
getErrors() - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
getErrors() - Method in class ambit2.tautomers.rules.JsonRuleParser
 
getErrorsAsString() - Method in class ambit2.reactions.ReactionDataBase
 
getErrorValue() - Method in class ambit2.base.data.study.EffectRecord
 
getErrQualifier() - Method in class ambit2.base.data.study.EffectRecord
 
getEscapeProcessing() - Method in class ambit2.db.results.AmbitRows
 
getEstimatedAtomCount(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getEvaluation() - Method in class ambit2.core.data.model.ModelWrapper
 
getExample() - Method in class ambit2.descriptors.FunctionalGroup
 
getExample() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getExcludeAtomIndices() - Method in class ambit2.tautomers.rules.TautomerRegion
 
getExcludeFilters(IAtomContainer) - Method in class ambit2.tautomers.FilterTautomers
 
getExe() - Method in class ambit2.base.external.Command
 
getExecutable(String, String) - Method in class ambit2.base.external.CommandShell
 
getExecutable() - Method in class ambit2.base.external.CommandShell
invokes CommandShell.getExecutable(String, String) with System.getProperty("os.name") as argument
getExitCode() - Method in class ambit2.base.external.CommandShell
 
getExperiment(CATEGORIES, SubstanceRecord, Protocol, ReliabilityParams) - Method in class ambit2.core.io.StringArrayHeader
 
getExperimentalConditionsInfo() - Method in class ambit2.reactions.GenericReaction
 
getExperimentalConditionsScore() - Method in class ambit2.reactions.GenericReaction
 
getExplanation() - Method in class ambit2.descriptors.VerboseDescriptorResult
 
getExplicitHAtomData(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
getExplicitHCount(IAtom, IAtomContainer) - Static method in class ambit2.groupcontribution.utils.MoleculeUtils
 
getExportJsonConfig() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getExportJsonConfig() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getExpressionAtomChirality(SmartsAtomExpression, SmartsAtomExpression) - Static method in class ambit2.smarts.StereoFromSmartsAtomExpression
 
getExpressionAtomType(SmartsAtomExpression, SmartsAtomExpression) - Method in class ambit2.smarts.SmartsToChemObject
 
getExpressionBondType(SmartsBondExpression, SmartsBondExpression) - Method in class ambit2.smarts.SmartsToChemObject
 
getExtension() - Method in class ambit2.base.io.MolFileFilter
 
getExtension() - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
getExtension() - Method in enum ambit2.export.isa.base.ISAConst.ISAFormat
 
getExtensionDescriptions(boolean) - Static method in class ambit2.core.io.FileState
 
getExtensions(boolean) - Static method in class ambit2.core.io.FileState
 
getExternalDataFile() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getExternalDataSet() - Method in class ambit2.groupcontribution.Learner
 
getExternalids() - Method in class ambit2.base.data.SubstanceRecord
 
getExternId() - Method in class ambit2.reactions.GenericReaction
 
getF(MatrixDouble, MatrixDouble, int) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getFacets() - Method in class ambit2.base.data.StructureRecord
 
getFacets() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getFacets() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getFacets() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getFactorValue(String, Object) - Static method in class ambit2.export.isa.v1_0.ISAJsonUtils1_0
 
getFactory() - Method in class ambit2.core.data.HashIntDescriptorResult
CDK 1.5.15
getFactory() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getFamily() - Method in class ambit2.descriptors.FunctionalGroup
 
getFastTautomerCountEstimation(TautomerManager, IAtomContainer) - Static method in class ambit2.tautomers.TautomerUtils
 
getFeatures() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
getFeatures() - Method in interface ambit2.model.IDataset
 
getFeatures(OTFeatures) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
 
getFeatures(OTFeatures) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
getFetchDirection() - Method in class ambit2.db.results.AmbitRows
 
getFetchSize() - Method in class ambit2.db.results.AmbitRows
 
getField(IStructureRecord, Property) - Method in class ambit2.db.results.StoredQueryTableModel
 
getField() - Method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
 
getFieldDelimiter() - Method in class ambit2.core.io.DelimitedFileFormat
 
getFieldFormat() - Method in class ambit2.core.groups.DataGroup
 
getFieldID() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getFieldID() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getFieldID() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getFieldID() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getFieldID() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getFieldID() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getFieldname() - Method in class ambit2.db.readers.RetrieveStructure
 
getFieldname() - Method in class ambit2.db.search.AbstractQuery
 
getFieldname() - Method in class ambit2.db.search.DictionaryQuery
 
getFieldname() - Method in class ambit2.db.search.property.TemplateQuery
 
getFieldname() - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
getFieldname() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getFieldname() - Method in class ambit2.db.update.bundle.ReadBundle
User name
getFieldname1() - Method in class ambit2.db.search.QueryInfo
 
getFieldname2() - Method in class ambit2.db.search.QueryInfo
 
getFieldname3() - Method in class ambit2.db.search.QueryInfo
 
getFieldnames() - Static method in class ambit2.db.search.QueryInfo
 
getFieldType() - Method in class ambit2.core.groups.DataGroup
 
getFieldType() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getFieldType() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getFieldType() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getFieldType() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getFieldType() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getFieldType() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getFile() - Method in class ambit2.core.io.FileState
 
getFile(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getFileExtension() - Method in class ambit2.base.processors.batch.BatchReporter
 
getFileExtension() - Method in class ambit2.core.processors.ProcessorFileExport
 
getFileExtension() - Method in class ambit2.db.reporters.ARFF3ColReporter
 
getFileExtension() - Method in class ambit2.db.reporters.ARFFReporter
 
getFileExtension() - Method in class ambit2.db.reporters.CMLReporter
 
getFileExtension() - Method in class ambit2.db.reporters.CSVReporter
 
getFileExtension() - Method in class ambit2.db.reporters.ImageAreaReporter
 
getFileExtension() - Method in class ambit2.db.reporters.PDFReporter
 
getFileExtension() - Method in class ambit2.db.reporters.RTFReporter
 
getFileExtension() - Method in class ambit2.db.reporters.SDFReporter
 
getFileExtension() - Method in class ambit2.db.reporters.SmilesReporter
 
getFileExtension() - Method in enum ambit2.db.reporters.SmilesReporter.Mode
 
getFileExtension() - Method in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
getFileExtension() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getFileExtension(String) - Static method in class ambit2.reactions.io.ReactionWriteUtils
 
getFileExtension() - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
getFileExtension() - Method in class ambit2.rest.QueryStaXReporter
 
getFileExtension() - Method in class ambit2.rest.RemoteStreamConvertor
 
getFileExtension() - Method in class ambit2.rest.reporters.TaskRDFReporter
 
getFileFormat() - Method in class ambit2.core.io.FileState
 
getFileFormat() - Method in interface ambit2.core.io.IInputState
 
getFileFormat() - Method in class ambit2.core.processors.batch.DefaultInputState
 
getFileHeader() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
getFilename() - Static method in class ambit2.base.config.Preferences
 
getFilename() - Method in class ambit2.base.data.study.StructureRecordValidator
 
getFilename() - Method in class ambit2.core.io.FileState
 
getFileNamePrefix() - Method in class ambit2.rest.RemoteStreamConvertor
 
getFilePath(String, String, String, IStructureRecord, String) - Method in class ambit2.db.reporters.AbstractImageReporter
 
getFileRuleName(String) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
getFiles() - Method in class ambit2.core.io.IteratingFolderReader
 
getFileTypeName(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getFilterConfig() - Method in class ambit2.rest.wrapper.WrappedService
 
getFingerprint(IAtomContainer) - Method in class ambit2.core.data.HashIntDescriptorResult
 
getFingerPrint(String, int) - Static method in class ambit2.core.data.MoleculeTools
 
getFingerPrint(String) - Static method in class ambit2.core.data.MoleculeTools
 
getFingerprint(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinter
Calculate 881 bit Pubchem fingerprint for a molecule.
getFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
CDK 1.5.15
getFingerprint(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsFingerprinter
 
getFingerprintAsBytes() - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinter
Returns the fingerprint generated for a molecule as a byte[].
getFingerprintAsBytes() - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
Returns the fingerprint generated for a molecule as a byte[].
getFingerprinter() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getFingerPrintLength() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
getFingerprintsCalculated() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
getFirst(int) - Method in class ambit2.smarts.BinaryCombinations
 
getFirstAtom() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getFirstLevel() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getFirstName() - Method in class ambit2.base.data.AmbitUser
 
getFirstPosAtomMappings(IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
getFirstStructure() - Method in interface ambit2.base.interfaces.IStructureRelation
 
getFirstStructure() - Method in class ambit2.base.relation.AbstractRelation
 
getFirstValue() - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
getFirstValue() - Method in class ambit2.core.filter.RecordIntervalCondition
 
getFirstValue(Form) - Method in enum ambit2.rest.OpenTox.params
 
getFisher() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getFlag(T) - Method in class ambit2.domain.stats.datastructures.Histogram
 
getFlag(T) - Method in class ambit2.similarity.stats.Histogram
 
getFlagAllowBondExpressionInRingClosure() - Method in class ambit2.sln.SLNParser
 
getFlagHAtomsTransformationMode() - Method in class ambit2.smarts.SMIRKSManager
 
getFlagSSMode() - Method in class ambit2.smarts.groups.GroupMatch
 
getFlagSSMode() - Method in class ambit2.smarts.SMIRKSManager
 
getFlagTolerateSpaces() - Method in class ambit2.sln.SLNParser
 
getFloat(int) - Method in class ambit2.db.results.AmbitRows
 
getFloat(String) - Method in class ambit2.db.results.AmbitRows
 
getFolders() - Method in class ambit2.db.reporters.CSVReporter
 
getFormat() - Method in class ambit2.base.data.StructureRecord
 
getFormat() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getFormat() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getFormat() - Method in class ambit2.core.data.model.Algorithm
 
getFormat() - Method in class ambit2.core.io.ArffWriter
 
getFormat() - Method in class ambit2.core.io.DelimitedFileReader
 
getFormat() - Method in class ambit2.core.io.DelimitedFileWriter
 
getFormat() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
getFormat() - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
getFormat() - Method in class ambit2.core.io.I5ReaderSimple
 
getFormat() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
getFormat() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
getFormat() - Method in class ambit2.core.io.IteratingFileReader
 
getFormat() - Method in class ambit2.core.io.IteratingFolderReader
 
getFormat() - Method in class ambit2.core.io.IteratingXLSReader
 
getFormat() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
getFormat() - Method in class ambit2.core.io.MDLReader
 
getFormat() - Method in class ambit2.core.io.pdb.RawIteratingPDBReader
 
getFormat() - Method in class ambit2.core.io.PDFWriter
 
getFormat() - Method in class ambit2.core.io.RawIteratingCSVReader
 
getFormat() - Method in class ambit2.core.io.RawIteratingMOLReader
 
getFormat() - Method in class ambit2.core.io.RawIteratingReader
 
getFormat() - Method in class ambit2.core.io.RawIteratingSDFReader
 
getFormat() - Method in class ambit2.core.io.RawIteratingWrapper
 
getFormat() - Method in class ambit2.core.io.ToXMLReaderSimple
 
getFormat() - Method in class ambit2.core.io.XLSFileWriter
 
getFormat() - Method in class ambit2.mopac.Mopac7Reader
 
getFormat() - Method in class ambit2.mopac.Mopac7Writer
 
getFormat() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getFormat() - Method in class ambit2.some.SOMERawReader
 
getFormat() - Method in class ambit2.ui.DelimitersPanel
 
getFormatName() - Method in class ambit2.core.io.DelimitedFileFormat
 
getFormatName() - Method in class ambit2.core.io.XLSFileFormat
 
getFormula() - Method in class ambit2.base.data.StructureRecord
 
getFormula() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getFormula() - Method in interface ambit2.base.interfaces.IChemical
 
getFormula() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getFormula() - Method in class ambit2.db.search.QueryInfo
 
getFPLength() - Method in class ambit2.core.processors.structure.FingerprintGenerator
 
getFpmode() - Method in class ambit2.descriptors.processors.BitSetGenerator
 
getFptable() - Method in class ambit2.db.update.fp.CreateFingerprintChemical
 
getFptable() - Method in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
getFragmenationRules() - Method in class ambit2.reactions.fragmentation.Fragmentation
 
getFragment() - Method in class ambit2.reactions.retrosynth.NodeComponent
 
getFragmentFromSequence(int) - Method in class ambit2.smarts.ChemObjectFactory
 
getFrequency() - Method in class ambit2.db.update.fp.Fingerprint
 
getFrequency() - Method in interface ambit2.db.update.fp.IFingerprint
 
getFrequency() - Method in class ambit2.descriptors.AtomEnvironment
 
getFrequency(int, int[], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getFrequency(double, double[], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getFrequency(GraphMatrices.DMAtomState, GraphMatrices.DMAtomState[], int) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getFrequency(T) - Method in class ambit2.domain.stats.datastructures.Histogram
 
getFrequency(T) - Method in class ambit2.similarity.stats.Histogram
 
getFrequencySum(boolean, MutableInt) - Method in class ambit2.domain.stats.datastructures.Histogram
 
getFrequencySum(boolean, MutableInt) - Method in class ambit2.similarity.stats.Histogram
 
getFromIndex() - Method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
Get one of the number of the column or row that contains the cell whose top left hand corner will be aligned with the top left hand corner of the image.
getFromString(String) - Static method in enum ambit2.reactions.rules.IRetroSynthRule.Type
 
getFromString(String) - Static method in enum ambit2.reactions.rules.IStrategyRule.Type
 
getFunction() - Method in class ambit2.base.relation.composition.Proportion
 
getFunctionalGroupByAtomSymbol(String) - Method in class ambit2.structure2name.rules.IUPACRuleDataBase
 
getFunctions() - Method in class ambit2.rules.functions.NestedFunctions
 
getFunctionValue(double) - Method in interface ambit2.rules.functions.IFunction
 
getFunctionValue(double) - Method in class ambit2.rules.functions.LinearFunction
 
getFunctionValue(double) - Method in class ambit2.rules.functions.NestedFunctions
 
getFunctionValue(double) - Method in class ambit2.rules.functions.ReciprocalFunction
 
getG2() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getGACode() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
getGeneralizedDistanceMatrix(IAtomContainer, double) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getGenerationInfo(int) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
getGenerator() - Method in enum ambit2.descriptors.processors.FPTable
 
getGenericReactionByID(int) - Method in class ambit2.reactions.ReactionDataBase
 
getGlobalDescriptorsFromString(String) - Method in class ambit2.groupcontribution.GCMParser
 
getGlobalDescriptorsFromString(String, String) - Method in class ambit2.groupcontribution.GCMParser
 
getGlobalDictionary() - Method in class ambit2.sln.SLNContainer
 
getGraphics() - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
Returns the Graphics2D for for this visitor.
getGrid(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getGridPoint(double) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getGroundTruth() - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
getGroup() - Method in class ambit2.reactions.sets.ReactionData
 
getGroupMatch() - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
getGroupProperties() - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
getGroupProperties() - Method in class ambit2.db.reporters.QueryHeaderReporter
 
getGroupProperties() - Method in class ambit2.db.reporters.SDFReporter
 
getGroupProperties() - Method in class ambit2.db.reporters.SmilesReporter
 
getGroupProperties() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getGroups() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getGroupsAsString() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getGroupsCount(IAtomContainer, GroupContributionModel) - Static method in class ambit2.groupcontribution.Calculator
 
getGroupSet() - Method in class ambit2.groupcontribution.groups.AtomGroup
 
getGroupSet() - Method in class ambit2.groupcontribution.groups.BondGroup
 
getGroupSet() - Method in class ambit2.groupcontribution.groups.DGroup
 
getGroupSet() - Method in class ambit2.groupcontribution.groups.GGroup
 
getGroupSet() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getGuardListAllowed() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getGuidance() - Method in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
getGuideline() - Method in class ambit2.base.data.study.Protocol
 
getGuidelineConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getHandler() - Method in class ambit2.rest.wrapper.WrappedService
 
getHashCode() - Method in class ambit2.core.io.FileState
 
getHasTopic() - Method in class ambit2.base.data.Bookmark
 
getHAtoms(SmartsAtomExpression) - Static method in class ambit2.smarts.smirks.HAtomManager
 
getHCount(IAtom, IAtomContainer) - Static method in class ambit2.groupcontribution.utils.MoleculeUtils
 
getHeader() - Method in class ambit2.core.io.FilesWithHeaderWriter
 
getHeader() - Method in class ambit2.core.io.FileWithHeaderWriter
 
getHeader() - Method in class ambit2.core.io.StringArrayHeader
 
getHeader() - Method in class ambit2.db.reporters.QueryHeaderReporter
 
getHeader(Form) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getHeaderActions() - Static method in class ambit2.ui.QueryBrowser
 
getHeaderColumn(int) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getHeaderEditor() - Method in class ambit2.ui.EditableHeaderTableColumn
 
getHeaders() - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
getHeight() - Method in class ambit2.db.chart.ChartGenerator
 
getHeight() - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
getHeight() - Method in class ambit2.search.csls.CSLSImageRequest
 
getHelp() - Method in class ambit2.ui.editors.SelectFieldsPanel
 
getHelp(Class) - Static method in class ambit2.ui.Utils
 
getHigh() - Method in class ambit2.similarity.stats.Bin
 
getHint() - Method in class ambit2.descriptors.FunctionalGroup
 
getHint() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
getHint() - Method in interface ambit2.smarts.query.ISmartsPattern
 
getHiRelation() - Method in interface ambit2.rules.conditions.value.IValueInterval
 
getHiRelation() - Method in class ambit2.rules.conditions.value.ValueInterval
 
getHistogram(Comparable, int) - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
getHistogram(Comparable, int) - Method in interface ambit2.similarity.stats.IModelHistogram
 
getHistogram(Comparable, int) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
getHiValue() - Method in interface ambit2.rules.conditions.value.IValueInterval
 
getHiValue() - Method in class ambit2.rules.conditions.value.ValueInterval
 
getHNeighbours(IAtom, IAtomContainer) - Static method in class ambit2.tautomers.CACTVSRanking
 
getHNMRKnowledgeBase() - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
getHNMRKnowledgeBase(File) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
getHome() - Method in class ambit2.dragon.AbstractDescriptorShell
 
getHome() - Method in class ambit2.dragon.DragonShell
 
getHome() - Method in class ambit2.vega.VegaShell
 
getHomeDir(File) - Method in class ambit2.balloon.ShellBalloon
 
getHomeDir(File) - Method in class ambit2.base.external.CommandShell
 
getHomeDir(File) - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
getHomeDir(File) - Method in class ambit2.dragon.DragonShell
 
getHomeDir(File) - Method in class ambit2.some.SOMEShell
 
getHomeDir(File) - Method in class ambit2.vega.VegaShell
 
getHomeFromConfig(String, String) - Method in class ambit2.base.external.CommandShell
 
getHost() - Method in class ambit2.pubchem.NCISearchProcessor
 
getHost(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getHostname() - Method in class ambit2.db.LoginInfo
 
getHostname() - Method in class ambit2.dbui.LoginInfoBean
 
getHPDCounters() - Method in interface ambit2.domain.stats.transforms.densityestimation.HighestDensityRegions
 
getHPDCounters() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
getHPDCounters() HighestDensityRegions interface
getHPDLevelsError(int) - Method in interface ambit2.domain.stats.transforms.densityestimation.HighestDensityRegions
 
getHPDLevelsError(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
getHPDLevelsError() HighestDensityRegions interface
getHShifts() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getHTMLByTemplate(Variant) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
getHTMLByTemplate(Status, String, String, String, Request) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
getHttpMethod() - Method in class ambit2.pubchem.HTTPRequest
 
getI5DReader(InputStream) - Static method in class ambit2.core.io.FileInputState
 
getI5DReader(File) - Static method in class ambit2.core.io.FileInputState
 
getI5UUIDInstance() - Static method in class ambit2.base.data.Property
 
getI5UUIDReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getI5ZReader(File) - Static method in class ambit2.core.io.FileInputState
 
getIcon() - Method in class ambit2.base.data.ClassHolder
 
getIcon(boolean) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getID() - Method in class ambit2.base.data.AbstractDataset
 
getId() - Method in class ambit2.base.data.Bookmark
 
getId() - Method in class ambit2.base.data.Dictionary
 
getId() - Method in interface ambit2.base.data.ILiteratureEntry
 
getID() - Method in interface ambit2.base.data.ISourceDataset
 
getId() - Method in class ambit2.base.data.LiteratureEntry
 
getId() - Method in class ambit2.base.data.Property
 
getId() - Method in class ambit2.base.data.SourceDataset
 
getID() - Method in class ambit2.base.data.SourceDataset
 
getId() - Method in class ambit2.base.data.study.ReliabilityParams
 
getID() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getId() - Method in class ambit2.base.data.Template
 
getID() - Method in class ambit2.base.external.CommandShell
 
getId() - Method in class ambit2.core.data.model.Algorithm
 
getId() - Method in class ambit2.core.data.model.ModelWrapper
 
getID() - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
getID() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
getID(T) - Method in class ambit2.db.chart.BarChartGenerator
 
getID(ISourceDataset) - Method in class ambit2.db.chart.BarChartGeneratorDataset
 
getID(SourceDataset) - Method in class ambit2.db.chart.FingerprintHistogramDataset
 
getID(ISourceDataset) - Method in class ambit2.db.chart.PieChartGenerator
 
getId() - Method in class ambit2.db.readers.PropertyValue
 
getId() - Method in class ambit2.db.search.AbstractQuery
 
getId() - Method in class ambit2.db.search.property.FilteredCount
 
getId() - Method in class ambit2.db.search.QueryCombined
 
getId() - Method in class ambit2.db.search.StoredQuery
 
getID() - Method in class ambit2.db.search.StoredQuery
 
getId() - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
getId() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getId() - Method in class ambit2.db.SessionID
 
getId() - Method in class ambit2.db.simiparity.space.QMap
 
getId() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getID() - Method in class ambit2.descriptors.FunctionalGroup
 
getId() - Method in class ambit2.descriptors.PKANode
 
getID() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getID() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
getID() - Method in interface ambit2.model.IDataset
 
getId() - Method in enum ambit2.model.numeric.ADomainMethodType
 
getId() - Method in class ambit2.model.numeric.DataCoverage
 
getId() - Method in class ambit2.reactions.GenericReaction
 
getId() - Method in class ambit2.reactions.Reaction
 
getID() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
getID() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getID() - Method in class ambit2.rest.model.predictor.ExternalModel
 
getId(String, Reference) - Method in enum ambit2.rest.OpenTox.URI
 
getId(String, Template) - Method in enum ambit2.rest.OpenTox.URI
 
getId() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getID() - Method in class ambit2.some.SOMEVisualizer
 
getIdchemical() - Method in class ambit2.base.data.StructureRecord
 
getIdchemical() - Method in interface ambit2.base.interfaces.IChemical
 
getIdchemical() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getIDColumn() - Method in class ambit2.ui.table.BrowsableTableModel
 
getIDColumn() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getIdentifier() - Method in enum ambit2.base.data.study.ReliabilityParams._r_flags
 
getIdentifier() - Method in class ambit2.base.data.substance.SubstanceProperty
 
getIdentifier1() - Method in class ambit2.db.search.QueryInfo
 
getIdentifier2() - Method in class ambit2.db.search.QueryInfo
 
getIdentifier3() - Method in class ambit2.db.search.QueryInfo
 
getIdentifiers() - Method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
getIdInstance(Object, URI) - Static method in class ambit2.export.isa.v1_0.ObjectUtils
 
getIdproperty() - Method in class ambit2.base.data.PropertyAnnotation
 
getIdresult() - Method in class ambit2.base.data.study.EffectRecord
 
getIdresult() - Method in class ambit2.base.data.study.ValueAnnotated
 
getIds(String, Reference) - Method in enum ambit2.rest.OpenTox.URI
 
getIds(String, Template) - Method in enum ambit2.rest.OpenTox.URI
 
getIdstructure() - Method in class ambit2.base.data.StructureRecord
 
getIdstructure() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getIdstructure() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getIdsubstance() - Method in class ambit2.base.data.SubstanceRecord
 
getImage() - Method in class ambit2.base.data.ClassHolder
 
getImage(IAtomContainer, String, int, int, boolean) - Method in interface ambit2.core.data.IStructureDiagramDepiction
 
getImage(IAtomContainer) - Method in interface ambit2.core.data.IStructureDiagramDepiction
 
getImage() - Method in enum ambit2.core.data.model.Algorithm.AlgorithmFormat
 
getImage(Object) - Method in interface ambit2.core.io.ICompoundImageTools
 
getImage(IAtomContainer) - Method in interface ambit2.core.io.ICompoundImageTools
 
getImage() - Method in class ambit2.core.smiles.OpenBabelDepiction
 
getImage(IAtomContainer) - Method in class ambit2.db.processors.DescriptorsCalculator
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.db.processors.DescriptorsCalculator
 
getImage(Connection, StructureRecord) - Method in class ambit2.db.readers.DbCompoundImageTools
 
getImage(IAtomContainer) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
getImage() - Method in class ambit2.rendering.CachedImage
 
getImage(Object) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(String) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer, IAtomContainerHighlights, boolean, boolean) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer, IAtomContainerHighlights, boolean, boolean, boolean) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer, IAtomContainerHighlights, boolean, boolean, boolean, CompoundImageTools.Mode2D) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(ArrayList<?>) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.rendering.CompoundImageTools
 
getImage(IAtomContainer) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getImage(IAtomContainer) - Method in class ambit2.some.DescriptorSOMEShell
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.some.DescriptorSOMEShell
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class ambit2.some.SOMEVisualizer
 
getImage(IAtomContainer) - Method in class ambit2.some.SOMEVisualizer
 
getImageMap() - Method in class ambit2.rendering.CachedImage
 
getImageMap() - Method in class ambit2.rendering.CompoundImageTools
 
getImageRenderer(IBrowserMode.BrowserMode) - Method in class ambit2.ui.QueryBrowser
 
getImageSize() - Method in interface ambit2.core.data.IStructureDiagramDepiction
 
getImageSize() - Method in interface ambit2.core.io.ICompoundImageTools
 
getImageSize() - Method in class ambit2.db.processors.DescriptorsCalculator
 
getImageSize() - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
getImageSize() - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
getImageSize() - Method in class ambit2.rendering.CompoundImageTools
 
getImageSize() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getImageSize() - Method in class ambit2.some.DescriptorSOMEShell
 
getImageSize() - Method in class ambit2.some.SOMEVisualizer
 
getImplementationDetails() - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
getImplementationDetails() - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getImplementationOf() - Method in class ambit2.core.data.model.Algorithm
 
getImportedRecord() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
getInchi() - Method in class ambit2.base.data.StructureRecord
 
getInchi() - Method in interface ambit2.base.interfaces.IChemical
 
getInchi() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getInchi() - Method in class ambit2.db.search.QueryInfo
 
getInChIInstance() - Static method in class ambit2.base.data.Property
 
getInchiKey() - Method in class ambit2.base.data.StructureRecord
 
getInchiKey() - Method in interface ambit2.base.interfaces.IChemical
 
getInchiKey() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getInchiKey(IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getInChIKeyInstance() - Static method in class ambit2.base.data.Property
 
getInchiOptions() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getInchiOptions() - Method in class ambit2.tautomers.FilterTautomers
 
getInChIStdInstance() - Static method in class ambit2.base.data.Property
 
getIndependentVariables() - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Independent variables
getIndependentVariables() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getIndex() - Method in enum ambit2.db.readers.AbstractStructureRetrieval._sqlids
 
getIndex() - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
getIndex() - Method in enum ambit2.db.substance.AbstractReadSubstance._sqlids
 
getIndex() - Method in enum ambit2.db.update.dataset.AbstractReadDataset._fields
 
getIndex() - Method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
 
getIndex() - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
Index of the array, if the Descrptor value is of type DoubleArrayResult or IntegerArrayResult
getIndexAt1() - Method in class ambit2.smarts.ClosureBond
 
getIndexAt2(boolean) - Method in class ambit2.smarts.ClosureBond
 
getInfo() - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
getInfo() - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
getInfo() - Method in class ambit2.groupcontribution.groups.AtomGroup
 
getInfo() - Method in class ambit2.groupcontribution.groups.BondGroup
 
getInfo() - Method in class ambit2.groupcontribution.groups.DGroup
 
getInfo() - Method in class ambit2.groupcontribution.groups.GGroup
 
getInfo() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getInfo() - Method in class ambit2.reactions.GenericReaction
 
getInfo() - Method in class ambit2.reactions.Reaction
 
getInfo() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
getInfo() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getInfo() - Method in class ambit2.reactions.sets.ReactionData
 
getInfo() - Method in class ambit2.reactions.sets.ReactionGroup
 
getInfo() - Method in class ambit2.reactions.sets.ReactionSet
 
getInfo() - Method in interface ambit2.rules.miscellaneous.IProgress
 
getInitialConnection(IIUPACComponent, IIUPACComponent) - Method in class ambit2.structure2name.IUPACNameGenerator
 
getInitialRuleCount() - Method in class ambit2.tautomers.TautomerManager
 
getInput() - Method in class ambit2.core.data.model.Algorithm
 
getInput() - Method in class ambit2.pubchem.rest.PUGRestRequest
 
getInputFile() - Method in class ambit2.base.external.CommandShell
 
getInputMolecule() - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
getInset() - Method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
Get the images offset from the edge of a cell.
getInstance() - Static method in class ambit2.base.data.LiteratureEntry
 
getInstance(String) - Static method in class ambit2.base.data.LiteratureEntry
 
getInstance(String, String) - Static method in class ambit2.base.data.LiteratureEntry
 
getInstance(String, String, int) - Static method in class ambit2.base.data.LiteratureEntry
 
getInstance(String, String) - Static method in class ambit2.base.data.Property
 
getInstance(String, ILiteratureEntry) - Static method in class ambit2.base.data.Property
 
getInstance(String, String, String) - Static method in class ambit2.base.data.Property
 
getInstance(SmilesParserWrapper.SMILES_PARSER) - Static method in class ambit2.core.smiles.SmilesParserWrapper
 
getInstance() - Static method in class ambit2.core.smiles.SmilesParserWrapper
 
getInstance(IChemObjectBuilder) - Static method in class ambit2.descriptors.IsotopeFactory
Returns an IsotopeFactory instance.
getInstance() - Static method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getInstances() - Method in class ambit2.rest.dataset.RDFInstancesParser
 
getInstances() - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
getInt(int) - Method in class ambit2.db.results.AmbitRows
 
getInt(String) - Method in class ambit2.db.results.AmbitRows
 
getInt(String) - Static method in class ambit2.reactions.GenericReaction
 
getInterpretation(int) - Method in class ambit2.db.update.fp.Fingerprint
 
getInterpretation(int) - Method in interface ambit2.db.update.fp.IFingerprint
 
getInterpretation_result() - Method in class ambit2.base.facet.SubstanceStudyFacet
 
getInterpretation_result() - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
getInterpretation_result() - Method in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
getInterpretationConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getInterpretationCriteria() - Method in class ambit2.base.data.study.ProtocolApplication
 
getInterpretationResult() - Method in class ambit2.base.data.study.ProtocolApplication
"interpretation": {}
getInterpretationResult() - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
getInterpretationResultConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getInterpretationResultCriteria(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getIntValue(Request) - Method in enum ambit2.rest.OpenTox.URI
 
getInverseTransformation() - Method in interface ambit2.groupcontribution.transformations.IValueTransformation
 
getInverseTransformation() - Method in class ambit2.groupcontribution.transformations.TransformationComposition
 
getInverseTransformation() - Method in class ambit2.groupcontribution.transformations.TransformationExp
 
getInverseTransformation() - Method in class ambit2.groupcontribution.transformations.TransformationLin
 
getInverseTransformation() - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
getInverseTransformation() - Method in class ambit2.groupcontribution.transformations.TransformationPow
 
getInvestigationUUID() - Method in class ambit2.base.data.study.ProtocolApplication
 
getIOSettings() - Method in class ambit2.core.io.DelimitedFileReader
 
getIOSettings() - Method in class ambit2.core.io.IteratingFileReader
 
getIOSettings() - Method in class ambit2.core.io.MDLReader
 
getIOSettings() - Method in class ambit2.core.io.RawIteratingWrapper
 
getIOSettings() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getISAFormat() - Method in interface ambit2.export.isa.IISAExport
 
getISAFormat() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getISAFormat() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getISAVersion() - Method in interface ambit2.export.isa.IISAExport
 
getISAVersion() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getISAVersion() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getIsomorphismMapping(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
This function returns null if no isomorphism is found
getIsomorphismMapping(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
This function returns null if no isomorphism is found
getIsomorphismPositions(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
 
getIsomorphismPositions(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
getIsomorphismTester() - Method in class ambit2.smarts.SMIRKSManager
 
getIsomorphismTesterFlagCheckStereoElements() - Method in class ambit2.smarts.SmartsManager
 
getIsoTester() - Method in class ambit2.smarts.groups.GroupMatch
 
getIsotopes(String) - Method in class ambit2.descriptors.IsotopeFactory
Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
getIsRobustStudy() - Method in class ambit2.base.data.study.ReliabilityParams
 
getIsStructureOnly() - Method in class ambit2.sln.SLNContainer
 
getIssue(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getIsUsedforClassification() - Method in class ambit2.base.data.study.ReliabilityParams
 
getIsUsedforMSDS() - Method in class ambit2.base.data.study.ReliabilityParams
 
getItem(int) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
getItemIdentifier(Property) - Method in class ambit2.db.reporters.ARFF3ColReporter
 
getItemReader(int) - Method in class ambit2.core.io.IteratingFolderReader
 
getItemReader(int) - Method in class ambit2.core.io.IteratingMolFolderReader
 
getItemReader(int) - Method in class ambit2.core.io.RawIteratingFolderReader
 
getItems() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
getIterator(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
getIterator(IQueryRetrieval<ResultType>) - Method in class ambit2.db.DbReader
 
getIterator(IInputState) - Method in class ambit2.db.processors.BatchDBProcessor
 
getIterator(List<IStructureRecord>) - Method in class ambit2.db.processors.BatchStructuresListProcessor
 
getIterator() - Method in class ambit2.domain.stats.datastructures.Histogram
 
getIterator(Reference) - Method in class ambit2.rest.RDFBatchParser
 
getIterator() - Method in class ambit2.similarity.stats.Histogram
 
getIUPACReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getJComponent() - Method in interface ambit2.base.interfaces.IAmbitEditor
 
getJComponent() - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
getJComponent() - Method in class ambit2.dbui.dictionary.OntologyEditor
 
getJComponent() - Method in class ambit2.dbui.ProfileEditor
 
getJComponent() - Method in class ambit2.dbui.QueryCombinedEditor
 
getJComponent() - Method in class ambit2.dbui.QueryEditor
 
getJComponent() - Method in class ambit2.dbui.QueryInfoEditor
 
getJComponent() - Method in class ambit2.dbui.QueryScopeEditor
 
getJComponent() - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
getJComponent() - Method in class ambit2.ui.editors.BeanEditor
 
getJComponent() - Method in class ambit2.ui.editors.FileSelector
 
getJComponent() - Method in class ambit2.ui.editors.ListEditor
 
getJComponent() - Method in class ambit2.ui.editors.PreferencesPanel
 
getJComponent() - Method in class ambit2.ui.editors.SelectFieldsPanel
 
getJComponent() - Method in class ambit2.ui.editors.TemplateEditor
 
getJComponent() - Method in class ambit2.ui.jmol.Panel3D
 
getJComponent() - Method in class ambit2.ui.Panel2D
 
getJComponent() - Method in class ambit2.ui.QueryBrowser
 
getJenaModel() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
getJenaModel() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
getJenaModel() - Method in class ambit2.rest.reporters.CatalogRDFReporter
 
getJenaModel() - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getJournal(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getJsonParams() - Method in class ambit2.db.search.SQLFileQueryParams
 
getK() - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
getKDE(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
getKDE
getKernelH() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getKey() - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException
 
getKey() - Method in class ambit2.core.processors.structure.key.EmptyKey
 
getKey() - Method in class ambit2.core.processors.structure.key.InchiKey
 
getKey() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey
 
getKey() - Method in interface ambit2.core.processors.structure.key.IStructureKey
 
getKey() - Method in class ambit2.core.processors.structure.key.NameKey
 
getKey() - Method in class ambit2.core.processors.structure.key.PropertyKey
 
getKey() - Method in class ambit2.core.processors.structure.key.SmilesKey
 
getKey() - Method in class ambit2.db.search.AbstractQuery
 
getKey() - Method in class ambit2.db.search.property.FilteredCount
 
getKey() - Method in class ambit2.db.search.QueryCombined
 
getKey() - Method in class ambit2.db.search.StoredQuery
 
getKey() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
getKey() - Method in class ambit2.db.search.structure.QuerySMARTS
 
getKey() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
getKey() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getKey() - Method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
 
getKey() - Method in enum ambit2.rest.OpenTox.URI
 
getKey(int) - Static method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
getKeyColumns() - Method in class ambit2.db.results.AmbitRows
 
getKeys() - Method in class ambit2.smarts.SmartsScreeningKeys
 
getKNN() - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
getKnowledgeBase() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getKnowledgeBase() - Method in class ambit2.tautomers.TautomerManager
 
getLabel() - Method in class ambit2.base.data.AbstractLabel
 
getLabel() - Method in class ambit2.base.data.Property
 
getLabel(IStructureRecord, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
getLabel(IAtom) - Method in class ambit2.rendering.AtomLabelGenerator
 
getLabelFile(IAtom) - Method in class ambit2.rendering.AtomLabelGenerator
 
getLambda() - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
getLastAtom() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getLastAtomToken() - Method in class ambit2.smarts.SmartsParser
 
getLastModified() - Method in class ambit2.core.io.FileState
 
getLastName() - Method in class ambit2.base.data.AmbitUser
 
getLastToken() - Method in class ambit2.smarts.SmartsAtomExpression
 
getLastValue() - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
getLastValue() - Method in class ambit2.core.filter.RecordIntervalCondition
 
getLeft() - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
getLegend(int, int) - Method in interface ambit2.core.data.IStructureDiagramDepiction
 
getLegend(int, int) - Method in class ambit2.db.processors.DescriptorsCalculator
 
getLegend(int, int) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
getLegend(int, int) - Method in class ambit2.rendering.CompoundImageTools
 
getLegend(int, int) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
getLegend(int, int) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getLegend(int, int) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
Evaluation evaluation = new Evaluation( trainDataset ); evaluation.evaluateModel( classifier, testDataset ); for (int i = 0; i < evaluation.predictions(); i++) { NominalPrediction prediction = (NominalPrediction) evaluation.predictions().elementAt(i); double[] distribution = prediction.distribution(); }
getLegend(int, int) - Method in class ambit2.rest.task.weka.WekaPredictor
Evaluation evaluation = new Evaluation( trainDataset ); evaluation.evaluateModel( classifier, testDataset ); for (int i = 0; i < evaluation.predictions(); i++) { NominalPrediction prediction = (NominalPrediction) evaluation.predictions().elementAt(i); double[] distribution = prediction.distribution(); }
getLegend(int, int) - Method in class ambit2.some.DescriptorSOMEShell
 
getLegend(int, int) - Method in class ambit2.some.SOMEVisualizer
 
getLength() - Method in class ambit2.core.io.FileState
 
getLevel(int) - Method in class ambit2.descriptors.AtomEnvironment
 
getLevel(int) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getLevel2String(int) - Method in class ambit2.descriptors.AtomEnvironment
 
getLevels() - Method in class ambit2.descriptors.AtomEnvironment
 
getLevels() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getLicense() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
getLicenseURI() - Method in class ambit2.base.data.AbstractDataset
 
getLicenseURI() - Method in interface ambit2.base.data.ISourceDataset
 
getLicenseURI() - Method in class ambit2.base.data.SourceDataset
 
getLicenseURI() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getLicenseURI() - Method in class ambit2.base.processors.batch.BatchReporter
 
getLicenseURI() - Method in class ambit2.core.processors.ProcessorFileExport
 
getLicenseURI() - Method in class ambit2.db.search.StoredQuery
 
getLicenseURI() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getLicenseURI() - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
getLicenseURI() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getLimitDiffForSwitchToCombinatorial() - Method in class ambit2.tautomers.RuleSelector
 
getList() - Method in class ambit2.ui.editors.ListEditor
 
getListeners() - Method in class ambit2.core.io.IteratingFileReader
 
getListeners() - Method in class ambit2.core.io.RawIteratingWrapper
 
getListeners() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getLocalDescriptors() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getLocalDescriptorsFromString(String) - Method in class ambit2.groupcontribution.GCMParser
 
getLocalDescriptorsFromString(String, String) - Method in class ambit2.groupcontribution.GCMParser
 
getLocalDictionary() - Method in class ambit2.sln.SLNContainer
 
getLocalPropertyType() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
getLocalSecrets() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getLocationAsIdentifier() - Method in class ambit2.export.isa.base.ExternalDataFileLocation
 
getLogfile() - Method in class ambit2.pubchem.BatchRetrievePubChem
 
getLoggedFromHost() - Method in class ambit2.base.data.AmbitUser
 
getLogger() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
getLoginInfo() - Method in class ambit2.rest.DBConnection
 
getLogOperation() - Method in class ambit2.sln.SLNExpressionToken
 
getLogOperation() - Method in class ambit2.smarts.SmartsExpressionToken
 
getLogOperationCharNumber(char) - Static method in class ambit2.smarts.SmartsConst
 
getLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getLonePairCount() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getLonePairNumber(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getLong(int) - Method in class ambit2.db.results.AmbitRows
 
getLong(String) - Method in class ambit2.db.results.AmbitRows
 
getLoQualifier() - Method in class ambit2.base.data.study.EffectRecord
 
getLoQualifier() - Method in interface ambit2.base.data.study.IParams
 
getLoQualifier() - Method in interface ambit2.base.data.study.IValue
 
getLoQualifier() - Method in class ambit2.base.data.study.Params
 
getLoQualifier() - Method in class ambit2.base.data.study.Value
 
getLoRelation() - Method in interface ambit2.rules.conditions.value.IValueInterval
 
getLoRelation() - Method in class ambit2.rules.conditions.value.ValueInterval
 
getLoValue() - Method in class ambit2.base.data.study.EffectRecord
 
getLoValue() - Method in interface ambit2.base.data.study.IParams
 
getLoValue() - Method in interface ambit2.base.data.study.IValue
lower value
getLoValue() - Method in class ambit2.base.data.study.Params
 
getLoValue() - Method in class ambit2.base.data.study.Value
 
getLoValue() - Method in interface ambit2.rules.conditions.value.IValueInterval
 
getLoValue() - Method in class ambit2.rules.conditions.value.ValueInterval
 
getLow() - Method in class ambit2.similarity.stats.Bin
 
getMadanChemicalDegree(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
getMAE() - Method in class ambit2.model.evaluation.EvaluationStats
 
getMainSQL() - Method in class ambit2.db.search.QueryCombined
 
getMainSQL() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
getMaintainer() - Method in class ambit2.base.data.AbstractDataset
 
getMaintainer() - Method in interface ambit2.base.data.ISourceDataset
 
getMaintainer() - Method in class ambit2.base.data.SourceDataset
 
getMaintainer() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getMaintainer() - Method in class ambit2.db.search.StoredQuery
 
getMajor() - Method in interface ambit2.db.DBVersion
 
getMajor() - Method in class ambit2.db.version.AmbitDBVersion
 
getMajorIsotope(int) - Method in class ambit2.descriptors.IsotopeFactory
Returns the most abundant (major) isotope with a given atomic number.
getMajorIsotope(String) - Method in class ambit2.descriptors.IsotopeFactory
Returns the most abundant (major) isotope whose symbol equals element.
getMap() - Method in class ambit2.base.data.StructureRecord
 
getMapFolder() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getMappings(IAtomContainer) - Method in class ambit2.smarts.groups.GroupMatch
 
getMappingsForGroup(IAtomContainer, IQueryAtomContainer, SmartsConst.SSM_MODE) - Method in class ambit2.smarts.SmartsManager
 
getMapStrategy() - Method in class ambit2.reactions.mapping.ReactionAtomMapping
 
getMatchColumnIndexes() - Method in class ambit2.db.results.AmbitRows
 
getMatchColumnNames() - Method in class ambit2.db.results.AmbitRows
 
getMatcher() - Method in enum ambit2.core.processors.structure.key.IStructureKey.Matcher
 
getMatchingStructure(IAtomContainer) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
getMatchingStructure(IAtomContainer) - Method in interface ambit2.smarts.query.ISmartsPattern
 
getMatchingStructure(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
getMatchingStructure(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getMaterialAttributeValue(Object, String, URI, String) - Static method in class ambit2.export.isa.v1_0.ISAJsonUtils1_0
 
getMaterials() - Method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
getMatricesAsString(String, boolean, boolean, boolean, boolean, boolean) - Method in class ambit2.groupcontribution.Learner
 
getMatrixDecDig() - Method in class ambit2.groupcontribution.Learner
 
getMatrixDig() - Method in class ambit2.groupcontribution.Learner
 
getMax() - Method in class ambit2.base.data.PropertyStats
 
getMaxAllAtoms() - Method in class ambit2.mopac.AbstractMopacShell
 
getMaxAttribute(int) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
getMaxdata() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
getMaxFieldSize() - Method in class ambit2.db.results.AmbitRows
 
getMaxFrequency() - Method in class ambit2.domain.stats.datastructures.Histogram
 
getMaxFrequency() - Method in class ambit2.similarity.stats.Histogram
 
getMaxHeavyAtoms() - Method in class ambit2.mopac.AbstractMopacShell
 
getMaximumBondOrder(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getMaxLevel() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getMaxLevels() - Method in class ambit2.core.data.HashIntDescriptorResult
 
getMaxLevels() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
getMaxLevels() - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
getMaxPages() - Method in class ambit2.ui.table.BrowsableTableModel
 
getMaxPages() - Method in interface ambit2.ui.table.IPageNavigator
 
getMaxPoints() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getMaxRecords() - Method in class ambit2.ui.table.BrowsableTableModel
 
getMaxRecords() - Method in interface ambit2.ui.table.IRecordNavigator
 
getMaxRows() - Method in class ambit2.db.results.AmbitRows
 
getMaxValue() - Method in class ambit2.base.data.Range
 
getMaxValue() - Method in class ambit2.db.search.QuerySmilesByID
 
getMaxValue() - Method in class ambit2.db.search.structure.NumberQuery
 
getMaxValue() - Method in class ambit2.db.search.structure.QueryDistance
 
getMaxValue() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
getMaxValue() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getMaxValue() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getMaxValue(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
getMaxValue(int) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
getMaxValue() - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
getMaxX() - Method in class ambit2.db.chart.BarChartGenerator
 
getMeanValue(int) - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
getMeasurements() - Method in class ambit2.base.data.SubstanceRecord
 
getMediaType() - Method in enum ambit2.core.data.model.Algorithm.AlgorithmFormat
 
getMediaType() - Method in enum ambit2.export.isa.base.ISAConst.ISAFormat
MIME type See https://github.com/ISA-tools/isa-api/issues/96
getMediaType() - Method in enum ambit2.pubchem.NCISearchProcessor.METHODS
 
getMediaType() - Method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OUTPUT
 
getMediaType(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
getMediaType(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
getMediaType() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
getMenuProfile() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getMessage() - Method in exception ambit2.base.processors.ProcessorException
 
getMessage(String, String, String, long) - Method in class ambit2.pubchem.BatchRetrievePubChem
 
getMetaData() - Method in class ambit2.db.results.AmbitRows
 
getMethod() - Method in class ambit2.db.search.QueryInfo
 
getMethod() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getMetric() - Method in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
getMetric() - Method in class ambit2.db.search.property.FilteredCount
 
getMetric() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getMetric() - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
getMetricName() - Method in class ambit2.model.numeric.DataCoverage
 
getMetricName() - Method in interface ambit2.model.numeric.IDataCoverage
 
getMetricName() - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
getMetricName() - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
getMIMEType() - Method in class ambit2.core.io.DelimitedFileFormat
 
getMIMEType() - Method in class ambit2.core.io.XLSFileFormat
 
getMimeType() - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
getMin() - Method in class ambit2.base.data.PropertyStats
 
getMinAttribute(int) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
getMindata() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
getMinimumBondOrder(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getMinInchiTautomer(List<IAtomContainer>) - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
getMinor() - Method in interface ambit2.db.DBVersion
 
getMinor() - Method in class ambit2.db.version.AmbitDBVersion
 
getMinValue() - Method in class ambit2.base.data.Range
 
getMinValue() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getMinValue(int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
getMinValue(int) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
getMinValue() - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
getMinX() - Method in class ambit2.db.chart.BarChartGenerator
 
getMixedColor(Color, float, Color, float) - Static method in class ambit2.ui.Utils
TODO resolve Duplicate with CompoundImageTools method
getMode() - Method in class ambit2.base.processors.search.AbstractFinder
 
getMode() - Method in class ambit2.core.io.RawIteratingFolderReader
 
getMode() - Method in class ambit2.db.reporters.SmilesReporter
 
getMode() - Method in class ambit2.db.search.structure.QuerySimilarityBitset
 
getMode() - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
getMode() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getModel() - Method in class ambit2.groupcontribution.Learner
 
getModel() - Method in class ambit2.rest.model.predictor.ExternalModel
 
getModel() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getModel() - Method in class ambit2.rest.model.task.CallableModelCreator
 
getModelColumn(QuerySolution, Reference) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getModelDescription() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getModelIndex() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getModelName() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getModelParams(Form) - Method in enum ambit2.rest.OpenTox.params
 
getModelReporter() - Method in class ambit2.rest.model.builder.ModelBuilder
 
getModelReporter() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getModelType() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getModelURI(QuerySolution) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getMolAttributes(SLNContainer) - Static method in class ambit2.sln.SLNHelper
 
getMolecule(String) - Static method in class ambit2.core.data.MoleculeTools
 
getMolecule() - Method in class ambit2.db.search.QueryInfo
 
getMolecule() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getMolecule() - Method in class ambit2.jchempaint.editor.AbstractMoleculeAction
 
getMolecule() - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
getMolecule() - Method in interface ambit2.tautomers.zwitterion.ICenter
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
getMolecule() - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
getMolecule() - Method in interface ambit2.ui.IMoleculeEditAction
 
getMoleculeForEdit(IAtomContainer) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
getMoleculeFromSmiles(String) - Static method in class ambit2.smarts.SmartsHelper
 
getMoleculeFromSmiles(String, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
getMoleculeStatus(IAtomContainer) - Static method in class ambit2.reactions.retrosynth.ReactionSequence
 
getMopac_commands() - Method in class ambit2.mopac.AbstractMopacShell
 
getMopac_commands() - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
getMopacCommands() - Method in class ambit2.mopac.Mopac7Writer
 
getMostDenseVector(double[]) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
getmostDenseVector
getMostDenseVector(double[]) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
getMostDenseVector
getMsgemptymolecule() - Static method in class ambit2.base.external.CommandShell
 
getMulticenter() - Method in class ambit2.core.groups.DataGroup
 
getMultiObject(ResultSet) - Method in class ambit2.db.readers.RetrieveProfileValues
 
getMultiplier() - Method in class ambit2.core.groups.MultipleGroup
 
getName() - Method in class ambit2.base.data.AbstractDataset
 
getName() - Method in class ambit2.base.data.AmbitUser
 
getName() - Method in interface ambit2.base.data.ILiteratureEntry
 
getName() - Method in interface ambit2.base.data.ISourceDataset
 
getName() - Method in class ambit2.base.data.LiteratureEntry
 
getName() - Method in class ambit2.base.data.Profile
 
getName() - Method in class ambit2.base.data.Property
 
getName() - Method in class ambit2.base.data.SourceDataset
 
getName() - Method in class ambit2.base.data.StringBean
 
getName() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getName() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getName() - Method in interface ambit2.base.interfaces.ICategory
 
getName() - Method in interface ambit2.base.interfaces.IStructureRelation
 
getName() - Method in class ambit2.base.relation.AbstractRelation
 
getName() - Method in class ambit2.core.data.model.Algorithm
 
getName() - Method in class ambit2.core.data.model.ModelWrapper
 
getName() - Method in class ambit2.core.data.model.Parameter
 
getName() - Method in class ambit2.core.groups.DataGroup
 
getName() - Method in class ambit2.db.search.AbstractQuery
 
getName() - Method in interface ambit2.db.search.IStoredQuery
 
getName() - Method in class ambit2.db.search.StoredQuery
 
getName() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getName() - Method in class ambit2.db.SessionID
 
getName() - Method in class ambit2.db.substance.study.facet.OwnerFacet
 
getName() - Method in class ambit2.descriptors.FunctionalGroup
 
getName() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
getName() - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
getName() - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
getName() - Method in enum ambit2.model.numeric.ADomainMethodType
 
getName() - Method in class ambit2.model.numeric.DataCoverage
 
getName() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
getName() - Method in enum ambit2.model.structure.AtomEnvironmentDistanceType
 
getName() - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
getName() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
getName() - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
getName() - Method in class ambit2.reactions.GenericReaction
 
getName() - Method in class ambit2.reactions.Reaction
 
getName() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
getName() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getName() - Method in class ambit2.reactions.sets.ReactionData
 
getName() - Method in class ambit2.reactions.sets.ReactionGroup
 
getName() - Method in class ambit2.reactions.sets.ReactionSet
 
getName() - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
getName() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
getName(Algorithm) - Method in class ambit2.rest.model.builder.ExpertModelBuilder
 
getName(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
getName() - Method in class ambit2.rest.task.Task
 
getName() - Method in class ambit2.rest.wrapper.WrappedService
 
getName() - Method in interface ambit2.rules.actions.IAction
 
getName() - Method in interface ambit2.rules.functions.IFunction
 
getName() - Method in class ambit2.rules.functions.LinearFunction
 
getName() - Method in class ambit2.rules.functions.NestedFunctions
 
getName() - Method in class ambit2.rules.functions.ReciprocalFunction
 
getName() - Method in interface ambit2.rules.IBasicRule
 
getName() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getName() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
getName() - Method in interface ambit2.smarts.query.ISmartsPattern
 
getNameColumn(QuerySolution, String) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getNameCondition() - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
getNamedConfig() - Method in class ambit2.rest.DBConnection
 
getNameExtensions() - Method in class ambit2.core.io.DelimitedFileFormat
 
getNameExtensions() - Method in class ambit2.core.io.XLSFileFormat
 
getNameInstance() - Static method in class ambit2.base.data.Property
 
getNamespace() - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
getNativeComparison(AtomEnvironmentList, AtomEnvironmentList) - Method in class ambit2.similarity.measure.AtomEnvironmentsDistance
 
getNativeComparison(BitSet, BitSet) - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
getNativeComparison(double[], double[]) - Method in class ambit2.similarity.measure.EuclideanDistance
 
getNativeComparison(BitSet, BitSet) - Method in class ambit2.similarity.measure.FingerprintDistance
 
getNativeComparison(int[], int[]) - Method in class ambit2.similarity.measure.HammingDistance
Count only nonzero items
getNativeComparison(T, T) - Method in interface ambit2.similarity.measure.IDistanceFunction
Calculates native comparison index between two objects (distance or similarity).
getNativeComparison(String, String) - Method in class ambit2.similarity.measure.LevensteinDistance
 
getNativeComparison(IAtomContainer, IAtomContainer) - Method in class ambit2.similarity.measure.MCSSDistance
 
getNaturalMass(IElement) - Method in class ambit2.descriptors.IsotopeFactory
Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
getNearestNeighbors(T, int) - Method in interface ambit2.similarity.knn.INearestNeighborsSearch
 
getNearestNeighbors(T, int) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
Returns k nearest neighbors, encapsulated in DistanceComparable.
getNearestNeighbors(T, int) - Method in interface ambit2.similarity.stats.INearestNeighborsSearch
 
getNearestNeighborsSearch() - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
getNegative() - Method in enum ambit2.base.interfaces.ICategory.CategoryType
 
getNegativeCategoryType() - Method in interface ambit2.base.interfaces.ICategory
 
getNextLevel() - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
getNextReader() - Method in class ambit2.core.io.IteratingFolderReader
 
getNitroGroupPositions(IAtomContainer) - Static method in class ambit2.tautomers.rules.CustomTautomerRegion
 
getNitroxidePositions(IAtomContainer) - Static method in class ambit2.tautomers.rules.CustomTautomerRegion
 
getNoDataText() - Method in class ambit2.ui.editors.EditorPanel
 
getNodeLevel() - Method in class ambit2.reactions.retrosynth.RetroSynthNode
 
getNodeNo(boolean) - Method in class ambit2.descriptors.PKANode
 
getNodes(Document, Element, String) - Static method in class ambit2.pubchem.PUGProcessor
 
getNodeTypeAsString(JsonNode) - Static method in class ambit2.core.json.JSONParserUtils
 
getNonIdenticalMappings(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
 
getNonIdenticalMappings(List<List<IAtom>>) - Static method in class ambit2.smarts.MappingUtils
 
getNonIdenticalMappings(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
getNonIdenticalMappings(IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
getNonOverlappingMappings(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
 
getNonOverlappingMappings(List<List<IAtom>>) - Static method in class ambit2.smarts.MappingUtils
 
getNonOverlappingMappings(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
getNonOverlappingMappings(IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
getNotionalUnitcell(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getNS() - Method in enum ambit2.rest.rdf.Annotea.Bookmark
 
getNS() - Method in enum ambit2.rest.rdf.BibTex.BTClass
 
getNS() - Method in enum ambit2.rest.rdf.OTA.OTAClass
 
getNS() - Method in enum ambit2.rest.rdf.OTEE.OTEEClass
 
getNum() - Method in class ambit2.rest.task.FilteredTasksIterator
 
getNumber() - Method in enum ambit2.base.data.study.Protocol._categories
 
getNumber() - Method in class ambit2.core.groups.AbstractGroup
 
getNumber(T) - Method in class ambit2.core.groups.FilteredList
 
getNumber() - Method in interface ambit2.core.groups.ISGroup
 
getNumberOfColumns() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getNumberOfDistinctValues(double[]) - Static method in class ambit2.tautomers.tools.TautomerAnalysis
 
getNumberOfHeaderLines() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getNumberofHeaderLines() - Method in class ambit2.db.reporters.CSVReporter
 
getNumberOfProperties() - Method in class ambit2.base.data.StructureRecord
 
getNumberOfProperties() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getNumberOfProperties() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getNumberOfStates() - Method in class ambit2.tautomers.CombinedRuleInstance
 
getNumberOfStates() - Method in interface ambit2.tautomers.IRuleInstance
 
getNumberOfStates() - Method in class ambit2.tautomers.RuleInstance
 
getNumOfAttributes() - Method in class ambit2.sln.SLNContainerAttributes
 
getNumOfOverlappedAtoms(RuleInstance, RuleInstance) - Static method in class ambit2.tautomers.RuleManager
 
getNumOfPairSwitches(int[], int[]) - Static method in class ambit2.smarts.ChiralPermutations
Calculates the number of pair switches needed to obtain permutation2 starting from permutation1 The number is not unique (since various paths are possible), but the parity (even/odd) of the switches number must always be the same
getOBabelHome() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
getOBabelHome() - Method in class ambit2.core.smiles.OpenBabelGen3D
 
getObject() - Method in class ambit2.base.data.PropertyAnnotation
 
getObject() - Method in interface ambit2.base.interfaces.IAmbitEditor
 
getObject(String) - Static method in class ambit2.core.config.Resources
 
getObject(ResultSet) - Method in class ambit2.db.cache.QueryCachedResultsBoolean
 
getObject(ResultSet) - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
getObject(ResultSet) - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
getObject(ResultSet) - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
getObject(ResultSet) - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
getObject(ResultSet) - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
getObject(ResultSet) - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
getObject(ResultSet) - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
getObject(ResultSet) - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
getObject(ResultSet) - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
getObject(ResultSet) - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
getObject(ResultSet) - Method in class ambit2.db.readers.ReadChemicalIds
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveAtomContainer
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveDatasets
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveDescriptor
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveField
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveFieldPropertyValue
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveFieldStructure
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveModelTemplates
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveModelTemplatesPropertyValue
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveProfileValues
 
getObject(ResultSet, IStructureRecord, int) - Method in class ambit2.db.readers.RetrieveProfileValues
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveStructure
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveTemplate
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveTemplatePropertyValue
 
getObject(ResultSet) - Method in class ambit2.db.readers.RetrieveTemplateStructure
 
getObject() - Method in class ambit2.db.results.AmbitRows
 
getObject(int) - Method in class ambit2.db.results.AmbitRows
 
getObject(String) - Method in class ambit2.db.results.AmbitRows
 
getObject(int, Map<String, Class<?>>) - Method in class ambit2.db.results.AmbitRows
 
getObject(String, Map<String, Class<?>>) - Method in class ambit2.db.results.AmbitRows
 
getObject(ResultSet) - Method in class ambit2.db.search.DictionaryQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
getObject(ResultSet, Property) - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
getObject(ResultSet) - Method in class ambit2.db.search.property.FilteredCount
 
getObject(ResultSet) - Method in class ambit2.db.search.property.FilteredCountNumeric
 
getObject(ResultSet) - Method in class ambit2.db.search.property.FreeTextPropertyQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.property.PropertiesByDataset
 
getObject(ResultSet) - Method in class ambit2.db.search.property.PropertyCount
 
getObject(ResultSet) - Method in class ambit2.db.search.property.PropertyRange
 
getObject(ResultSet) - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getObject(ResultSet) - Method in class ambit2.db.search.property.PropertyStatsString
 
getObject(ResultSet) - Method in class ambit2.db.search.property.QueryMetricRange
 
getObject(ResultSet) - Method in class ambit2.db.search.property.QueryOntology
 
getObject(ResultSet) - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
getObject(ResultSet) - Method in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
getObject(ResultSet) - Method in class ambit2.db.search.property.RetrieveProfile
 
getObject(ResultSet) - Method in class ambit2.db.search.property.TemplateQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.qlabel.QueryConsensus
 
getObject(ResultSet) - Method in class ambit2.db.search.qlabel.QueryQLabel
 
getObject(ResultSet) - Method in class ambit2.db.search.QueryCombined
 
getObject(ResultSet) - Method in class ambit2.db.search.QuerySmilesByID
 
getObject(ResultSet) - Method in class ambit2.db.search.QueryUser
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.ChemicalByQueryFolder
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.FingerprintsByStatus
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.FreeTextQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairs
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
getObject(ResultSet, IStructureRecord, int) - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.QueryDataset
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.QueryStructure
 
getObject(ResultSet) - Method in class ambit2.db.search.structure.ScopeQuery
 
getObject(ResultSet) - Method in class ambit2.db.simiparity.space.QueryQMap
 
getObject(ResultSet) - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
getObject(ResultSet) - Method in class ambit2.db.substance.AbstractReadSubstance
 
getObject(ResultSet) - Method in class ambit2.db.substance.ids.ReadChemIdentifiersByComposition
 
getObject(ResultSet) - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
getObject(ResultSet) - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
getObject(ResultSet) - Method in class ambit2.db.substance.QueryCountEndpoints
 
getObject(ResultSet) - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
getObject(ResultSet) - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
getObject(ResultSet) - Method in class ambit2.db.substance.QueryCountSubstanceTypes
 
getObject(ResultSet) - Method in class ambit2.db.substance.ReadSubstance
 
getObject(ResultSet) - Method in class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
getObject(ResultSet) - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
getObject(ResultSet) - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.ReadSubstanceProperty
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
getObject(ResultSet) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
protected ProtocolApplication record;
getObject(ResultSet) - Method in class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
getObject(ResultSet) - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
getObject(ResultSet) - Method in class ambit2.db.update.bookmark.ReadBookmark
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.BundleOwnerByNumber
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.endpoints.ReadEndpointsByBundle
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.ReadBundle
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.substance.ReadSubstanceChemicalsUnionByBundle
 
getObject(ResultSet) - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
getObject(ResultSet) - Method in class ambit2.db.update.dataset.AbstractReadDataset
 
getObject(ResultSet) - Method in class ambit2.db.update.dataset.QueryCount
 
getObject(ResultSet) - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
getObject(ResultSet) - Method in class ambit2.db.update.fp.QueryFingerprints
 
getObject(ResultSet) - Method in class ambit2.db.update.model.AbstractModelQuery
 
getObject(ResultSet) - Method in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
getObject(ResultSet) - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
getObject(ResultSet) - Method in class ambit2.db.update.reference.ReadReference
 
getObject(ResultSet) - Method in class ambit2.db.update.storedquery.ReadStoredQuery
 
getObject(ResultSet) - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
getObject(ResultSet) - Method in class ambit2.db.update.structure.ChemicalByDataset
 
getObject(ResultSet) - Method in class ambit2.db.version.DBVersionQuery
 
getObject() - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
getObject() - Method in class ambit2.dbui.dictionary.OntologyEditor
 
getObject() - Method in class ambit2.dbui.ProfileEditor
 
getObject() - Method in class ambit2.dbui.QueryCombinedEditor
 
getObject() - Method in class ambit2.dbui.QueryEditor
 
getObject() - Method in class ambit2.dbui.QueryInfoEditor
 
getObject() - Method in class ambit2.dbui.QueryScopeEditor
 
getObject() - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
getObject() - Method in class ambit2.similarity.measure.DistanceComparable
 
getObject() - Method in class ambit2.ui.editors.BeanEditor
 
getObject() - Method in class ambit2.ui.editors.FileSelector
 
getObject() - Method in class ambit2.ui.editors.ListEditor
 
getObject() - Method in class ambit2.ui.editors.PreferencesPanel
 
getObject() - Method in class ambit2.ui.editors.SelectFieldsPanel
 
getObject() - Method in class ambit2.ui.editors.TemplateEditor
 
getObject() - Method in class ambit2.ui.jmol.Panel3D
 
getObject() - Method in class ambit2.ui.Panel2D
 
getObject() - Method in class ambit2.ui.QueryBrowser
 
getObjectToVerify(IAtomContainer) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
getObjectToVerify(IAtomContainer) - Method in interface ambit2.smarts.query.ISmartsPattern
 
getObjectToVerify(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
getObjectToVerify(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getObjectType() - Method in interface ambit2.sln.dictionary.ISLNDictionaryObject
 
getObserved() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
getObserved() - Method in interface ambit2.model.IDataset
 
getObserved() - Method in class ambit2.similarity.stats.ValuePair
 
getOffset() - Method in class ambit2.core.io.FileState
 
getOffset() - Method in class ambit2.dbui.CachedRowSetTableModel
 
getOntClass(OntModel) - Method in enum ambit2.rest.rdf.Annotea.Bookmark
 
getOntClass(OntModel) - Method in enum ambit2.rest.rdf.BibTex.BTClass
 
getOntClass(OntModel) - Method in enum ambit2.rest.rdf.OTA.OTAClass
 
getOntClass(OntModel) - Method in enum ambit2.rest.rdf.OTEE.OTEEClass
 
getOntologyAnotation(String) - Method in class ambit2.export.isa.v1_0.OntologyManager1_0
 
getOntologyService() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getOntologyURI() - Method in enum ambit2.base.data.study.Protocol._categories
 
getOpenSSOService() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getOpenToxEntry() - Method in enum ambit2.pubchem.NCISearchProcessor.METHODS
 
getOperation() - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
getOperation() - Method in class ambit2.db.processors.ProcessorOntology
 
getOperation() - Method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OPERATION
 
getOperation() - Method in class ambit2.pubchem.rest.PUGRestRequest
 
getOption() - Method in class ambit2.pubchem.NCISearchProcessor
 
getOptionalInChIHeader() - Method in class ambit2.core.io.FileInputState
 
getOptionalInChIHeader() - Method in class ambit2.core.io.RawIteratingCSVReader
 
getOptionalInChIKeyHeader() - Method in class ambit2.core.io.FileInputState
 
getOptionalInChIKeyHeader() - Method in class ambit2.core.io.RawIteratingCSVReader
 
getOptionalSMILESHeader() - Method in class ambit2.core.io.FileInputState
 
getOptionalSMILESHeader() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getOptionalSMILESHeader() - Method in class ambit2.core.io.RawIteratingCSVReader
 
getOptions() - Method in class ambit2.base.data.SelectionBean
 
getOptions() - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
getOptions() - Method in class ambit2.pubchem.rest.PUGRestRequest
 
getOptions() - Method in class ambit2.search.csls.CSLSImageRequest
 
getOptions() - Method in class ambit2.search.csls.CSLSRequest
 
getOrder() - Method in class ambit2.base.data.Property
 
getOrder() - Method in class ambit2.core.groups.ComponentGroup
 
getOrder(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getOrder() - Method in class ambit2.db.update.fp.QueryFingerprints
 
getOrder() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getOriginal() - Method in class ambit2.db.results.AmbitRows
 
getOriginalPositions() - Method in class ambit2.tautomers.FilterTautomers
 
getOriginalRow() - Method in class ambit2.db.results.AmbitRows
 
getOriginalRuleString() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
getOriginalRuleString() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getOtherSide() - Method in class ambit2.db.processors.ProcessorOntology
 
getOut() - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
getOutFile(int, String) - Method in class ambit2.mopac.AbstractMopacShell
 
getOutput() - Method in class ambit2.base.processors.batch.BatchReporter
 
getOutput() - Method in class ambit2.core.processors.ProcessorFileExport
 
getOutput() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getOutput() - Method in class ambit2.pubchem.rest.PUGRestRequest
 
getOutput(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getOutput() - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
getOutputDir() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
getOutputDir() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getOutputDir() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getOutputFile() - Method in class ambit2.base.external.CommandShell
 
getOutputFileName() - Method in class ambit2.balloon.ShellBalloon
 
getOutputFileName() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
getOutputFileName() - Method in class ambit2.core.smiles.OpenBabelDepiction
 
getOutputFileName() - Method in class ambit2.core.smiles.OpenBabelGen3D
 
getOutputMolecules() - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
getOutputOption() - Method in class ambit2.balloon.ShellBalloon
 
getOutputOption() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
getOutputOption() - Method in class ambit2.core.smiles.OpenBabelDepiction
 
getOutputOption() - Method in class ambit2.core.smiles.OpenBabelGen3D
 
getOverlappedMappingClusters(List<List<IAtom>>) - Method in class ambit2.smarts.IsomorphismTester
 
getOverlappedMappingClusters(List<List<IAtom>>) - Static method in class ambit2.smarts.MappingUtils
 
getOwnerConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getOwnerName() - Method in class ambit2.base.data.SubstanceRecord
Name of the company, which is the substance owner (usually the substance manufacturer)
getOwnerNameReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getOwnerUUID() - Method in class ambit2.base.data.SubstanceRecord
UUID of the company, which is the substance owner (usually the substance manufacturer)
getOwnerUUID() - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
getPage() - Method in class ambit2.db.search.AbstractQuery
 
getPage() - Method in class ambit2.db.search.property.FilteredCount
 
getPage() - Method in class ambit2.db.search.StoredQuery
 
getPage() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
getPage() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getPage(int, int) - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
getPage(int, int) - Method in interface ambit2.rest.legacy.IOTPageable
Deprecated.
 
getPage(int, int) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
getPage(int, int) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
getPage(int, int) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
getPage() - Method in class ambit2.rest.SimpleTaskResource
 
getPage(int, int, boolean) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getPage(int, int, boolean, boolean, boolean) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getPage(int, int, boolean) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
getPage() - Method in class ambit2.ui.table.BrowsableTableModel
 
getPage() - Method in interface ambit2.ui.table.IPageNavigator
 
getPagedReference(Reference, int, int) - Static method in class ambit2.rest.legacy.OTObject
Deprecated.
 
getPages(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getPageSize() - Method in class ambit2.db.results.AmbitRows
 
getPageSize() - Method in class ambit2.db.search.AbstractQuery
 
getPageSize() - Method in class ambit2.db.search.property.FilteredCount
 
getPageSize() - Method in class ambit2.db.search.StoredQuery
 
getPageSize() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
getPageSize() - Method in class ambit2.db.search.structure.QueryMissingDescriptor
 
getPageSize() - Method in class ambit2.db.search.structure.QueryMissingDistances
 
getPageSize() - Method in class ambit2.db.search.structure.QueryMissingProperty
 
getPageSize() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getPageSize() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getPageSize() - Method in class ambit2.rest.SimpleTaskResource
 
getPageSize() - Method in class ambit2.ui.table.BrowsableTableModel
 
getPageSize() - Method in interface ambit2.ui.table.IPageNavigator
 
getPairwise(IDataset<ID, Features, ResultType>, IDataset<ID, Features, ResultType>) - Method in class ambit2.similarity.AbstractSimilarityModel
 
getPairwise(Features, Features) - Method in class ambit2.similarity.AbstractSimilarityModel
 
getPairwise(Features, Features) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
getPairwiseSimilarity() - Method in interface ambit2.similarity.ISimilarityResultType
 
getPapp() - Method in exception ambit2.base.exceptions.NoDocumentUUIDException
 
getParam() - Method in class ambit2.db.chart.ChartGenerator
 
getParam(Property) - Method in enum ambit2.db.readers.RetrieveProfileValues.SearchMode
 
getParam(String) - Method in class ambit2.db.substance.QueryCountSubstanceTypes
 
getParam(String) - Method in class ambit2.db.update.dataset.QueryCount
 
getParam(ModelQueryResults, String) - Method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
 
getParam(ReadStoredQuery) - Method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
 
getParameter(QueryDatasetByFeatures) - Method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
 
getParameter(Object) - Method in class ambit2.model.AbstractModel
 
getParameter(Object) - Method in interface ambit2.model.IModelDefinition
 
getParameter(Form, String, String, boolean) - Method in class ambit2.rest.AbstractResource
Returns parameter value and throwsan exception if value is missing of mandatory parameter
getParameter(Form, String, String) - Method in class ambit2.rest.AbstractResource
Calls #getParameter(Form, String, boolean) with false for the last argument
getParameter(Object) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
getParameterNames() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getParameterNames() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
Gets the parameterNames attribute of the AtomHybridizationDescriptor object
getParameterNames() - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
Gets the parameterNames attribute of the AtomHybridizationDescriptor object
getParameterNames() - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getParameterNames() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.InChI
 
getParameterNames() - Method in class ambit2.descriptors.MolecularWeight
Gets the parameterNames attribute of the WeightDescriptor object.
getParameterNames() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.SizeDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.SpherosityDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getParameterNames() - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getParameterNames() - Method in class ambit2.dragon.DescriptorDragonShell
 
getParameterNames() - Method in interface ambit2.groupcontribution.transformations.IValueTransformation
 
getParameterNames() - Method in class ambit2.groupcontribution.transformations.TransformationComposition
 
getParameterNames() - Method in class ambit2.groupcontribution.transformations.TransformationExp
 
getParameterNames() - Method in class ambit2.groupcontribution.transformations.TransformationLin
 
getParameterNames() - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
getParameterNames() - Method in class ambit2.groupcontribution.transformations.TransformationPow
 
getParameterNames() - Method in class ambit2.mopac.DescriptorMopacShell
 
getParameterNames() - Method in class ambit2.some.DescriptorSOMEShell
 
getParameters() - Method in class ambit2.base.data.study.ProtocolApplication
"parameters": {}
getParameters() - Method in class ambit2.core.data.model.Algorithm
 
getParameters() - Method in class ambit2.core.data.model.ModelWrapper
 
getParameters() - Method in class ambit2.db.cache.QueryCachedResults
 
getParameters() - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
getParameters(int) - Method in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
getParameters() - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
getParameters() - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
getParameters(int) - Method in class ambit2.db.chemrelation.UpdateStructureRelation
 
getParameters() - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
getParameters() - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
getParameters() - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
getParameters() - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
getParameters() - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
getParameters() - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
getParameters() - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
getParameters() - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
getParameters() - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
getParameters() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
getParameters() - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
getParameters() - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
getParameters() - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
getParameters() - Method in class ambit2.db.model.QueryCountModels
 
getParameters() - Method in class ambit2.db.readers.AbstractStructureRetrieval
 
getParameters() - Method in class ambit2.db.readers.ReadChemicalIds
 
getParameters() - Method in class ambit2.db.readers.RetrieveDatasets
 
getParameters() - Method in class ambit2.db.readers.RetrieveDescriptor
 
getParameters() - Method in class ambit2.db.readers.RetrieveField
 
getParameters() - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
getParameters() - Method in class ambit2.db.readers.RetrieveModelTemplates
 
getParameters() - Method in class ambit2.db.readers.RetrieveProfileValues
 
getParameters() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getParameters() - Method in class ambit2.db.readers.RetrieveStructure
 
getParameters() - Method in class ambit2.db.readers.RetrieveTemplate
 
getParameters() - Method in class ambit2.db.search.DictionaryQuery
 
getParameters() - Method in class ambit2.db.search.property.FilteredCount
 
getParameters() - Method in class ambit2.db.search.property.FilteredCountNominal
 
getParameters() - Method in class ambit2.db.search.property.FilteredCountNumeric
 
getParameters() - Method in class ambit2.db.search.property.FreeTextPropertyQuery
 
getParameters() - Method in class ambit2.db.search.property.ModelTemplates
 
getParameters() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getParameters() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getParameters() - Method in class ambit2.db.search.property.PropertyCount
 
getParameters() - Method in class ambit2.db.search.property.PropertyRange
 
getParameters() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getParameters() - Method in class ambit2.db.search.property.PropertyStatsString
 
getParameters() - Method in class ambit2.db.search.property.QueryMetricRange
 
getParameters() - Method in class ambit2.db.search.property.QueryOntology
 
getParameters() - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
getParameters() - Method in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
getParameters() - Method in class ambit2.db.search.property.RetieveFeatures
 
getParameters() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getParameters() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getParameters() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getParameters() - Method in class ambit2.db.search.property.RetrieveProfile
 
getParameters() - Method in class ambit2.db.search.property.TemplateQuery
 
getParameters() - Method in class ambit2.db.search.qlabel.QueryConsensus
 
getParameters() - Method in class ambit2.db.search.qlabel.QueryQLabel
 
getParameters() - Method in class ambit2.db.search.QueryCombined
SQL Parameters
getParameters() - Method in class ambit2.db.search.QuerySmilesByID
 
getParameters() - Method in class ambit2.db.search.QueryUser
 
getParameters() - Method in class ambit2.db.search.SQLFileQueryParams
 
getParameters() - Method in class ambit2.db.search.StoredQuery
Selects should be in the form
getParameters() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
getParameters() - Method in class ambit2.db.search.structure.ChemicalByQueryFolder
 
getParameters() - Method in class ambit2.db.search.structure.FingerprintsByStatus
 
getParameters() - Method in class ambit2.db.search.structure.FreeTextQuery
 
getParameters() - Method in class ambit2.db.search.structure.MissingFingerprintsQuery
 
getParameters() - Method in class ambit2.db.search.structure.MissingInChIsQuery
 
getParameters() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getParameters() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsDataset
 
getParameters() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsMixed
 
getParameters() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset
 
getParameters() - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
getParameters() - Method in class ambit2.db.search.structure.QueryAtomEnvironment
 
getParameters() - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
getParameters() - Method in class ambit2.db.search.structure.QueryComplement
 
getParameters() - Method in class ambit2.db.search.structure.QueryDataset
 
getParameters() - Method in class ambit2.db.search.structure.QueryDatasetByID
 
getParameters() - Method in class ambit2.db.search.structure.QueryDistance
 
getParameters() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
getParameters() - Method in class ambit2.db.search.structure.QueryField
 
getParameters() - Method in class ambit2.db.search.structure.QueryFieldMultiple
 
getParameters() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
getParameters() - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
getParameters() - Method in class ambit2.db.search.structure.QueryLookupStructure
 
getParameters() - Method in class ambit2.db.search.structure.QueryMissingDescriptor
 
getParameters() - Method in class ambit2.db.search.structure.QueryMissingDistances
 
getParameters() - Method in class ambit2.db.search.structure.QueryMissingProperty
 
getParameters() - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
getParameters() - Method in class ambit2.db.search.structure.QuerySimilarityBitset
 
getParameters() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getParameters() - Method in class ambit2.db.search.structure.QuerySMARTS
 
getParameters() - Method in class ambit2.db.search.structure.QueryStoredResults
 
getParameters() - Method in class ambit2.db.search.structure.QueryStoredResultsByName
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructure
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
getParameters() - Method in class ambit2.db.search.structure.QueryStructureType
 
getParameters() - Method in class ambit2.db.search.structure.QueryStrucType
 
getParameters() - Method in class ambit2.db.search.structure.ScopeQuery
 
getParameters() - Method in class ambit2.db.simiparity.space.QueryQMap
 
getParameters() - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
getParameters() - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
getParameters(int) - Method in class ambit2.db.substance.CreateSubstance
 
getParameters(int) - Method in class ambit2.db.substance.DeleteSubstance
 
getParameters() - Method in class ambit2.db.substance.FacetedSearchSubstance
 
getParameters() - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
getParameters(int) - Method in class ambit2.db.substance.ids.UpdateSubstanceIdentifiers
 
getParameters() - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
getParameters() - Method in class ambit2.db.substance.QueryCountBundles
 
getParameters() - Method in class ambit2.db.substance.QueryCountEndpoints
 
getParameters() - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
getParameters() - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
getParameters() - Method in class ambit2.db.substance.QueryCountSubstances
 
getParameters() - Method in class ambit2.db.substance.QueryCountSubstanceTypes
 
getParameters() - Method in class ambit2.db.substance.ReadByReliabilityFlags
 
getParameters() - Method in class ambit2.db.substance.ReadSubstance
 
getParameters() - Method in class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
getParameters() - Method in class ambit2.db.substance.ReadSubstanceByName
 
getParameters() - Method in class ambit2.db.substance.ReadSubstanceByOwner
 
getParameters() - Method in class ambit2.db.substance.ReadSubstanceByStudy
 
getParameters() - Method in class ambit2.db.substance.ReadSubstanceByType
 
getParameters() - Method in class ambit2.db.substance.ReadSubstances
 
getParameters() - Method in class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
getParameters(int) - Method in class ambit2.db.substance.relation.DeleteSubstanceRelation
 
getParameters() - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
getParameters() - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
getParameters(int) - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
getParameters(int) - Method in class ambit2.db.substance.study.DeleteEffectRecords
 
getParameters(int) - Method in class ambit2.db.substance.study.DeleteStudy
 
getParameters() - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
getParameters() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getParameters() - Method in class ambit2.db.substance.study.ReadEffectRecord
 
getParameters() - Method in class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
getParameters() - Method in class ambit2.db.substance.study.ReadSubstanceProperty
 
getParameters() - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
getParameters() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getParameters(int) - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
getParameters(int) - Method in class ambit2.db.substance.study.UpdateSubstanceStudy
 
getParameters(int) - Method in class ambit2.db.substance.UpdateSubstance
 
getParameters(int) - Method in class ambit2.db.update.bookmark.CreateBookmark
 
getParameters(int) - Method in class ambit2.db.update.bookmark.DeleteBookmark
 
getParameters() - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
getParameters() - Method in class ambit2.db.update.bookmark.ReadBookmark
 
getParameters(int) - Method in class ambit2.db.update.bookmark.UpdateBookmark
 
getParameters() - Method in class ambit2.db.update.bundle.BundleOwnerByNumber
 
getParameters(int) - Method in class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
getParameters() - Method in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.CreateBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
getParameters(int) - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
getParameters(int) - Method in class ambit2.db.update.bundle.DeleteBundle
 
getParameters() - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
getParameters() - Method in class ambit2.db.update.bundle.effects.ReadEffectRecordByBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
getParameters() - Method in class ambit2.db.update.bundle.endpoints.ReadEndpointsByBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixFromBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixProtocolApplicationValue
 
getParameters(int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixValue
 
getParameters() - Method in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
getParameters() - Method in class ambit2.db.update.bundle.ReadBundle
 
getParameters() - Method in class ambit2.db.update.bundle.ReadBundleVersion
 
getParameters(int) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
getParameters(int) - Method in class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
getParameters() - Method in class ambit2.db.update.bundle.substance.ReadSubstanceChemicalsUnionByBundle
 
getParameters() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
getParameters() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds
 
getParameters(int) - Method in class ambit2.db.update.bundle.UpdateBundle
 
getParameters(int) - Method in class ambit2.db.update.chemical.CreateChemical
 
getParameters(int) - Method in class ambit2.db.update.chemical.DeleteChemical
 
getParameters(int) - Method in class ambit2.db.update.chemical.UpdateChemical
 
getParameters(int) - Method in class ambit2.db.update.dataset.CreateDataset
 
getParameters(int) - Method in class ambit2.db.update.dataset.DatasetAddStructure
 
getParameters(int) - Method in class ambit2.db.update.dataset.DatasetDeleteStructure
 
getParameters() - Method in class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
getParameters(int) - Method in class ambit2.db.update.dataset.DeleteDataset
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCount
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCountChemicalInDataset
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCountDataset
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCountProperties
 
getParameters() - Method in class ambit2.db.update.dataset.QueryCountValues
 
getParameters() - Method in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
getParameters() - Method in class ambit2.db.update.dataset.ReadDataset
 
getParameters() - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
getParameters(int) - Method in class ambit2.db.update.dataset.UpdateDataset
 
getParameters(int) - Method in class ambit2.db.update.dictionary.CreateDictionary
 
getParameters(int) - Method in class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
getParameters(int) - Method in class ambit2.db.update.dictionary.DeleteDictionary
 
getParameters(int) - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
getParameters(int) - Method in class ambit2.db.update.dictionary.TemplateDeleteProperty
 
getParameters(int) - Method in class ambit2.db.update.fp.CreateFingerprintChemical
 
getParameters(int) - Method in class ambit2.db.update.fp.CreateFingerprintStructure
 
getParameters() - Method in class ambit2.db.update.fp.QueryFingerprints
 
getParameters() - Method in class ambit2.db.update.fp.ReadStructuresByFingerprint
 
getParameters(int) - Method in class ambit2.db.update.fpae.CreateAtomEnvironment
 
getParameters(int) - Method in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
getParameters(int) - Method in class ambit2.db.update.fpae.DeleteAtomEnvironment
 
getParameters(int) - Method in class ambit2.db.update.model.CreateModel
 
getParameters(int) - Method in class ambit2.db.update.model.DeleteModel
 
getParameters() - Method in class ambit2.db.update.model.QueryModel
 
getParameters() - Method in class ambit2.db.update.model.ReadModel
 
getParameters(int) - Method in class ambit2.db.update.model.UpdateModel
 
getParameters(int) - Method in class ambit2.db.update.property.CreateProperty
 
getParameters(int) - Method in class ambit2.db.update.property.CreatePropertyReferenceID
 
getParameters(int) - Method in class ambit2.db.update.property.DeleteProperty
 
getParameters() - Method in class ambit2.db.update.property.ReadProperty
 
getParameters(int) - Method in class ambit2.db.update.property.UpdateProperty
 
getParameters(int) - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
getParameters(int) - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
getParameters(int) - Method in class ambit2.db.update.propertyannotations.DeletePropertyAnnotation
 
getParameters() - Method in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
getParameters(int) - Method in class ambit2.db.update.propertyannotations.UpdatePropertyAnnotation
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateQLabelCAS
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateQLabelEINECS
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateQLabelFingerprints
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateQLabelPair
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateStructureQLabel
 
getParameters(int) - Method in class ambit2.db.update.qlabel.CreateValueQLabel
 
getParameters(int) - Method in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
getParameters(int) - Method in class ambit2.db.update.qlabel.DeleteValueQLabel
 
getParameters(int) - Method in class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
getParameters(int) - Method in class ambit2.db.update.qlabel.SmilesUniquenessCheck
 
getParameters(int) - Method in class ambit2.db.update.qlabel.ValuesQualityCheck
 
getParameters(int) - Method in class ambit2.db.update.queryfolder.CreateQueryFolder
 
getParameters(int) - Method in class ambit2.db.update.queryfolder.DeleteQueryFolder
 
getParameters() - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
getParameters(int) - Method in class ambit2.db.update.queryfolder.UpdateQueryFolder
 
getParameters(int) - Method in class ambit2.db.update.reference.CreateReference
 
getParameters(int) - Method in class ambit2.db.update.reference.DeleteReference
 
getParameters() - Method in class ambit2.db.update.reference.ReadReference
 
getParameters(int) - Method in class ambit2.db.update.reference.UpdateReference
 
getParameters(int) - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
getParameters(int) - Method in class ambit2.db.update.storedquery.DeleteStoredQuery
 
getParameters(int) - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
getParameters(int) - Method in class ambit2.db.update.storedquery.QueryAddTemplate
 
getParameters(int) - Method in class ambit2.db.update.storedquery.QueryDeleteStructure
 
getParameters(int) - Method in class ambit2.db.update.storedquery.QueryDeleteTemplate
 
getParameters() - Method in class ambit2.db.update.storedquery.ReadStoredQuery
 
getParameters() - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
getParameters(int) - Method in class ambit2.db.update.storedquery.SelectStoredQuery
 
getParameters(int) - Method in class ambit2.db.update.storedquery.UpdateSelectedRecords
 
getParameters(int) - Method in class ambit2.db.update.storedquery.UpdateStoredQuery
 
getParameters() - Method in class ambit2.db.update.structure.ChemicalByDataset
 
getParameters(int) - Method in class ambit2.db.update.structure.CreateStructure
 
getParameters(int) - Method in class ambit2.db.update.structure.CreateStrucType
 
getParameters(int) - Method in class ambit2.db.update.structure.DeleteStructure
 
getParameters(int) - Method in class ambit2.db.update.structure.UpdateStructure
 
getParameters(int) - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
getParameters(int) - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
getParameters(int) - Method in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
getParameters(int) - Method in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
getParameters() - Method in class ambit2.db.version.DBVersionQuery
 
getParameters() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getParameters() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getParameters() - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
getParameters() - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getParameters() - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getParameters() - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
getParameters() - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getParameters() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getParameters() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getParameters() - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getParameters() - Method in class ambit2.descriptors.InChI
 
getParameters() - Method in class ambit2.descriptors.MolecularWeight
Gets the parameters attribute of the WeightDescriptor object.
getParameters() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getParameters(Property) - Method in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
getParameters() - Method in class ambit2.descriptors.SizeDescriptor
 
getParameters() - Method in class ambit2.descriptors.SpherosityDescriptor
 
getParameters() - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getParameters() - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getParameters() - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getParameters() - Method in class ambit2.dragon.DescriptorDragonShell
 
getParameters() - Method in interface ambit2.groupcontribution.transformations.IValueTransformation
 
getParameters() - Method in class ambit2.groupcontribution.transformations.TransformationComposition
 
getParameters() - Method in class ambit2.groupcontribution.transformations.TransformationExp
 
getParameters() - Method in class ambit2.groupcontribution.transformations.TransformationLin
 
getParameters() - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
getParameters() - Method in class ambit2.groupcontribution.transformations.TransformationPow
 
getParameters() - Method in class ambit2.mopac.DescriptorMopacShell
 
getParameters() - Method in class ambit2.rendering.ImageMapGenerator
 
getParameters() - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
getParameters() - Method in class ambit2.some.DescriptorSOMEShell
 
getParametersAsArray() - Method in class ambit2.core.data.model.Algorithm
 
getParametersConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getParameterType(String) - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getParameterType(String) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getParameterType(String) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.InChI
 
getParameterType(String) - Method in class ambit2.descriptors.MolecularWeight
Gets the parameterType attribute of the WeightDescriptor object.
getParameterType(String) - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.SizeDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.SpherosityDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getParameterType(String) - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getParameterType(String) - Method in class ambit2.dragon.DescriptorDragonShell
 
getParameterType(String) - Method in class ambit2.mopac.DescriptorMopacShell
 
getParameterType(String) - Method in class ambit2.some.DescriptorSOMEShell
 
getParamName() - Method in class ambit2.rest.legacy.OTAlgorithms
Deprecated.
 
getParamName() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
getParamName() - Method in class ambit2.rest.legacy.OTDatasets
Deprecated.
 
getParamName() - Method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
getParams() - Method in interface ambit2.rules.functions.IFunction
 
getParams() - Method in class ambit2.rules.functions.LinearFunction
 
getParams() - Method in class ambit2.rules.functions.NestedFunctions
 
getParams() - Method in class ambit2.rules.functions.ReciprocalFunction
 
getParent() - Method in class ambit2.descriptors.PKANode
 
getParent(Component) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
getParentComponent() - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
getParentTemplate() - Method in class ambit2.base.data.Dictionary
 
getParser() - Method in class ambit2.core.smiles.SmilesParserWrapper
 
getParser() - Method in class ambit2.rendering.CompoundImageTools
 
getParser() - Method in class ambit2.smarts.groups.GroupMatch
 
getParserType() - Method in class ambit2.smarts.query.SmartsPatternFactory
 
getPartnerAtom() - Method in class ambit2.smarts.NodeExplorer
 
getPassword() - Method in class ambit2.base.data.AmbitUser
 
getPassword() - Method in class ambit2.db.LoginInfo
 
getPassword() - Method in class ambit2.db.results.AmbitRows
 
getPassword() - Method in class ambit2.dbui.LoginInfoBean
 
getPassword() - Method in class ambit2.rest.ProtectedResource
 
getPath(File) - Method in class ambit2.balloon.ShellBalloon
 
getPath(File) - Method in class ambit2.base.external.CommandShell
 
getPath(File) - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
getPath(File) - Method in class ambit2.dragon.AbstractDescriptorShell
 
getPath(File) - Method in class ambit2.mopac.AbstractMopacShell
 
getPath(File) - Method in class ambit2.some.SOMEShell
 
getPathLenght() - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
getPathString(IAtom[]) - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
getPca() - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
getPca() - Method in class ambit2.rest.task.weka.WekaPredictor
 
getPctCorrect() - Method in class ambit2.model.evaluation.EvaluationStats
 
getPctInCorrect() - Method in class ambit2.model.evaluation.EvaluationStats
 
getPercentage() - Method in interface ambit2.rules.miscellaneous.IProgress
 
getPercentCompleted() - Method in class ambit2.rest.task.Task
 
getPercentCompleted() - Method in class ambit2.rest.task.TaskResult
 
getPka() - Method in class ambit2.descriptors.PKANode
 
getPka_range() - Method in class ambit2.descriptors.PKANode
 
getPoints() - Method in class ambit2.model.numeric.DataCoverage
 
getPolicy() - Method in class ambit2.rest.task.TaskResult
 
getPolicyError() - Method in class ambit2.rest.task.Task
 
getPolicyService() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getPort() - Method in class ambit2.db.LoginInfo
 
getPort() - Method in class ambit2.dbui.LoginInfoBean
 
getPos(int, int[]) - Static method in class ambit2.smarts.ChiralPermutations
 
getPositionDistance(int) - Method in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
getPredefinedLocalDescriptors() - Static method in class ambit2.groupcontribution.descriptors.LocalDescriptorManager
 
getPredicate() - Method in class ambit2.base.data.PropertyAnnotation
 
getPredicted() - Method in class ambit2.core.data.model.ModelWrapper
 
getPredicted() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
getPredicted() - Method in interface ambit2.model.IDataset
 
getPredicted() - Method in class ambit2.similarity.stats.ValuePair
 
getPredictedVariables() - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Predicted variables
getPredictedVariables() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getPredictionFeature(Form) - Method in class ambit2.rest.task.CallableBuilder
 
getPredictor() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getPredictor() - Method in class ambit2.rest.model.task.CallableModelPredictor
 
getPredictors() - Method in class ambit2.core.data.model.ModelWrapper
 
getPreferredNameExtension() - Method in class ambit2.core.io.DelimitedFileFormat
 
getPreferredNameExtension() - Method in class ambit2.core.io.XLSFileFormat
 
getPrefix() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
 
getPrefix() - Method in class ambit2.base.data.study.StructureRecordValidator
 
getPrefix() - Method in class ambit2.rest.structure.CompoundURIReporter
 
getPrefixedUUID(Object, Object) - Static method in class ambit2.base.data.I5Utils
IUCLID style UUID
getPriorityScore() - Method in class ambit2.reactions.GenericReaction
 
getProbability(double) - Method in class ambit2.tautomers.TautomerRanking
 
getProbabilityDistribution(List<IAtomContainer>) - Method in class ambit2.tautomers.TautomerRanking
 
getProcessorChain() - Method in interface ambit2.base.interfaces.IBatchProcessor
 
getProcessorChain() - Method in class ambit2.base.processors.batch.BatchProcessor
 
getProcessors() - Method in class ambit2.base.processors.batch.BatchReporter
 
getProducts() - Method in class ambit2.reactions.Reaction
 
getProfile() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
getProfile() - Method in class ambit2.db.search.property.ValuesReader
 
getProfile() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
getProfile() - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
getProfile() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
getProperties() - Static method in class ambit2.base.config.Preferences
 
getProperties(boolean) - Method in class ambit2.base.data.Profile
 
getProperties() - Method in class ambit2.core.io.SimpleIOListener
 
getProperties() - Method in class ambit2.ui.AmbitSettingsListener
 
getProperties() - Static method in class ambit2.ui.EditorPreferences
 
getProperties() - Method in class ambit2.vega.VegaShell
 
getPropertiesAsString() - Method in class ambit2.groupcontribution.dataset.DataSetObject
 
getProperty(String) - Static method in class ambit2.base.config.Preferences
 
getProperty() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
 
getProperty(String) - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
 
getProperty() - Method in class ambit2.base.data.PropertyTemplateStats
 
getProperty() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
getProperty(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PropertyKey
 
getProperty() - Method in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
getProperty() - Method in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
getProperty() - Method in class ambit2.db.chart.PieChartGenerator
 
getProperty() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
getProperty() - Method in class ambit2.db.processors.quality.QualityValueWriter
 
getProperty() - Method in class ambit2.db.readers.PropertyValue
 
getProperty() - Method in enum ambit2.db.reporters.SmilesReporter.Mode
 
getProperty() - Method in class ambit2.db.search.property.FilteredCount
 
getProperty() - Method in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
getProperty() - Method in class ambit2.db.simiparity.space.QMap
 
getProperty() - Method in class ambit2.db.update.qlabel.ValuesQualityCheck
 
getProperty() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
getProperty() - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
getProperty() - Method in class ambit2.descriptors.processors.BitSetGenerator
 
getProperty() - Method in enum ambit2.descriptors.processors.FPTable
 
getProperty() - Method in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
getProperty() - Method in class ambit2.rendering.CachedImage
 
getProperty(String) - Method in class ambit2.rest.DBConnection
 
getProperty(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
getProperty(Model) - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
getProperty() - Method in class ambit2.similarity.measure.DistanceComparable
 
getProperty() - Method in class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
getProperty() - Method in class ambit2.smarts.processors.SMARTSPropertiesReader
 
getProperty(String) - Static method in class ambit2.ui.EditorPreferences
 
getPropertyChangeSupport() - Static method in class ambit2.base.config.Preferences
 
getPropertyChangeSupport() - Static method in class ambit2.ui.EditorPreferences
 
getPropertyDoubleValue(String) - Method in class ambit2.groupcontribution.dataset.DataSetObject
 
getPropertyHeader(Property) - Method in class ambit2.db.reporters.ARFFReporter
 
getPropertyIterator(Model) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
getPropertyIterator(Model) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
getPropertyKey() - Method in class ambit2.db.processors.PropertyImporter
 
getPropertyKey() - Method in class ambit2.db.processors.RepositoryWriter
 
getPropertyname() - Method in class ambit2.db.results.AmbitRows
 
getPropertyNames(Target) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
getPropertyNames(DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
getPropertyNames(DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorWriter
 
getPropertyNames(IStructureRecord) - Method in class ambit2.db.processors.PropertyValuesWriter
 
getPropertyNames(DescriptorValue) - Method in class ambit2.descriptors.processors.DescriptorValue2Property
 
getPropertyNames() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
getPropertyNode(Property, RDFNode) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
getPropertyQuery() - Method in class ambit2.db.readers.ValuesByTemplateReader
 
getPropertyReporter() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getPropertyReporter() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
getPropertySQL() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getPropertyType() - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
getPropertyValue(Property, RDFNode) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
getPropertyWhere() - Method in class ambit2.db.readers.RetrieveProfileValues
 
getPropertyWhere() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getPropertyX() - Method in class ambit2.db.chart.BarChartGenerator
 
getPropertyX() - Method in class ambit2.db.chart.PropertiesChartGenerator
 
getPropertyX() - Method in class ambit2.db.chart.XTabChartGenerator
 
getPropertyY() - Method in class ambit2.db.chart.BarChartGenerator
 
getPropertyY() - Method in class ambit2.db.chart.PropertiesChartGenerator
 
getPropertyY() - Method in class ambit2.db.chart.XTabChartGenerator
 
getProtocol(String) - Method in enum ambit2.base.data.study.Protocol._categories
 
getProtocol() - Method in class ambit2.base.data.study.ProtocolApplication
"protocol": { ...
getProtocol() - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
getProtocolapp_remarks() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
getProtocolConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getPThreshold() - Method in class ambit2.model.numeric.DataCoverage
 
getPThreshold() - Method in interface ambit2.model.numeric.IDataCoverage
 
getPublicName() - Method in class ambit2.base.data.SubstanceRecord
Public name of the substance
getPurposeFlag() - Method in class ambit2.base.data.study.ReliabilityParams
 
getQ2F1(MatrixDouble, MatrixDouble, double) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getQ2F2(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getQ2F3(MatrixDouble, MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getQmap() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getQModifier() - Method in class ambit2.db.search.structure.QueryAtomEnvironment
 
getQueries() - Method in class ambit2.db.search.QueryCombined
 
getQuery() - Method in class ambit2.db.processors.ProcessorSetQueryScope
 
getQuery() - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
getQuery(IStructureRecord) - Method in class ambit2.db.processors.RepositoryWriter
 
getQuery() - Method in class ambit2.db.results.AmbitRows
 
getQuery() - Method in enum ambit2.db.results.StoredQueryTableModel.FIELDS
 
getQuery() - Method in class ambit2.db.results.StoredQueryTableModel
 
getQuery() - Method in interface ambit2.db.search.IStoredQuery
 
getQuery() - Method in class ambit2.db.search.property.FilteredCount
 
getQuery() - Method in class ambit2.db.search.StoredQuery
 
getQuery() - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
getQuery() - Method in class ambit2.descriptors.FunctionalGroup
 
getQuery(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getQuery(Form) - Method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
getQuery() - Method in class ambit2.rest.wrapper.WrappedService
 
getQuery() - Method in class ambit2.smarts.query.FastSmartsMatcher
 
getQuery() - Method in interface ambit2.smarts.query.ISmartsPattern
 
getQuery() - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
getQuery() - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getQueryAtomContainer(IAtomContainer, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
getQueryContaner() - Method in class ambit2.smarts.SmartsManager
 
getQueryCreate() - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
getQueryDelete() - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
getQueryID() - Method in class ambit2.core.data.model.ModelWrapper
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.ChEMBLCompoundURI
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.DSSToxID
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.EmptyKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.InchiKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey
 
getQueryKey() - Method in interface ambit2.core.processors.structure.key.IStructureKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.NameKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.PropertyKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.PropertyNameKey
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.PubchemCID
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.PubchemSID
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
getQueryKey() - Method in class ambit2.core.processors.structure.key.SmilesKey
 
getQueryName() - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
getQueryName() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
getQueryName() - Method in class ambit2.db.reporters.AbstractImageReporter
 
getQueryObject(Reference, Reference, Context, Series<Cookie>, String, String) - Static method in class ambit2.rest.task.CallableQueryProcessor
 
getQueryObject(Reference, Reference, Context, String, String, String) - Static method in class ambit2.rest.task.CallableQueryProcessor
 
getQueryOperator() - Method in class ambit2.core.groups.DataGroup
 
getQueryString(OTDataset, boolean, OTFeatures, boolean, OTFeatures, String, int, int, String) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getQueryTimeout() - Method in class ambit2.db.results.AmbitRows
 
getQueryType() - Method in class ambit2.core.groups.DataGroup
 
getQueryUpdate() - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
getR2(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getRandomPermutation(int) - Method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
getRandomSelection(Map<GenericReaction, List<List<IAtom>>>) - Static method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
getRangeTitle(ISourceDataset) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
getRank() - Method in class ambit2.structure2name.components.AbstractComponent
 
getRank() - Method in interface ambit2.structure2name.components.IIUPACComponent
 
getRanks(double[], boolean) - Static method in class ambit2.tautomers.tools.TautomerAnalysis
 
getRawFingerprint(IAtomContainer) - Method in class ambit2.core.data.HashIntDescriptorResult
 
getRawFingerprint(IAtomContainer) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getRawFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.CircularFingerprintInterpretable
 
getRawFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
getRawReader(InputStream, String, IChemFormat) - Static method in class ambit2.core.io.FileInputState
 
getRDFwriter() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getReactants() - Method in class ambit2.reactions.Reaction
 
getReactDB() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getReaction() - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
getReactionByID(int) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
getReactionCenterIndices() - Method in class ambit2.reactions.GenericReaction
 
getReactionClass() - Method in class ambit2.reactions.GenericReaction
 
getReactionClass() - Method in class ambit2.reactions.Reaction
 
getReactionClass() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getReactionDataBase() - Method in class ambit2.reactions.reactor.Reactor
 
getReactionFromJsonNode(JsonNode) - Static method in class ambit2.reactions.GenericReaction
 
getReactionFromTokens(String[], Map<String, Integer>) - Static method in class ambit2.reactions.GenericReaction
 
getReactionGroups() - Method in class ambit2.reactions.sets.ReactionSet
 
getReactionInstance() - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
getReactionKnowledgeBase() - Method in class ambit2.reactions.retrosynth.RetroSynthesis
 
getReactionMapping(IAtomContainer, IAtomContainer) - Method in class ambit2.reactions.mapping.ReactionAtomMapping
 
getReactions() - Method in class ambit2.reactions.sets.ReactionGroup
 
getReactions() - Method in class ambit2.reactions.sets.ReactionSet
 
getReactionScore() - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
getReactionSequence() - Method in interface ambit2.reactions.retrosynth.IReactionSequenceHandler
 
getReactionSequenceHandler() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getReactionsMetaInfo() - Static method in class ambit2.reactions.io.ReactionReadUtils
 
getReactionType() - Method in class ambit2.reactions.GenericReaction
 
getReader() - Method in class ambit2.core.io.FileInputState
 
getReader(File) - Static method in class ambit2.core.io.FileInputState
 
getReader(InputStream, String) - Static method in class ambit2.core.io.FileInputState
 
getReader(File, IChemFormat) - Static method in class ambit2.core.io.FileInputState
 
getReader(InputStream, String, IChemFormat) - Static method in class ambit2.core.io.FileInputState
 
getReader() - Method in interface ambit2.core.io.IInputState
 
getReader() - Method in class ambit2.core.processors.batch.DefaultInputState
 
getReader(InputStream, String) - Static method in class ambit2.groupcontribution.dataset.DataSet
 
getReader(InputStream, String) - Method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
getReader(InputStream, String) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
getReaderClassName() - Method in class ambit2.core.io.DelimitedFileFormat
 
getReaderClassName() - Method in class ambit2.core.io.XLSFileFormat
 
getReal_lower() - Method in class ambit2.base.relation.composition.Proportion
 
getReal_lowervalue() - Method in class ambit2.base.relation.composition.Proportion
 
getReal_unit() - Method in class ambit2.base.relation.composition.Proportion
 
getReal_upper() - Method in class ambit2.base.relation.composition.Proportion
 
getReal_uppervalue() - Method in class ambit2.base.relation.composition.Proportion
 
getRecalls() - Method in class ambit2.base.data.Bookmark
 
getReciprocalDistanceMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getRecord() - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
getRecord() - Method in class ambit2.db.readers.RetrieveProfileValues
 
getRecord() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getRecord() - Method in class ambit2.db.readers.RetrieveTemplateStructure
 
getRecord(int, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
getRecord() - Method in class ambit2.db.simiparity.space.QMapSpace
 
getRecord() - Method in class ambit2.db.substance.AbstractReadSubstance
 
getRecord() - Method in class ambit2.db.substance.FacetedSearchSubstance
 
getRecord() - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
getRecord() - Method in class ambit2.db.substance.ReadByReliabilityFlags
 
getRecord() - Method in class ambit2.db.substance.ReadSubstance
 
getRecord() - Method in class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
getRecord() - Method in class ambit2.db.substance.ReadSubstanceByName
 
getRecord() - Method in class ambit2.db.substance.ReadSubstanceByOwner
 
getRecord() - Method in class ambit2.db.substance.ReadSubstanceByStudy
 
getRecord() - Method in class ambit2.db.substance.ReadSubstanceByType
 
getRecord() - Method in class ambit2.db.substance.ReadSubstances
 
getRecord() - Method in class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
getRecord() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getRecord() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getRecord() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
getRecord() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds
 
getRecord() - Method in class ambit2.ui.table.BrowsableTableModel
 
getRecord() - Method in interface ambit2.ui.table.IRecordNavigator
 
getRecordLocationAsIdentifier() - Method in class ambit2.export.isa.base.ExternalDataFileLocation
 
getRecordMarker(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
getRecordProperties() - Method in class ambit2.base.data.StructureRecord
 
getRecordProperties() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getRecordProperties() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getRecordProperty(Property) - Method in class ambit2.base.data.StructureRecord
 
getRecordProperty(Property) - Method in interface ambit2.base.interfaces.IStructureRecord
 
getRecordProperty(Property) - Method in class ambit2.base.relation.composition.CompositionRelation
 
getRecords() - Method in class ambit2.base.processors.StructureRecordsAppender
 
getRecords() - Method in class ambit2.dbui.CachedRowSetTableModel
 
getRecords() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getRecords() - Method in class ambit2.ui.table.StructureRecordsTableModel
 
getRecords_to_delete() - Method in class ambit2.base.data.study.ProtocolApplicationAnnotated
 
getRecordsNumber() - Method in class ambit2.db.results.ResultSetTableModel
 
getRecordType() - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
getRecordURI(QuerySolution) - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
This is considered record ID
getRecursiveAtoms(IQueryAtomContainer) - Method in class ambit2.smarts.groups.GroupMatch
 
getRecursiveAtoms(IQueryAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
getRecursiveExpressionAtomType(SmartsAtomExpression, int) - Method in class ambit2.smarts.SmartsToChemObject
 
getRef(int) - Method in class ambit2.db.results.AmbitRows
 
getRef(String) - Method in class ambit2.db.results.AmbitRows
 
getReference() - Method in class ambit2.base.data.Property
 
getReference() - Method in class ambit2.base.data.SourceDataset
 
getReference() - Method in class ambit2.base.data.StructureRecord
 
getReference() - Method in class ambit2.base.data.study.ProtocolApplication
 
getReference() - Method in interface ambit2.base.interfaces.ICiteable
 
getReference() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getReference() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getReference() - Method in class ambit2.core.io.I5ReaderSimple
 
getReference() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
getReference() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getReference() - Method in class ambit2.core.io.IteratingXLSReader
 
getReference() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
getReference() - Method in class ambit2.core.io.RawIteratingCSVReader
 
getReference() - Method in class ambit2.core.io.RawIteratingReader
 
getReference() - Method in class ambit2.core.io.RawIteratingWrapper
 
getReference(ProtocolEffectRecord<String, IParams, String>) - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
getReference() - Method in class ambit2.db.processors.BatchDBProcessor
 
getReference() - Method in class ambit2.rest.task.TaskResult
 
getReferenceID() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getReferenceOwner() - Method in class ambit2.base.data.study.ProtocolApplication
 
getReferenceSubstanceUUID() - Method in class ambit2.base.data.study.ProtocolApplication
 
getReferenceSubstanceUUID() - Method in class ambit2.base.data.SubstanceRecord
referenceSubstance (link to reference structure).Typical use IStructureRecord
getReferenceUUID() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getReferenceYear() - Method in class ambit2.base.data.study.ProtocolApplication
 
getRelatedStructures() - Method in class ambit2.base.data.SubstanceRecord
CompositionRelation
getRelation() - Method in interface ambit2.base.interfaces.IStructureRelation
 
getRelation() - Method in class ambit2.base.relation.AbstractRelation
 
getRelation() - Method in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
getRelation() - Method in interface ambit2.rules.conditions.value.IValue
 
getRelation() - Method in class ambit2.rules.conditions.value.Value
 
getRelationFromString(String) - Static method in enum ambit2.rules.conditions.value.IValue.Relation
 
getRelationGraphAsString(boolean) - Method in class ambit2.tautomers.TautomerRelationGraph
 
getRelationGraphAsString(boolean, TautomerRelationGraph.StructureFormat) - Method in class ambit2.tautomers.TautomerRelationGraph
 
getRelationName() - Method in class ambit2.db.reporters.ARFF3ColReporter
 
getRelationName() - Method in class ambit2.db.reporters.ARFFReporter
 
getRelationship() - Method in class ambit2.base.data.Dictionary
 
getRelationString() - Method in enum ambit2.rules.conditions.value.IValue.Relation
 
getRelationType() - Method in interface ambit2.base.interfaces.IStructureRelation
 
getRelationType() - Method in class ambit2.base.relation.AbstractRelation
 
getRelativeAtomicWeights(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
getRelativeURI() - Method in class ambit2.base.data.Property
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstanceName
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstanceOwner
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstanceProperty
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstancePropertyCategory
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstancePublicName
 
getRelativeURI() - Method in class ambit2.base.data.substance.SubstanceUUID
 
getRelevance() - Method in class ambit2.base.data.Bookmark
 
getReliability() - Method in class ambit2.base.data.study.ProtocolApplication
"reliability": {}
getReliabilityScore() - Method in class ambit2.reactions.GenericReaction
 
getRemark() - Method in class ambit2.base.data.study.ValueAnnotated
 
getRemarks() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
getRemarks() - Method in class ambit2.base.facet.BundleRoleFacet
 
getRendererModel() - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
Returns the current RendererModel.
getReport() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getReportConfig() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getReportLevel() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getRepresentation(String) - Method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_INPUT
 
getRepresentation() - Method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OUTPUT
 
getRepresentation(Variant) - Method in class ambit2.rest.AbstractResource
 
getRepresentation() - Method in exception ambit2.rest.exception.RResourceException
 
getRepresentation(Variant) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
getRepresentation(Status, Request, Response) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
getRepresentation() - Method in class ambit2.search.csls.CSLSRequest
 
getRequest() - Method in class ambit2.rest.reporters.CatalogURIReporter
 
getRequestref() - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getRequestref() - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
getRequiredDataFeatures() - Method in class ambit2.core.io.DelimitedFileFormat
 
getRequiredDataFeatures() - Method in class ambit2.core.io.XLSFileFormat
 
getRequirement() - Method in class ambit2.core.data.model.Algorithm
 
getResolutionStep() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getResource(Model) - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
getResourceBundle() - Static method in class ambit2.core.config.Resources
 
getResourceID() - Method in enum ambit2.rest.OpenTox.URI
 
getResourceRef(Request) - Method in class ambit2.rest.ProtectedResource
 
getResourceRef() - Method in class ambit2.rest.reporters.CatalogURIReporter
 
getResponseType() - Method in interface ambit2.base.interfaces.IInputOutputState
 
getResponseType() - Method in class ambit2.core.io.FileState
 
getResponseType() - Method in class ambit2.core.processors.batch.DefaultIOState
 
getResult(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
getResult() - Method in class ambit2.db.substance.study.facet.ResultsCountFacet
 
getResult() - Method in class ambit2.descriptors.VerboseDescriptorResult
 
getResult() - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
getResult() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
getResult() - Method in interface ambit2.rules.actions.IAction
 
getResult() - Method in class ambit2.similarity.AbstractSimilarityModel
 
getResultAsJson() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getResultConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getResultDir() - Method in class ambit2.pubchem.BatchRetrievePubChem
 
getResultFile(String, File) - Method in class ambit2.pubchem.BatchRetrievePubChem
 
getResults() - Method in class ambit2.core.data.HashDescriptorResult
 
getResultSet() - Method in class ambit2.db.DbReader
 
getResultSet() - Method in class ambit2.db.results.ResultSetTableModel
 
getResultsURL(String...) - Method in class ambit2.base.facet.AbstractFacet
 
getResultsURL(String...) - Method in class ambit2.base.facet.BundleRoleFacet
 
getResultsURL(String...) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
getResultsURL(String...) - Method in class ambit2.db.facets.bundle.BundleSummaryFacet
 
getResultsURL(String...) - Method in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
getResultsURL(String...) - Method in class ambit2.db.facets.datasets.EndpointCompoundFacet
params[0] root URL params[1] full compound URL
getResultsURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetConsensusLabelFacet
 
getResultsURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetStructureQLabelFacet
 
getResultsURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeFacet
 
getResultType() - Method in class ambit2.db.search.QueryExecutor
 
getResultTypeConcurency() - Method in class ambit2.db.search.QueryExecutor
 
getRetrieveConformers(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getRetrieveSDF(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getRetroSynthRuleMetaInfo() - Static method in class ambit2.reactions.rules.ReactionParser
 
getRight() - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
getrightsHolder() - Method in class ambit2.base.data.AbstractDataset
 
getrightsHolder() - Method in interface ambit2.base.data.ISourceDataset
 
getrightsHolder() - Method in class ambit2.base.data.SourceDataset
 
getrightsHolder() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getrightsHolder() - Method in class ambit2.db.search.StoredQuery
 
getRindData(IAtomContainer, IRingSet) - Static method in class ambit2.smarts.SmartsParser
 
getRindData2(IAtomContainer, IRingSet) - Static method in class ambit2.smarts.SmartsParser
 
getRingNumber(IAtomContainer) - Method in class ambit2.structure2name.IUPACNameGenerator
 
getRingNumberInRingSet(IAtomContainer, IRingSet) - Static method in class ambit2.smarts.SmartsParser
 
getRingSet() - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
getRMSE() - Method in class ambit2.model.evaluation.EvaluationStats
 
getRow() - Method in class ambit2.db.results.AmbitRows
 
getRowCount() - Method in class ambit2.base.data.PropertiesTableModel
 
getRowCount() - Method in class ambit2.db.results.StoredQueryTableModel
 
getRowCount() - Method in class ambit2.dbui.CachedRowSetTableModel
 
getRowCount() - Method in class ambit2.similarity.stats.ConfusionMatrix
 
getRowCount() - Method in class ambit2.ui.table.BrowsableTableModel
 
getRowCount() - Method in class ambit2.ui.table.StructureRecordsTableModel
 
getRows() - Method in interface ambit2.db.search.IStoredQuery
 
getRows() - Method in class ambit2.db.search.StoredQuery
 
getRowSet() - Method in class ambit2.db.results.AmbitRows
 
getRowSetWarnings() - Method in class ambit2.db.results.AmbitRows
 
getRSS(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getRule() - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
getRule() - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
getRule() - Method in class ambit2.tautomers.CombinedRuleInstance
 
getRule() - Method in interface ambit2.tautomers.IRuleInstance
 
getRule() - Method in class ambit2.tautomers.RuleInstance
 
getRuleDataBase() - Method in class ambit2.structure2name.IUPACNameGenerator
 
getRuleInstanceScore(IRetroSynthRuleInstance, IAtomContainer) - Method in interface ambit2.reactions.rules.IStrategyRule
 
getRuleNumberLimit() - Method in class ambit2.tautomers.RuleSelector
 
getRules() - Static method in class ambit2.reactions.fragmentation.DefaultFragmentationRules
 
getRuleScore(IAtomContainer) - Method in interface ambit2.reactions.rules.IStrategyRule
 
getRuleSelector() - Method in class ambit2.tautomers.TautomerManager
 
getSameAs() - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
getSampleID() - Method in class ambit2.base.data.study.EffectRecord
 
getScale(int) - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
getScale(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
 
getScheme() - Method in class ambit2.db.LoginInfo
 
getScheme() - Method in class ambit2.dbui.LoginInfoBean
 
getScope() - Method in class ambit2.core.data.model.Parameter
 
getScope() - Method in class ambit2.db.search.QueryCombined
 
getScope() - Method in class ambit2.db.search.QueryInfo
 
getScopeSQL() - Method in class ambit2.db.search.QueryCombined
 
getScopeSQL() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
getScore(IAtomContainer) - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
getScore(IAtomContainer) - Method in class ambit2.reactions.generator.score.components.KnimeWorkflowScore
 
getScore(IAtomContainer) - Method in interface ambit2.reactions.generator.score.IScoreComponent
 
getScore(IAtomContainer) - Method in class ambit2.reactions.generator.score.ScoreFunction
 
getScore() - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
getScore() - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
getScreeningDataForTarget(IAtomContainer) - Method in class ambit2.smarts.Screening
The ScreeningData for the target structure
getSD() - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
getSD() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
getSD() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
getSD() - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
getSD() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getSD() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getSD() - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
getSDFContent(IStructureRecord) - Method in class ambit2.db.reporters.SDFReporter
 
getSearchMode() - Method in class ambit2.db.readers.RetrieveField
 
getSearchMode() - Method in class ambit2.db.readers.RetrieveProfileValues
 
getSearchMode() - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
getSearchPropertyID() - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
getSearchReference(Context, Request, Response) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
getSearchServiceURI(String) - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getSecondStructure() - Method in interface ambit2.base.interfaces.IStructureRelation
 
getSecondStructure() - Method in class ambit2.base.relation.AbstractRelation
 
getSecret() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getSeeAlso() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
getSelected() - Method in class ambit2.base.data.SelectionBean
 
getSelected() - Method in class ambit2.ui.editors.ListEditor
 
getSelectedAttributes(Features) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
getSelectedAttributes(AtomEnvironmentList) - Method in class ambit2.similarity.knn.NNAtomEnvironmentSimilarity
 
getSelectedAttributes(BitSet) - Method in class ambit2.similarity.knn.NNFingerprintSimilarity
 
getSelectedColor() - Method in class ambit2.ui.ImageCellRenderer
 
getSelectedItem() - Method in class ambit2.ui.HeaderComboBoxModel
 
getSelectedPartColor(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.getSelectedPartColor()
getSelection() - Method in interface ambit2.base.data.ISelectableRecords
 
getSelection() - Method in class ambit2.db.results.StoredQueryTableModel
 
getSelection() - Method in class ambit2.ui.table.BrowsableTableModel
 
getSelectionMode() - Method in class ambit2.tautomers.RuleSelector
 
getSelectionOrder() - Method in class ambit2.tautomers.RuleSelector
 
getSelectionRadius(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
 
getSelectionShape(RendererModel) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.getSelectionShape()
getSelector() - Method in class ambit2.ui.Panel2D
 
getSelf() - Method in class ambit2.similarity.stats.SelfBin
 
getSeparator() - Method in class ambit2.db.reporters.CSVReporter
 
getSequence() - Method in class ambit2.smarts.groups.GroupMatch
 
getSequence() - Method in class ambit2.smarts.IsomorphismTester
 
getSequence() - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
getServer() - Method in class ambit2.pubchem.DepictRequest
 
getService() - Method in class ambit2.rest.wrapper.WrappedService
 
getSession() - Method in class ambit2.db.processors.DBProcessorsChain
 
getSession() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
getSetting(String) - Method in class ambit2.core.io.IteratingFileReader
 
getSetting(String, Class<S>) - Method in class ambit2.core.io.IteratingFileReader
 
getSetting(String) - Method in class ambit2.core.io.RawIteratingWrapper
 
getSetting(String, Class<S>) - Method in class ambit2.core.io.RawIteratingWrapper
 
getSetting(String) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getSetting(String, Class<S>) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getSettings() - Method in class ambit2.core.io.IteratingFileReader
 
getSettings() - Method in class ambit2.core.io.RawIteratingWrapper
 
getSettings() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
getSheet() - Method in class ambit2.core.io.XLSFileWriter
 
getShort(int) - Method in class ambit2.db.results.AmbitRows
 
getShort(String) - Method in class ambit2.db.results.AmbitRows
 
getShortName() - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
getShortName() - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
getShortName() - Method in enum ambit2.tautomers.TautomerConst.GAT
 
getShortName() - Method in enum ambit2.tautomers.TautomerConst.RSM
 
getShortString(ReactionSequence.MoleculeStatus) - Static method in enum ambit2.reactions.retrosynth.ReactionSequence.MoleculeStatus
 
getShowDeleted() - Method in class ambit2.db.results.AmbitRows
 
getSimilarityColumn() - Method in class ambit2.db.reporters.CSVReporter
 
getSimilarityOrderOption() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getSimilarityThreshold() - Method in class ambit2.db.simiparity.space.QMap
 
getSimMatrixFormat() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
getSimMatrixFormat() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
getSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getSingleElectronCount() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getSingleElectronNumber(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer
 
getSize() - Method in class ambit2.base.data.ProfileListModel
 
getSize() - Method in class ambit2.core.data.HashIntDescriptorResult
 
getSize() - Method in class ambit2.core.smiles.OpenBabelDepiction
 
getSize() - Method in class ambit2.db.results.MemoryRowsModel
 
getSize() - Method in class ambit2.db.results.RowsModel
 
getSize() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getSize() - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinter
 
getSize() - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
Get the size of the fingerprint.
getSize() - Method in class ambit2.descriptors.IsotopeFactory
Returns the number of isotopes defined by this class.
getSize() - Method in class ambit2.ui.HeaderComboBoxModel
 
getSizeDescriptorResult(IAtomContainer) - Method in class ambit2.descriptors.SpherosityDescriptor
 
getSlnObjectType() - Method in class ambit2.sln.SLNContainer
 
getSmarts() - Method in class ambit2.descriptors.FunctionalGroup
 
getSmarts() - Method in class ambit2.descriptors.PKANode
 
getSmarts() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getSmarts() - Method in class ambit2.smarts.groups.GroupMatch
 
getSmarts() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
getSmarts() - Method in interface ambit2.smarts.query.ISmartsPattern
 
getSmarts() - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getSmartsParser() - Method in class ambit2.smarts.SMIRKSManager
 
getSmartsPositions(String, IAtomContainer, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
getSmartsQuery() - Method in class ambit2.smarts.groups.GroupMatch
 
getSmartsToChemObjectConvertor() - Method in class ambit2.smarts.SMIRKSReaction
 
getSmiles() - Method in class ambit2.base.data.StructureRecord
 
getSMILES() - Method in enum ambit2.base.data.substance.ParticleTypes
 
getSmiles() - Method in interface ambit2.base.interfaces.IChemical
 
getSmiles() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getSmiles() - Method in class ambit2.db.search.QueryInfo
 
getSMILES(IAtomContainer) - Method in class ambit2.smarts.ChemObjectToSmiles
 
getSmilesGenerator() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
getSmilesHeader(int) - Method in class ambit2.core.io.IteratingDelimitedFileReader
 
getSmilesHeader(int) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
getSMILESInstance() - Static method in class ambit2.base.data.Property
 
getSmirks() - Method in class ambit2.reactions.GenericReaction
 
getSmirks() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getSmirks() - Method in class ambit2.reactions.sets.ReactionData
 
getSMIRKS() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
getSmirksFlag() - Method in class ambit2.reactions.GenericReaction
 
getSMIRKSManager() - Method in class ambit2.reactions.reactor.Reactor
 
getSmirksReaction() - Method in class ambit2.reactions.GenericReaction
 
getSmrkMan() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getSolrServices() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
getSolvers() - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
getSortedCodesIndices(int[]) - Static method in class ambit2.smarts.AtomEquivalenceInfo
 
getSortedCodesIndices(List<Integer>) - Static method in class ambit2.smarts.AtomEquivalenceInfo
 
getSortingOrder() - Method in enum ambit2.base.data.study.Protocol._categories
 
getSortingOrder() - Method in class ambit2.base.facet.SubstanceStudyFacet
 
getSource() - Method in class ambit2.base.data.AbstractDataset
 
getSource() - Method in interface ambit2.base.data.ISourceDataset
 
getSource() - Method in class ambit2.base.data.SourceDataset
 
getSource() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getSource() - Method in class ambit2.db.search.StoredQuery
 
getSource(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getSource() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
getSparql(String) - Static method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getSparseFingerprint(IAtomContainer) - Method in class ambit2.descriptors.fingerprints.CircularFingerprintInterpretable
 
getSparseFingerprint(IAtomContainer) - Method in interface ambit2.descriptors.fingerprints.ISparseFingerprint
 
getSpecification() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getSpecification() - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
getSpecification() - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
getSpecification() - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.AtomCountHybridizationDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.AverageMolecularWeightDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.CubicRootMolecularWeightDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.HeteroAtomCountDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
getSpecification() - Method in class ambit2.descriptors.constitutional.SquareRootMolecularWeightDescriptor
 
getSpecification() - Method in class ambit2.descriptors.CrossSectionalDiameterDescriptor
 
getSpecification() - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
getSpecification() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
getSpecification() - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
getSpecification() - Method in class ambit2.descriptors.InChI
 
getSpecification() - Method in class ambit2.descriptors.MaximumDiameterDescriptor
 
getSpecification() - Method in class ambit2.descriptors.MolecularWeight
 
getSpecification() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getSpecification() - Method in class ambit2.descriptors.PlanarityDescriptor
 
getSpecification() - Method in class ambit2.descriptors.SizeDescriptor
 
getSpecification() - Method in class ambit2.descriptors.SpherosityDescriptor
 
getSpecification() - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
getSpecification() - Method in class ambit2.descriptors.topological.CTIDescriptor
 
getSpecification() - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
getSpecification() - Method in class ambit2.dragon.DescriptorDragonShell
 
getSpecification() - Method in class ambit2.mopac.DescriptorMopacShell
 
getSpecification() - Method in class ambit2.mopac.MopacOriginalStructure
 
getSpecification() - Method in class ambit2.some.DescriptorSOMEShell
 
getSQL() - Method in class ambit2.db.cache.QueryCachedResults
 
getSQL() - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
getSQL(T) - Method in class ambit2.db.chart.BarChartGenerator
 
getSQL(ISourceDataset) - Method in class ambit2.db.chart.BarChartGeneratorDataset
 
getSQL() - Method in class ambit2.db.chart.FingerprintHistogramDataset
 
getSQL(ISourceDataset) - Method in class ambit2.db.chart.HistogramChartGenerator
 
getSQL(ISourceDataset) - Method in class ambit2.db.chart.PieChartGenerator
 
getSQL(ISourceDataset) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
getSQL() - Method in class ambit2.db.chemrelation.DeleteStructureRelation
 
getSQL() - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
getSQL() - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
getSQL() - Method in class ambit2.db.chemrelation.UpdateStructureRelation
 
getSQL() - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
getSQL() - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
getSQL() - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
getSQL() - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
getSQL() - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
getSQL() - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
getSQL() - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
getSQL() - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
getSQL() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
getSQL() - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
getSQL() - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
getSQL() - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
getSQL() - Method in class ambit2.db.model.QueryCountModels
 
getSql() - Method in class ambit2.db.processors.ConnectionStatisticsProcessor
 
getSQL(IStoredQuery) - Method in class ambit2.db.processors.QueryStatisticsProcessor
 
getSQL(IStructureRecord) - Method in class ambit2.db.processors.StructureStatisticsProcessor
 
getSQL() - Method in class ambit2.db.readers.AbstractStructureRetrieval
 
getSQL() - Method in class ambit2.db.readers.ReadChemicalIds
 
getSQL() - Method in class ambit2.db.readers.RetrieveDatasets
 
getSQL() - Method in class ambit2.db.readers.RetrieveDescriptor
 
getSQL() - Method in class ambit2.db.readers.RetrieveField
 
getSQL() - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
getSQL() - Method in class ambit2.db.readers.RetrieveModelTemplates
 
getSQL() - Method in class ambit2.db.readers.RetrieveProfileValues
 
getSQL() - Method in enum ambit2.db.readers.RetrieveProfileValues.SearchMode
 
getSQL() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getSQL() - Method in class ambit2.db.readers.RetrieveStructure
 
getSQL() - Method in class ambit2.db.readers.RetrieveTemplate
 
getSQL() - Method in class ambit2.db.search.DictionaryQuery
 
getSQL() - Method in enum ambit2.db.search.property.AbstractPropertyRetrieval.SearchMode
 
getSQL() - Method in class ambit2.db.search.property.FilteredCountNominal
 
getSQL() - Method in class ambit2.db.search.property.FilteredCountNumeric
 
getSQL() - Method in class ambit2.db.search.property.FreeTextPropertyQuery
 
getSQL() - Method in class ambit2.db.search.property.ModelTemplates
 
getSQL() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getSQL(PropertiesByDataset) - Method in enum ambit2.db.search.property.PropertiesByDataset.QField
 
getSQL() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getSQL(PropertiesByQuery) - Method in enum ambit2.db.search.property.PropertiesByQuery.QField
 
getSQL() - Method in class ambit2.db.search.property.PropertyCount
 
getSQL() - Method in class ambit2.db.search.property.PropertyRange
 
getSQL() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getSQL() - Method in class ambit2.db.search.property.PropertyStatsString
 
getSQL() - Method in class ambit2.db.search.property.QueryMetricRange
 
getSQL() - Method in class ambit2.db.search.property.QueryOntology
 
getSQL() - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
getSQL() - Method in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
getSQL() - Method in class ambit2.db.search.property.RetieveFeatures
 
getSQL() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getSQL() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getSQL() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getSQL() - Method in class ambit2.db.search.property.RetrieveProfile
 
getSQL() - Method in class ambit2.db.search.property.TemplateQuery
 
getSQL() - Method in class ambit2.db.search.qlabel.QueryConsensus
 
getSQL() - Method in class ambit2.db.search.qlabel.QueryQLabel
 
getSQL() - Method in class ambit2.db.search.QueryCombined
 
getSQL(Q) - Method in class ambit2.db.search.QueryExecutor
 
getSQL() - Method in class ambit2.db.search.QuerySmilesByID
 
getSQL() - Method in class ambit2.db.search.QueryUser
 
getSQL() - Method in class ambit2.db.search.SQLFileQueryParams
 
getSQL() - Method in class ambit2.db.search.StoredQuery
 
getSQL() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
getSQL() - Method in class ambit2.db.search.structure.ChemicalByQueryFolder
 
getSQL() - Method in class ambit2.db.search.structure.FingerprintsByStatus
 
getSQL() - Method in class ambit2.db.search.structure.FreeTextQuery
 
getSQL() - Method in class ambit2.db.search.structure.MissingFingerprintsQuery
 
getSQL() - Method in class ambit2.db.search.structure.MissingInChIsQuery
 
getSQL() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getSQL() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsDataset
 
getSQL() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsMixed
 
getSQL() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset
 
getSQL() - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
getSQL() - Method in class ambit2.db.search.structure.QueryAtomEnvironment
 
getSQL() - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
getSQL() - Method in class ambit2.db.search.structure.QueryComplement
 
getSQL() - Method in class ambit2.db.search.structure.QueryDataset
 
getSQL() - Method in class ambit2.db.search.structure.QueryDatasetByID
 
getSQL() - Method in class ambit2.db.search.structure.QueryDistance
 
getSQL() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
getSQL() - Method in class ambit2.db.search.structure.QueryField
 
getSQL() - Method in class ambit2.db.search.structure.QueryFieldMultiple
 
getSQL() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
getSQL() - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
getSQL() - Method in class ambit2.db.search.structure.QueryLookupStructure
 
getSQL() - Method in class ambit2.db.search.structure.QueryMissingDescriptor
 
getSQL() - Method in class ambit2.db.search.structure.QueryMissingDistances
 
getSQL() - Method in class ambit2.db.search.structure.QueryMissingProperty
 
getSQL() - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
getSQL() - Method in class ambit2.db.search.structure.QuerySimilarityBitset
select ? as idquery,idchemical,idstructure,1 as selected,Tanimoto as metric
getSQL() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getSQL() - Method in class ambit2.db.search.structure.QuerySMARTS
 
getSQL() - Method in class ambit2.db.search.structure.QueryStoredResults
 
getSQL() - Method in class ambit2.db.search.structure.QueryStoredResultsByName
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructure
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
getSQL() - Method in class ambit2.db.search.structure.QueryStructureType
 
getSQL() - Method in class ambit2.db.search.structure.QueryStrucType
 
getSQL() - Method in class ambit2.db.search.structure.ScopeQuery
 
getSQL() - Method in class ambit2.db.simiparity.space.QueryQMap
 
getSQL() - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
getSQL() - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
getSQL() - Method in class ambit2.db.substance.CreateSubstance
 
getSQL() - Method in class ambit2.db.substance.DeleteSubstance
 
getSQL() - Method in class ambit2.db.substance.FacetedSearchSubstance
 
getSQL() - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
getSQL() - Method in class ambit2.db.substance.ids.UpdateSubstanceIdentifiers
 
getSQL() - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
getSQL() - Method in class ambit2.db.substance.QueryCountBundles
 
getSQL() - Method in class ambit2.db.substance.QueryCountEndpoints
 
getSQL() - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
getSQL() - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
getSQL() - Method in class ambit2.db.substance.QueryCountSubstances
 
getSQL() - Method in class ambit2.db.substance.QueryCountSubstanceTypes
 
getSQL() - Method in class ambit2.db.substance.ReadByReliabilityFlags
 
getSQL() - Method in class ambit2.db.substance.ReadSubstance
 
getSQL() - Method in class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
getSQL() - Method in class ambit2.db.substance.ReadSubstanceByName
 
getSQL() - Method in class ambit2.db.substance.ReadSubstanceByOwner
 
getSQL() - Method in class ambit2.db.substance.ReadSubstanceByStudy
 
getSQL() - Method in class ambit2.db.substance.ReadSubstanceByType
 
getSQL() - Method in class ambit2.db.substance.ReadSubstances
 
getSQL() - Method in class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
getSQL() - Method in class ambit2.db.substance.relation.DeleteSubstanceRelation
 
getSQL() - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
getSQL() - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
getSQL() - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
getSQL() - Method in class ambit2.db.substance.study.DeleteEffectRecords
 
getSQL() - Method in class ambit2.db.substance.study.DeleteStudy
 
getSQL() - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
getSQL() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getSQL() - Method in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
getSQL() - Method in class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
getSQL() - Method in class ambit2.db.substance.study.ReadSubstanceProperty
 
getSQL() - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
getSQL() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getSQL() - Method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
 
getSQL() - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
getSQL() - Method in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
getSQL() - Method in class ambit2.db.substance.study.UpdateSubstanceStudy
 
getSQL() - Method in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
getSQL() - Method in class ambit2.db.substance.UpdateSubstance
 
getSQL() - Method in class ambit2.db.update.bookmark.CreateBookmark
 
getSQL() - Method in class ambit2.db.update.bookmark.DeleteBookmark
 
getSQL() - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
getSQL() - Method in class ambit2.db.update.bookmark.ReadBookmark
 
getSQL() - Method in class ambit2.db.update.bookmark.UpdateBookmark
 
getSQL() - Method in class ambit2.db.update.bundle.BundleOwnerByNumber
 
getSQL() - Method in class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
getSQL() - Method in class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
getSQL() - Method in class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
getSQL() - Method in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
getSQL() - Method in class ambit2.db.update.bundle.CreateBundle
 
getSQL() - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
getSQL() - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
getSQL() - Method in class ambit2.db.update.bundle.DeleteBundle
 
getSQL() - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
getSQL() - Method in class ambit2.db.update.bundle.effects.ReadEffectRecordByBundle
 
getSQL() - Method in class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
getSQL() - Method in class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
getSQL() - Method in class ambit2.db.update.bundle.endpoints.ReadEndpointsByBundle
 
getSQL() - Method in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
getSQL() - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixFromBundle
 
getSQL() - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixProtocolApplicationValue
 
getSQL() - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixValue
 
getSQL() - Method in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
getSQL() - Method in class ambit2.db.update.bundle.ReadBundle
 
getSQL() - Method in class ambit2.db.update.bundle.ReadBundleVersion
 
getSQL() - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
getSQL() - Method in class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
getSQL() - Method in class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
getSQL() - Method in class ambit2.db.update.bundle.substance.ReadSubstanceChemicalsUnionByBundle
 
getSQL() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
getSQL() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds
 
getSQL() - Method in class ambit2.db.update.bundle.UpdateBundle
 
getSQL() - Method in class ambit2.db.update.chemical.CreateChemical
 
getSQL() - Method in class ambit2.db.update.chemical.DeleteChemical
 
getSQL() - Method in class ambit2.db.update.chemical.UpdateChemical
 
getSQL() - Method in class ambit2.db.update.dataset.CreateDataset
 
getSQL() - Method in class ambit2.db.update.dataset.DatasetAddStructure
 
getSQL() - Method in class ambit2.db.update.dataset.DatasetDeleteStructure
 
getSQL() - Method in class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
getSQL() - Method in class ambit2.db.update.dataset.DeleteDataset
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCount
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCountChemicalInDataset
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCountDataset
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCountProperties
 
getSQL() - Method in class ambit2.db.update.dataset.QueryCountValues
 
getSQL(String) - Method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
 
getSQL() - Method in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
getSQL() - Method in class ambit2.db.update.dataset.ReadDataset
 
getSQL() - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
getSQL() - Method in class ambit2.db.update.dataset.UpdateDataset
 
getSQL() - Method in class ambit2.db.update.dictionary.CreateDictionary
 
getSQL() - Method in class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
getSQL() - Method in class ambit2.db.update.dictionary.DeleteDictionary
 
getSQL() - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
getSQL() - Method in class ambit2.db.update.dictionary.TemplateDeleteProperty
 
getSQL() - Method in class ambit2.db.update.fp.CreateFingerprintChemical
 
getSQL() - Method in class ambit2.db.update.fp.CreateFingerprintStructure
 
getSQL() - Method in enum ambit2.db.update.fp.QueryFingerprints._order
 
getSQL() - Method in class ambit2.db.update.fp.QueryFingerprints
 
getSQL() - Method in class ambit2.db.update.fp.ReadStructuresByFingerprint
 
getSQL() - Method in class ambit2.db.update.fpae.CreateAtomEnvironment
 
getSQL() - Method in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
getSQL() - Method in class ambit2.db.update.fpae.DeleteAtomEnvironment
 
getSQL() - Method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
 
getSQL() - Method in class ambit2.db.update.model.CreateModel
 
getSQL() - Method in class ambit2.db.update.model.DeleteModel
 
getSQL() - Method in class ambit2.db.update.model.QueryModel
 
getSQL() - Method in class ambit2.db.update.model.ReadModel
 
getSQL() - Method in class ambit2.db.update.model.UpdateModel
 
getSQL() - Method in class ambit2.db.update.property.CreateProperty
 
getSQL() - Method in class ambit2.db.update.property.CreatePropertyReferenceID
 
getSQL() - Method in class ambit2.db.update.property.DeleteProperty
 
getSQL() - Method in class ambit2.db.update.property.ReadProperty
 
getSQL() - Method in class ambit2.db.update.property.UpdateProperty
 
getSQL() - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
getSQL() - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
getSQL() - Method in class ambit2.db.update.propertyannotations.DeletePropertyAnnotation
 
getSQL() - Method in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
getSQL() - Method in class ambit2.db.update.propertyannotations.UpdatePropertyAnnotation
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateQLabelCAS
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateQLabelEINECS
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateQLabelFingerprints
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateQLabelPair
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateStructureQLabel
 
getSQL() - Method in class ambit2.db.update.qlabel.CreateValueQLabel
 
getSQL() - Method in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
getSQL() - Method in class ambit2.db.update.qlabel.DeleteValueQLabel
 
getSQL() - Method in class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
getSQL() - Method in class ambit2.db.update.qlabel.SmilesUniquenessCheck
 
getSQL() - Method in class ambit2.db.update.qlabel.ValuesQualityCheck
 
getSQL() - Method in class ambit2.db.update.queryfolder.CreateQueryFolder
 
getSQL() - Method in class ambit2.db.update.queryfolder.DeleteQueryFolder
 
getSQL() - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
getSQL() - Method in class ambit2.db.update.queryfolder.UpdateQueryFolder
 
getSQL() - Method in class ambit2.db.update.reference.CreateReference
 
getSQL() - Method in class ambit2.db.update.reference.DeleteReference
 
getSQL() - Method in class ambit2.db.update.reference.ReadReference
 
getSQL() - Method in class ambit2.db.update.reference.UpdateReference
 
getSQL() - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
getSQL() - Method in class ambit2.db.update.storedquery.DeleteStoredQuery
 
getSQL() - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
getSQL() - Method in class ambit2.db.update.storedquery.QueryAddTemplate
 
getSQL() - Method in class ambit2.db.update.storedquery.QueryDeleteStructure
 
getSQL() - Method in class ambit2.db.update.storedquery.QueryDeleteTemplate
 
getSQL(ReadStoredQuery) - Method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
 
getSQL() - Method in class ambit2.db.update.storedquery.ReadStoredQuery
 
getSQL() - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
getSQL() - Method in class ambit2.db.update.storedquery.SelectStoredQuery
 
getSQL() - Method in class ambit2.db.update.storedquery.UpdateSelectedRecords
 
getSQL() - Method in class ambit2.db.update.storedquery.UpdateStoredQuery
 
getSQL() - Method in class ambit2.db.update.structure.ChemicalByDataset
 
getSQL() - Method in class ambit2.db.update.structure.CreateStructure
 
getSQL() - Method in class ambit2.db.update.structure.CreateStrucType
 
getSQL() - Method in class ambit2.db.update.structure.DeleteStructure
 
getSQL() - Method in class ambit2.db.update.structure.UpdateStructure
 
getSQL() - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
getSQL() - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
getSQL() - Method in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
getSQL() - Method in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
getSQL() - Method in class ambit2.db.version.DBVersionQuery
 
getSQL_and() - Method in class ambit2.db.search.QueryCombined
SQLs of simple queries, join-ed
getSQL_or() - Method in class ambit2.db.search.QueryCombined
SQLs of simple queries, union-ed.
getSqlDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
getSqlDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
getSqlDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldString
 
getSQLFile() - Method in class ambit2.db.processors.DbCreateDatabase
 
getSQLPropertyQuery() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
getSqlRDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldGeneric
 
getSqlRDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
getSqlRDataset() - Method in class ambit2.db.update.dataset.DatasetQueryFieldString
 
getSQLStructureQuery() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
getSQLStructureQuery() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds
 
getSQLStructureQuery() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset
 
getSQLStructureQuery() - Method in class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults
 
getSQLTemplate() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
getSQLTemplate() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds
 
getSQLTemplate() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset
 
getSQLTemplate() - Method in class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults
 
getSQLTemplate() - Method in class ambit2.db.substance.ids.ReadChemIdentifiersByComposition
 
getSQLTemplate() - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
getStars() - Method in class ambit2.base.data.AbstractDataset
 
getStars() - Method in interface ambit2.base.data.ISourceDataset
 
getStars() - Method in class ambit2.base.data.SourceDataset
 
getStars() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getStars() - Method in class ambit2.core.data.model.ModelWrapper
 
getStars() - Method in class ambit2.db.search.StoredQuery
 
getStartChainID() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getStarted() - Method in class ambit2.rest.task.Task
 
getStartingMaterialsDataBase() - Method in class ambit2.reactions.SimilarityManager
 
getStartInsertionCode() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getStartMatDB() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getStartSequenceNumber() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getState() - Method in class ambit2.structure2name.components.AbstractComponent
 
getState() - Method in interface ambit2.structure2name.components.IIUPACComponent
 
getState() - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
getState() - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
getState() - Method in interface ambit2.tautomers.zwitterion.IAcidicCenter
 
getState() - Method in interface ambit2.tautomers.zwitterion.IBasicCenter
 
getState() - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
getState() - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
getState() - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
getState() - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
getStatement() - Method in class ambit2.db.results.AmbitRows
 
getStats() - Method in class ambit2.model.AbstractModel
 
getStats() - Method in class ambit2.model.evaluation.EvaluationStats
 
getStats(Comparable) - Method in class ambit2.similarity.stats.AbstractModelStatistics
 
getStatsAt(IStructureRecord) - Method in class ambit2.db.results.StoredQueryTableModel
 
getStatus() - Method in class ambit2.base.data.AbstractDataset
 
getStatus() - Method in interface ambit2.base.data.ISourceDataset
 
getStatus() - Method in class ambit2.base.data.SourceDataset
 
getStatus() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getStatus() - Method in class ambit2.db.search.StoredQuery
 
getStatus() - Method in class ambit2.db.update.bundle.ReadBundle
 
getStatus() - Method in class ambit2.descriptors.AtomEnvironment
 
getStatus() - Method in interface ambit2.model.IModelStatistics
 
getStatus() - Method in exception ambit2.pubchem.ServerError
 
getStatus(Throwable, Request, Response) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
getStatus() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
getStatus() - Method in class ambit2.rest.task.Task
 
getStatus() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
getStatus() - Method in class ambit2.tautomers.TautomerManager
 
getStatusInfo() - Method in class ambit2.reactions.reactor.ReactorResult
 
getStatusProperty() - Method in enum ambit2.descriptors.processors.FPTable
 
getStep() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
getStereo(SmartsAtomExpression) - Static method in class ambit2.smarts.StereoFromSmartsAtomExpression
 
getStereoElementsStatus(IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
getStereoInfo() - Method in class ambit2.smarts.DoubleBondAromaticityNotSpecified
 
getStereoInfo() - Method in class ambit2.smarts.DoubleNonAromaticBond
 
getStereoInfo() - Method in class ambit2.smarts.SmartsBondExpression
 
getStereoRemovedTokens() - Method in class ambit2.smarts.SmartsAtomExpression
 
getStorageMode() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
getStoredProcedureOutVars(CallableStatement) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getStoredProcedureOutVars(CallableStatement) - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
getStoredProcedureOutVars(CallableStatement) - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
getStoredProcedureOutVars(CallableStatement) - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
getStoredProcedureOutVars(CallableStatement) - Method in class ambit2.db.update.dataset.DeleteDataset
 
getStoredQuery() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
getStoredQuery() - Method in class ambit2.db.search.QueryInfo
 
getStrategy() - Method in class ambit2.reactions.reactor.Reactor
 
getStrategy() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getStrategy() - Method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
getString(String) - Static method in class ambit2.core.config.Resources
 
getString(int) - Method in class ambit2.db.results.AmbitRows
 
getString(String) - Method in class ambit2.db.results.AmbitRows
 
getString(RDFNode) - Static method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
getString(RDFNode) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getStringArray(String) - Static method in class ambit2.core.config.Resources
 
getStrokeMap() - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
Returns the current stroke map.
getStructure() - Method in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
getStructure() - Method in class ambit2.db.processors.ValueWriter
 
getStructure(int) - Method in class ambit2.db.RepositoryReader
 
getStructure() - Method in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
getStructure() - Method in class ambit2.descriptors.processors.DescriptorValue2Property
 
getStructureIterator(Object) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
getStructureKeyBits(IAtomContainer) - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
getStructureKeyBits(IAtomContainer) - Method in class ambit2.smarts.Screening
 
getStructureRecord(JsonNode, JSONParsingUtils.STRUCTURE_RECORD_INPUT_INFO) - Static method in class ambit2.rules.json.JSONParsingUtils
 
getStructureRecords(JsonNode, String, JSONParsingUtils.STRUCTURE_RECORD_INPUT_INFO, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
getStructureSearchExample() - Static method in class ambit2.chebi.ChEBIClient
 
getStructureType() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
getStructureURI(String) - Method in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
getStructureWhere() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
getStudyResultType() - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
getStudyResultType() - Method in class ambit2.base.data.study.ReliabilityParams
 
getStudyResultType() - Method in class ambit2.base.data.substance.SubstanceProperty
 
getSubAtomEnvironment(int) - Method in class ambit2.descriptors.AtomEnvironment
 
getSubBlocks() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
getSubcategoryTitle() - Method in class ambit2.base.facet.AbstractFacet
 
getSubcategoryTitle() - Method in class ambit2.base.facet.BundleRoleFacet
 
getSubcategoryTitle() - Method in class ambit2.base.facet.SubstanceStudyFacet
 
getSubcategoryTitle() - Method in class ambit2.db.facets.bundle.BundleSummaryFacet
 
getSubcategoryTitle() - Method in class ambit2.db.facets.qlabel.DatasetConsensusLabelFacet
 
getSubcategoryTitle() - Method in class ambit2.db.facets.qlabel.DatasetStructureQLabelFacet
 
getSubcategoryTitle() - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeFacet
 
getSubcategoryTitle() - Method in class ambit2.db.substance.study.facet.OwnerFacet
 
getSubcategoryTitle() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getSubCategoryURL(String...) - Method in class ambit2.base.facet.AbstractFacet
 
getSubCategoryURL(String...) - Method in class ambit2.base.facet.BundleRoleFacet
 
getSubCategoryURL(String...) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.facets.bundle.BundleSummaryFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetConsensusLabelFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetStructureQLabelFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.substance.study.facet.OwnerFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getSubCategoryURL(String...) - Method in class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
getSubExpressions(SmartsAtomExpression, int) - Static method in class ambit2.smarts.SmartsToChemObject
 
getSubExpressions(SmartsBondExpression, int) - Method in class ambit2.smarts.SmartsToChemObject
 
getSubExpressions(SmartsAtomExpression, int) - Static method in class ambit2.smarts.StereoFromSmartsAtomExpression
 
getSubGroup() - Method in class ambit2.reactions.sets.ReactionData
 
getSublevel() - Method in class ambit2.descriptors.AtomEnvironment
 
getSubscript() - Method in class ambit2.core.groups.AbstractGroup
 
getSubscript() - Method in interface ambit2.core.groups.ISGroup
 
getSubstanceName() - Method in class ambit2.base.data.SubstanceRecord
Substance name, as assigned by the owner
getSubstancesCount() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getSubstancetype() - Method in class ambit2.base.data.SubstanceRecord
IUCLID5: monoconsituent, multiconstituent, UVCB (Unknown or Variable composition, Complex reaction products or Biological materials) http://echa .europa.eu/documents/10162/13643/nutshell_guidance_substance_en.pdf
getSubstanceType(String) - Static method in class ambit2.core.data.MoleculeTools
 
getSubstanceUUID() - Method in class ambit2.base.data.study.ProtocolApplication
 
getSubstanceUUID() - Method in class ambit2.base.data.SubstanceRecord
Substance UUID, as assigned by the owner
getSubstanceUUID() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getSubstanceUUID() - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
getSubstituentPosAtomIndicex(int) - Method in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
getSubSubGroup() - Method in class ambit2.reactions.sets.ReactionData
 
getSuffix(String) - Static method in class ambit2.base.io.AmbitFileFilter
 
getSuffix(File) - Static method in class ambit2.base.io.AmbitFileFilter
 
getSuffix(String) - Static method in class ambit2.base.io.MolFileFilter
 
getSuffix(File) - Static method in class ambit2.base.io.MolFileFilter
 
getSulfonylGroupPositions(IAtomContainer) - Static method in class ambit2.tautomers.rules.CustomTautomerRegion
 
getSupportDoubleBondAromaticityNotSpecified() - Method in class ambit2.smarts.SmartsManager
 
getSupportedDataFeatures() - Method in class ambit2.core.io.DelimitedFileFormat
 
getSupportedDataFeatures() - Method in class ambit2.core.io.DelimitedFileWriter
 
getSupportedDataFeatures() - Method in class ambit2.core.io.PDFWriter
 
getSupportedDataFeatures() - Method in class ambit2.core.io.XLSFileFormat
 
getSupportedExtDescriptions() - Method in class ambit2.core.io.FileState
 
getSupportedExtensions() - Method in class ambit2.core.io.FileState
 
getSupportMOEExtension() - Method in class ambit2.smarts.SmartsManager
 
getSupportOpenBabelExtension() - Method in class ambit2.smarts.SmartsManager
 
getSupportOpenEyeExtension() - Method in class ambit2.smarts.SmartsManager
 
getSyncProvider() - Method in class ambit2.db.results.AmbitRows
 
getSyntPathScore() - Method in class ambit2.reactions.retrosynth.RetroSynthPath
 
getSystemDesignator() - Method in class ambit2.base.data.substance.ExternalIdentifier
 
getSystemIdentifier() - Method in class ambit2.base.data.substance.ExternalIdentifier
 
getT() - Method in class ambit2.tautomers.TautomerRanking
 
getTable() - Method in enum ambit2.descriptors.processors.FPTable
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ambit2.ui.BrowserModeCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ambit2.ui.ColorTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ambit2.ui.ImageCellRenderer
 
getTableColumn() - Method in enum ambit2.db.search.property.ModelTemplates._ModelTemplates
 
getTableIndex() - Method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
 
getTableName() - Method in class ambit2.db.results.AmbitRows
 
getTag() - Method in enum ambit2.base.data.study._FIELDS_RELIABILITY
 
getTag() - Method in class ambit2.base.facet.BundleRoleFacet
 
getTag() - Method in class ambit2.db.processors.ProcessorCreateProfileQuery
 
getTag() - Method in enum ambit2.db.reporters.SmilesReporter.Mode
 
getTag() - Method in class ambit2.domain.stats.datastructures.SubcategoryBin
 
getTag() - Method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
 
getTarget() - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
getTarget() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getTarget() - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
getTarget() - Method in interface ambit2.rules.actions.IAction
 
getTargetProperty() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getTargetURI() - Method in class ambit2.model.builder.AbstractModelBuilder
 
getTask() - Method in class ambit2.rest.task.ExecutableTask
 
getTaskCategory() - Method in class ambit2.rest.task.CallableProtectedTask
 
getTasks() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
getTasks() - Method in class ambit2.rest.SimpleTaskResource
 
getTasks() - Method in class ambit2.rest.task.TaskStorage
 
getTaskStorage() - Method in class ambit2.rest.TaskApplication
 
getTautomerCountEstimation(TautomerManager, IAtomContainer) - Static method in class ambit2.tautomers.TautomerUtils
 
getTautomerManager() - Method in class ambit2.tautomers.processor.TautomerProcessor
 
getTautomerRelationGraph() - Method in class ambit2.tautomers.TautomerManager
 
getTempFolder() - Static method in class ambit2.core.io.ZipReader
 
getTemplate() - Method in class ambit2.base.data.Dictionary
 
getTemplate() - Method in class ambit2.base.data.PropertyTemplateStats
 
getTemplate() - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException
 
getTemplate(ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
getTemplate() - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
getTemplate() - Method in class ambit2.db.reporters.QueryHeaderReporter
 
getTemplate() - Method in class ambit2.db.reporters.SDFReporter
 
getTemplate() - Method in class ambit2.db.reporters.SmilesReporter
 
getTemplate() - Method in interface ambit2.db.search.IStoredQuery
 
getTemplate() - Method in class ambit2.db.search.StoredQuery
 
getTemplate() - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
getTemplate(Reference) - Method in enum ambit2.rest.OpenTox.URI
 
getTemplate() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
getTemplateName() - Method in class ambit2.db.search.DictionaryObjectQuery
 
getTemplateName() - Method in class ambit2.db.search.DictionaryQuery
 
getTemplateName() - Method in class ambit2.db.search.DictionarySubjectQuery
 
getTemplateName() - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
getTemplateName() - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
getTemplateName() - Method in class ambit2.rest.freemarker.FreeMarkerSupport
 
getTerm() - Method in class ambit2.pubchem.EntrezSearchOptions
 
getTerm() - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
getTestInstances() - Method in class ambit2.core.data.model.ModelWrapper
 
getTestUser() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getTestUserPass() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
getTetrahedralChiralityStatusString(int) - Static method in class ambit2.smarts.StereoChemUtils
 
getText() - Method in class ambit2.base.data.AbstractLabel
 
getText() - Method in class ambit2.db.search.structure.QueryStructureByID
 
getText(InputStream, String) - Static method in class ambit2.ui.Utils
 
getTextDelimiter() - Method in class ambit2.core.io.DelimitedFileFormat
 
getTextResultConfig(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
getTextValue() - Method in class ambit2.base.data.study.EffectRecord
 
getTextValue() - Method in class ambit2.base.data.study.ValueAnnotated
 
getThreshold() - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
getThreshold() - Method in class ambit2.db.search.QueryInfo
 
getThreshold() - Method in class ambit2.db.search.structure.QuerySimilarity
 
getThreshold() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
getThreshold() - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
getThreshold_a() - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
getThreshold_dactivity() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getThreshold_similarity() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
getTime(int) - Method in class ambit2.db.results.AmbitRows
 
getTime(String) - Method in class ambit2.db.results.AmbitRows
 
getTime(int, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getTime(String, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getTime_elapsed() - Method in class ambit2.descriptors.AtomEnvironment
 
getTimeCompleted() - Method in class ambit2.rest.task.Task
 
getTimeout() - Method in interface ambit2.base.interfaces.IBatchProcessor
 
getTimeout() - Method in class ambit2.base.processors.batch.BatchProcessor
 
getTimeout() - Method in class ambit2.base.processors.batch.BatchReporter
 
getTimeout() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
getTimeout() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getTimeout() - Method in class ambit2.pubchem.HTTPRequest
 
getTimeout(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getTimeProperty() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
getTimeProperty() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
getTimeProperty() - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
getTimeProperty() - Method in class ambit2.descriptors.processors.BitSetGenerator
 
getTimeProperty() - Method in enum ambit2.descriptors.processors.FPTable
 
getTimeProperty() - Method in class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
getTimestamp(int) - Method in class ambit2.db.results.AmbitRows
 
getTimestamp(String) - Method in class ambit2.db.results.AmbitRows
 
getTimestamp(int, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getTimestamp(String, Calendar) - Method in class ambit2.db.results.AmbitRows
 
getTitle() - Method in class ambit2.base.data.AmbitUser
 
getTitle() - Method in class ambit2.base.data.Bookmark
 
getTitle() - Method in class ambit2.base.data.ClassHolder
 
getTitle() - Method in interface ambit2.base.data.ILiteratureEntry
 
getTitle() - Method in enum ambit2.base.data.ISourceDataset.license
 
getTitle() - Method in class ambit2.base.data.LiteratureEntry
 
getTitle() - Method in class ambit2.base.data.Property
 
getTitle() - Method in class ambit2.base.data.SelectionBean
 
getTitle() - Method in class ambit2.base.data.SourceDataset
 
getTitle() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getTitle() - Method in class ambit2.base.facet.AbstractFacet
 
getTitle() - Method in interface ambit2.base.processors.IAmbitResult
 
getTitle() - Method in enum ambit2.base.processors.search.AbstractFinder.SITE
 
getTitle() - Method in enum ambit2.core.data.model.AlgorithmType
 
getTitle() - Method in class ambit2.core.groups.SuppleAtomContainer
 
getTitle(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getTitle() - Method in class ambit2.db.substance.study.facet.OwnerFacet
 
getTitle() - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
getTitle() - Method in interface ambit2.model.IModelStatistics
 
getTitle() - Method in class ambit2.mopac.Mopac7Writer
 
getTitle() - Method in enum ambit2.rest.legacy.OTCompound._titles
Deprecated.
 
getTitle(RDFNode) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
getTitle() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
getTitle() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getTitle(Class) - Static method in class ambit2.ui.Utils
 
getTman() - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
getToIndex() - Method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
Get one of the number of the column or row that contains the cell whose top left hand corner will be aligned with the bottom right hand corner of the image.
getToken() - Method in class ambit2.rest.ProtectedResource
 
getToken() - Method in class ambit2.rest.task.CallableProtectedTask
 
getTokenFromCookies(Request) - Method in class ambit2.rest.ProtectedResource
 
getTooltip() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
getTopCategory() - Method in enum ambit2.base.data.study.Protocol._categories
 
getTopCategory() - Method in class ambit2.base.data.study.Protocol
 
getTopcategory() - Method in class ambit2.base.data.substance.SubstanceProperty
 
getTopcategory() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
getTopDistanceMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getTotalEnergy(String) - Method in class ambit2.mopac.MopacUtilities
 
getTotalEnergy(IAtomContainer) - Method in class ambit2.mopac.MopacUtilities
 
getTradeNameInstance(String) - Static method in class ambit2.base.data.Property
 
getTradeNameReference() - Static method in class ambit2.base.data.LiteratureEntry
 
getTrainDataSet() - Method in class ambit2.groupcontribution.Learner
 
getTrainingData() - Method in class ambit2.model.builder.AbstractModelBuilder
 
getTrainingDataset() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
getTrainingInstances() - Method in class ambit2.core.data.model.ModelWrapper
 
getTransactionIsolation() - Method in class ambit2.db.results.AmbitRows
 
getTransformationName() - Method in interface ambit2.groupcontribution.transformations.IValueTransformation
 
getTransformationName() - Method in class ambit2.groupcontribution.transformations.TransformationComposition
 
getTransformationName() - Method in class ambit2.groupcontribution.transformations.TransformationExp
 
getTransformationName() - Method in class ambit2.groupcontribution.transformations.TransformationLin
 
getTransformationName() - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
getTransformationName() - Method in class ambit2.groupcontribution.transformations.TransformationPow
 
getTransformations() - Method in class ambit2.reactions.SimilarityManager
 
getTransformations() - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
getTransformedMaterials() - Method in class ambit2.reactions.SimilarityManager
 
getTransformType() - Method in class ambit2.reactions.GenericReaction
 
getTree() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
getTSS(MatrixDouble, double) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
getTuple(SourceDataset) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
getTuple(SourceDataset) - Method in class ambit2.db.processors.ValueWriter
 
getType() - Method in class ambit2.base.data.AmbitUser
 
getType() - Method in class ambit2.base.data.Bookmark
 
getType() - Method in interface ambit2.base.data.ILiteratureEntry
 
getType() - Method in class ambit2.base.data.LiteratureEntry
 
getType() - Method in class ambit2.base.data.PropertyAnnotation
 
getType() - Method in class ambit2.base.data.StructureRecord
 
getType() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getType() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getType() - Method in class ambit2.core.data.model.Algorithm
 
getType() - Method in interface ambit2.core.data.model.IEvaluation
 
getType() - Method in class ambit2.core.groups.ContainerGroup
 
getType() - Method in class ambit2.core.processors.structure.key.CASKey
 
getType() - Method in class ambit2.core.processors.structure.key.ChEMBLCompoundURI
 
getType() - Method in class ambit2.core.processors.structure.key.DSSToxID
 
getType() - Method in class ambit2.core.processors.structure.key.EINECSKey
 
getType() - Method in class ambit2.core.processors.structure.key.EmptyKey
 
getType() - Method in class ambit2.core.processors.structure.key.InchiKey
 
getType() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey
 
getType() - Method in interface ambit2.core.processors.structure.key.IStructureKey
 
getType() - Method in class ambit2.core.processors.structure.key.NameKey
 
getType() - Method in class ambit2.core.processors.structure.key.NoneKey
 
getType() - Method in class ambit2.core.processors.structure.key.PropertyKey
 
getType() - Method in class ambit2.core.processors.structure.key.PropertyNameKey
 
getType() - Method in class ambit2.core.processors.structure.key.PubchemCID
 
getType() - Method in class ambit2.core.processors.structure.key.PubchemSID
 
getType() - Method in class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
getType() - Method in class ambit2.core.processors.structure.key.SmilesKey
 
getType() - Method in class ambit2.db.results.AmbitRows
 
getType() - Method in class ambit2.db.update.fp.Fingerprint
 
getType() - Method in interface ambit2.db.update.fp.IFingerprint
 
getType() - Method in enum ambit2.descriptors.AtomEnvironentMatrix._param
 
getType() - Method in enum ambit2.descriptors.AtomEnvironmentDescriptor._param
 
getType() - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
getType() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
getType() - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
getType() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getType() - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
getType() - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
getType() - Method in class ambit2.groupcontribution.groups.AtomGroup
 
getType() - Method in class ambit2.groupcontribution.groups.BondGroup
 
getType() - Method in class ambit2.groupcontribution.groups.DGroup
 
getType() - Method in class ambit2.groupcontribution.groups.GGroup
 
getType() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getType() - Method in interface ambit2.groupcontribution.rules.ILocalDescriptorRule
 
getType() - Method in class ambit2.model.evaluation.EvaluationStats
 
getType() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
getType() - Method in class ambit2.reactions.rules.RetroSynthRule
 
getType() - Method in class ambit2.reactions.sets.ReactionData
 
getType() - Method in class ambit2.structure2name.components.AcyclicComponent
 
getType() - Method in class ambit2.structure2name.components.Chain
 
getType() - Method in class ambit2.structure2name.components.CyclicComponent
 
getType() - Method in class ambit2.structure2name.components.FunctionalGroup
 
getType() - Method in interface ambit2.structure2name.components.IIUPACComponent
 
getTypeMap() - Method in class ambit2.db.results.AmbitRows
 
getTyperClass() - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
getTyperClass() - Method in class ambit2.descriptors.SaturationCheckerVerifier
 
getTypical() - Method in class ambit2.base.relation.composition.Proportion
 
getTypical_unit() - Method in class ambit2.base.relation.composition.Proportion
 
getTypical_value() - Method in class ambit2.base.relation.composition.Proportion
 
getUnicodeStream(int) - Method in class ambit2.db.results.AmbitRows
 
getUnicodeStream(String) - Method in class ambit2.db.results.AmbitRows
 
getUniqueMatchingAtoms() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
getUniqueMatchingAtoms() - Method in interface ambit2.smarts.query.ISmartsPattern
Just for backward compatibility
getUniqueMatchingAtoms(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
getUniqueMatchingAtoms() - Method in class ambit2.smarts.query.SmartsPatternCDK
For backward compatibility
getUnit() - Method in class ambit2.base.data.study.EffectRecord
 
getUnits() - Method in class ambit2.base.data.Property
 
getUnits() - Method in interface ambit2.base.data.study.IParams
 
getUnits() - Method in interface ambit2.base.data.study.IValue
 
getUnits() - Method in class ambit2.base.data.study.Params
 
getUnits() - Method in class ambit2.base.data.study.Value
 
getUnits(Property) - Method in class ambit2.db.reporters.CSVReporter
 
getUnits() - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
getUnits() - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
getUpdated() - Method in class ambit2.base.data.study.ProtocolApplication
 
getUpdated() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getUpQualifier() - Method in class ambit2.base.data.study.EffectRecord
 
getUpQualifier() - Method in interface ambit2.base.data.study.IParams
 
getUpQualifier() - Method in interface ambit2.base.data.study.IValue
 
getUpQualifier() - Method in class ambit2.base.data.study.Params
 
getUpQualifier() - Method in class ambit2.base.data.study.Value
 
getUpValue() - Method in class ambit2.base.data.study.EffectRecord
 
getUpValue() - Method in interface ambit2.base.data.study.IParams
 
getUpValue() - Method in interface ambit2.base.data.study.IValue
Upper value
getUpValue() - Method in class ambit2.base.data.study.Params
 
getUpValue() - Method in class ambit2.base.data.study.Value
 
getURI() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Class
 
getURI() - Method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
 
getURI() - Method in enum ambit2.base.data.ISourceDataset.license
 
getURI(String, SubstanceRecord) - Static method in class ambit2.base.data.SubstanceRecord
 
getURI() - Method in enum ambit2.base.processors.search.AbstractFinder.SITE
 
getURI(IStructureRecord) - Method in class ambit2.db.reporters.CSVReporter
 
getURI(String, Algorithm) - Method in class ambit2.rest.algorithm.AlgorithmURIReporter
 
getURI(String, M) - Method in class ambit2.rest.dataset.DatasetURIReporter
 
getUri() - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
getUri() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
getURI(String, ModelQueryResults) - Method in class ambit2.rest.model.ModelURIReporter
 
getURI() - Method in enum ambit2.rest.OpenTox.URI
 
getURI(String, Property) - Method in class ambit2.rest.property.PropertyURIReporter
 
getURI() - Static method in class ambit2.rest.rdf.BibTex
 
getURI() - Static method in class ambit2.rest.rdf.OTA
 
getURI() - Static method in class ambit2.rest.rdf.OTEE
 
getURI(RDFNode) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
getURI(String, T) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
getURI(T) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
getURI(String, UUID) - Method in class ambit2.rest.reporters.TaskURIReporter
 
getURI(String, IStructureRecord) - Method in class ambit2.rest.structure.CompoundURIReporter
 
getURI(String, IStructureRecord) - Method in class ambit2.rest.structure.ConformerURIReporter
 
getURI() - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
getURI(String, SubstanceRecord) - Method in class ambit2.rest.substance.SubstanceURIReporter
 
getUri() - Method in class ambit2.rest.task.Task
 
getUri() - Method in class ambit2.rest.task.TaskResult
 
getURI() - Method in class ambit2.rest.wrapper.WrappedService
 
getURIParameter() - Method in enum ambit2.rendering.CompoundImageTools.Mode2D
 
getUriReporter() - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
getUriReporter() - Method in class ambit2.rest.QueryStaXReporter
 
getURL() - Method in interface ambit2.base.data.ILiteratureEntry
 
getURL() - Method in class ambit2.base.data.LiteratureEntry
 
getUrl() - Method in class ambit2.base.data.Property
 
getURL() - Method in class ambit2.base.data.SourceDataset
 
getURL() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getUrl() - Method in exception ambit2.base.exceptions.HttpException
 
getURL() - Method in class ambit2.base.facet.AbstractFacet
 
getUrl() - Method in class ambit2.db.results.AmbitRows
 
getURL(int) - Method in class ambit2.db.results.AmbitRows
 
getURL(String) - Method in class ambit2.db.results.AmbitRows
 
getUrl() - Method in class ambit2.pubchem.HTTPRequest
 
getUrl() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
getUrlPrefix() - Method in class ambit2.db.reporters.ARFFReporter
 
getUrlPrefix() - Method in class ambit2.db.reporters.CSVReporter
 
getUsedInchies() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
getUseMOEvPrimitive() - Method in class ambit2.smarts.SmartsManager
 
getUser() - Method in class ambit2.base.data.AbstractLabel
 
getUser() - Method in class ambit2.db.LoginInfo
 
getUser() - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
getUser() - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
getUser() - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
getUser() - Method in class ambit2.dbui.LoginInfoBean
 
getUser() - Method in class ambit2.rest.model.task.CallableModelCreator
 
getUserid() - Method in class ambit2.rest.task.Task
 
getUsername() - Method in class ambit2.base.data.SourceDataset
 
getUserName() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getUsername() - Method in class ambit2.db.results.AmbitRows
 
getUserName() - Method in class ambit2.rest.ProtectedResource
 
getUserPass() - Method in class ambit2.db.processors.DbCreateDatabase
 
getUserToken(String) - Method in class ambit2.rest.task.LauncherResource
 
getUuid() - Method in class ambit2.base.data.Bookmark
 
getUuid() - Method in class ambit2.rest.task.CallableMockup
 
getUuid() - Method in class ambit2.rest.task.CallableProtectedTask
 
getUuid() - Method in class ambit2.rest.task.Task
 
getValencySum(IAtomContainer) - Static method in class ambit2.tautomers.FilterTautomers
 
getValidationConfig() - Method in class ambit2.groupcontribution.GroupContributionModel
 
getValue() - Method in class ambit2.base.data.study.ReliabilityParams
 
getValue() - Method in class ambit2.base.facet.AbstractFacet
 
getValue() - Method in class ambit2.core.data.AbstractDescriptorResultType
 
getValue() - Method in class ambit2.core.data.model.Parameter
 
getValue(String) - Static method in class ambit2.core.io.SGroupMDL2000Helper
Extracts first 6 chars, replaces spaces with underscore '_' and calls SGROUP_LINE.valueof method.
getValue(int) - Method in class ambit2.core.io.StringArrayHeader
 
getValue(DescriptorValue, Property, int) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
getValue(IAtomContainer) - Method in class ambit2.db.processors.PropertyImporter
 
getValue(IStructureRecord, Property, int) - Method in class ambit2.db.processors.PropertyValuesWriter
 
getValue(Target, Property, int) - Method in class ambit2.db.processors.ValueWriter
 
getValue() - Method in class ambit2.db.readers.PropertyValue
 
getValue() - Method in class ambit2.db.search.AbstractQuery
 
getValue() - Method in class ambit2.db.search.property.FilteredCount
 
getValue() - Method in class ambit2.db.search.property.PropertyStatsString
 
getValue() - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
getValue() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
getValue() - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
getValue() - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
getValue(DescriptorValue, Property, int) - Method in class ambit2.descriptors.processors.DescriptorValue2Property
 
getValue(AMBITAppConfigProperties) - Method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
 
getValue() - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
getValue(Request) - Method in enum ambit2.rest.OpenTox.URI
 
getValue() - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
getValue() - Method in interface ambit2.rules.conditions.IValueCondition
 
getValue() - Method in interface ambit2.rules.conditions.value.IValue
 
getValue() - Method in class ambit2.rules.conditions.value.Value
 
getValue() - Method in class ambit2.rules.conditions.ValueCondition
 
getValue() - Method in class ambit2.similarity.stats.MutableInt
 
getValue() - Method in class ambit2.sln.SLNLogicalExpression
 
getValue() - Method in class ambit2.smarts.SmartsLogicalExpression
 
getValue() - Method in class ambit2.ui.table.BrowsableTableModel
 
getValue() - Method in interface ambit2.ui.table.IFindNavigator
 
getValueAt(int, int) - Method in class ambit2.base.data.PropertiesTableModel
 
getValueAt(int, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
getValueAt(int, int) - Method in class ambit2.dbui.CachedRowSetTableModel
 
getValueAt(int, int) - Method in class ambit2.similarity.stats.ConfusionMatrix
 
getValueAt(int, int) - Method in class ambit2.ui.table.BrowsableTableModel
 
getValueAt(int, int) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
getValueColumn(QuerySolution) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
getValueID() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getValueID() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getValueID() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getValueID() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getValueID() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getValueID() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getValueInterval() - Method in interface ambit2.rules.conditions.IValueIntervalCondition
 
getValuesArray(Form) - Method in enum ambit2.rest.OpenTox.params
 
getValuesReader() - Method in class ambit2.rest.model.task.CallableModelPredictor
 
getValueTransformation() - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
getValueTransformation() - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
getValueTransformation() - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
getValueTransformation() - Method in interface ambit2.groupcontribution.groups.IGroup
 
getValueTransformation() - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
getValueTransformation() - Method in interface ambit2.groupcontribution.transformations.IHasValueTransformation
 
getValueType() - Method in class ambit2.db.search.property.PropertiesByDataset
 
getValueType() - Method in class ambit2.db.search.property.PropertiesByQuery
 
getValueType() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
getValueType() - Method in class ambit2.db.search.property.RetrieveFieldNames
 
getValueType() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
getValueType() - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
getVariant() - Method in exception ambit2.rest.exception.RResourceException
 
getVariants() - Method in class ambit2.rest.AbstractResource
 
getVersion() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
getVersionDescription() - Method in class ambit2.core.data.HashIntDescriptorResult
 
getVersionDescription() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
getVersionDescription() - Method in class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
getVersionLong() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
getVersionShort() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
getVertexEccentricity(int[][]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
getViewer() - Method in class ambit2.ui.jmol.ImageTools3D
 
getVisibleIndex(int) - Method in class ambit2.base.data.ProfileListModel
 
getVolume(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getWait(CommandLine) - Static method in class ambit2.pubchem.SearchApplication
 
getWait_ms() - Method in class ambit2.pubchem.NCISearchProcessor
 
getWarnFilters(IAtomContainer) - Method in class ambit2.tautomers.FilterTautomers
 
getWarnings() - Method in class ambit2.db.results.AmbitRows
 
getWarnings() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
getWeight() - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
getWeight() - Method in class ambit2.reactions.generator.score.components.KnimeWorkflowScore
 
getWeight() - Method in interface ambit2.reactions.generator.score.IScoreComponent
 
getWhereQuery() - Method in class ambit2.db.search.structure.QueryFieldMultiple
 
getWidth() - Method in class ambit2.db.chart.ChartGenerator
 
getWidth() - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
getWidth() - Method in class ambit2.search.csls.CSLSImageRequest
 
getWorkFolder() - Method in class ambit2.base.external.CommandShell
 
getWritableContent() - Method in class ambit2.base.data.StructureRecord
 
getWritableContent() - Method in interface ambit2.base.interfaces.IStructureRecord
 
getWritableContent() - Method in class ambit2.base.relation.composition.CompositionRelation
 
getWriter() - Method in class ambit2.core.io.FileOutputState
 
getWriter(OutputStream, String) - Static method in class ambit2.core.io.FileOutputState
 
getWriter(String) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
getWriter() - Method in interface ambit2.core.io.IOutputState
 
getWriter() - Method in class ambit2.rest.model.task.CallableModelPredictor
 
getWriterClassName() - Method in class ambit2.core.io.DelimitedFileFormat
 
getWriterClassName() - Method in class ambit2.core.io.XLSFileFormat
 
getWww() - Method in class ambit2.base.data.AmbitUser
 
getXmlISAConfig() - Method in class ambit2.export.isa.json.ISAJsonExporter
 
getXmlISAConfig() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
getXSDType() - Method in enum ambit2.db.search.property.AbstractPropertyRetrieval._PROPERTY_TYPE
 
getYear(Row) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
getYieldHi() - Method in class ambit2.reactions.GenericReaction
 
getYieldLo() - Method in class ambit2.reactions.GenericReaction
 
getZeroColumns() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
gf - Static variable in class ambit2.dbui.QuerySmartsEditor
 
GGroup - Class in ambit2.groupcontribution.groups
 
GGroup() - Constructor for class ambit2.groupcontribution.groups.GGroup
 
globalDescriptors - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
globalDescriptorsString - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
GlobDictOffseet - Static variable in class ambit2.sln.SLNConst
 
googleAnalytics - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
GraphMatrices - Class in ambit2.descriptors.utils
 
GraphMatrices() - Constructor for class ambit2.descriptors.utils.GraphMatrices
 
GraphMatrices.DMAtomState - Enum in ambit2.descriptors.utils
 
Grid2ContourGrid(double[]) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
Grid2ContourGrid uses precalculated MultivariateHPDLevels to store HPD values for each grid cell
groundTruth - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
group - Static variable in class ambit2.db.search.structure.AbstractStructureQuery
 
group - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
groupBy() - Method in class ambit2.db.search.QueryCombined
 
groupBy() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
groupByInterpretationResult - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
GroupContributionCli - Class in ambit2.groupcontribution.cli
 
GroupContributionCli() - Constructor for class ambit2.groupcontribution.cli.GroupContributionCli
 
GroupContributionModel - Class in ambit2.groupcontribution
 
GroupContributionModel() - Constructor for class ambit2.groupcontribution.GroupContributionModel
 
GroupContributionModel.GCMConfigInfo - Class in ambit2.groupcontribution
 
GroupContributionModel.Type - Enum in ambit2.groupcontribution
 
GroupException - Exception in ambit2.core.groups
 
GroupException(String) - Constructor for exception ambit2.core.groups.GroupException
 
GroupException(String, Exception) - Constructor for exception ambit2.core.groups.GroupException
 
groupFrequencies - Variable in class ambit2.groupcontribution.fragmentation.Fragmentation
 
GroupInfo - Class in ambit2.groupcontribution.groups
 
GroupInfo() - Constructor for class ambit2.groupcontribution.groups.GroupInfo
 
groupMatch - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
groupMatch - Variable in class ambit2.groupcontribution.nmr.Substituent
 
GroupMatch - Class in ambit2.smarts.groups
 
GroupMatch(String, SmartsParser, IsomorphismTester) - Constructor for class ambit2.smarts.groups.GroupMatch
 
groupMatchRepository - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
GroupNotFoundException - Exception in ambit2.core.groups
 
GroupNotFoundException(String) - Constructor for exception ambit2.core.groups.GroupNotFoundException
 
groupProperties - Variable in class ambit2.db.reporters.AbstractStructureRecordReporter
 
groupProperties - Variable in class ambit2.db.reporters.QueryHeaderReporter
 
groupProperties - Variable in class ambit2.db.reporters.SDFReporter
 
groupProperties - Variable in class ambit2.db.reporters.SmilesReporter
 
groupProperties - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
groups - Variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
GUARD_ENABLED - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
GUARD_LIST - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
guessLabel(String) - Static method in class ambit2.base.data.Property
public constructors for web services
guidance - Variable in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 

H

h16 - Variable in class ambit2.db.processors.FP1024Writer
 
h16 - Variable in class ambit2.db.update.fp.CreateFingerprintChemical
 
h16 - Variable in class ambit2.db.update.fp.CreateFingerprintStructure
 
ha - Variable in class ambit2.db.processors.DescriptorsCalculator
 
hAdder - Variable in class ambit2.core.processors.structure.FingerprintGenerator
 
hadder - Variable in class ambit2.core.processors.structure.MoleculeReader
 
hAdder - Variable in class ambit2.db.search.structure.QuerySMARTS
 
hAdder - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
hAdder - Variable in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
hadder - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
HammingDistance - Class in ambit2.similarity.measure
The Hamming distance between two strings of equal length is the number of positions for which the corresponding symbols are different/
HammingDistance() - Constructor for class ambit2.similarity.measure.HammingDistance
 
handleDoubleClick(Object) - Method in class ambit2.ui.editors.ListEditor
 
handleError(String) - Method in class ambit2.core.io.IteratingFileReader
handleError(String, Exception) - Method in class ambit2.core.io.IteratingFileReader
handleError(String, int, int, int) - Method in class ambit2.core.io.IteratingFileReader
handleError(String, int, int, int, Exception) - Method in class ambit2.core.io.IteratingFileReader
handleError(String) - Method in class ambit2.core.io.RawIteratingWrapper
handleError(String, Exception) - Method in class ambit2.core.io.RawIteratingWrapper
handleError(String, int, int, int) - Method in class ambit2.core.io.RawIteratingWrapper
handleError(String, int, int, int, Exception) - Method in class ambit2.core.io.RawIteratingWrapper
handleError(Exception) - Method in class ambit2.model.dataset.DoubleArrayDataset
 
handleError(Exception) - Method in interface ambit2.model.IDataset
 
handleError(String) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
handleError(String, Exception) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
handleError(String, int, int, int) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
handleError(String, int, int, int, Exception) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
handleException(Exception) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
handleFormat(IStructureRecord.MOL_TYPE, IStructureRecord) - Method in class ambit2.core.processors.structure.MoleculeReader
 
handleGroupRecursiveAtoms(IAtomContainer, IQueryAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
handleOutput(InputStream, Status, Reference) - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
handleOutputRDF(InputStream, Status) - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
handleOverlappingHAtomEnvironmentInstances() - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
handlePrescreen - Variable in class ambit2.db.DbReader
 
handler - Variable in class ambit2.rest.wrapper.WrappedService
 
handleReactionInstances(Map<GenericReaction, List<List<IAtom>>>, IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
has2DCoordinates(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor
 
has3DCoordinates(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor
 
hasAlleneAtomsInCycle(IAtomContainer) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
hasBondOrderUnsetAromatic(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
 
hasCapability(Capabilities.Capability) - Method in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
hasDxProperties(IStructureRecord) - Static method in class ambit2.core.io.dx.DXParser
 
hasErrors() - Method in class ambit2.smarts.SMIRKSManager
 
hasExtension(String) - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
hasExtension(File) - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
hashCode() - Method in class ambit2.base.data.LiteratureEntry
 
hashCode() - Method in class ambit2.base.data.Property
 
hashCode() - Method in class ambit2.base.data.study.EffectRecord
 
hashCode() - Method in class ambit2.base.data.study.Params
 
hashCode() - Method in class ambit2.base.data.study.ProtocolApplication
 
hashCode() - Method in class ambit2.base.data.study.ReliabilityParams
 
hashCode() - Method in class ambit2.base.data.substance.SubstanceProperty
 
hashCode - Variable in class ambit2.core.io.FileState
 
hashCode() - Method in class ambit2.core.io.StringArrayHeader
 
hashCode() - Method in class ambit2.descriptors.SizeDescriptor
 
hashCode() - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
hashCode() - Method in class ambit2.similarity.stats.ValuePair
 
hashCode() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
HashDescriptorResult<V> - Class in ambit2.core.data
 
HashDescriptorResult(Map<String, V>) - Constructor for class ambit2.core.data.HashDescriptorResult
 
HashIntDescriptorResult - Class in ambit2.core.data
 
HashIntDescriptorResult(Map<String, Integer>) - Constructor for class ambit2.core.data.HashIntDescriptorResult
 
hasHydrogens(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor
 
hasID() - Method in interface ambit2.base.data.ILiteratureEntry
 
hasID() - Method in class ambit2.base.data.LiteratureEntry
 
hasID() - Method in class ambit2.base.data.SourceDataset
 
hasImplicitHStereoLigand - Variable in class ambit2.smarts.SmartsAtomExpression
 
hasIsomorphism(IAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
 
hasIsomorphism(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
hasLegend() - Method in class ambit2.db.chart.ChartGenerator
 
hasNewAlleneAtoms(IAtomContainer) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
hasNewAlleneAtomsInCycle(IAtomContainer) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
hasNext() - Method in class ambit2.chebi.ChEBIClient
 
hasNext() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator
 
hasNext() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
hasNext() - Method in class ambit2.core.io.I5ReaderSimple
 
hasNext() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
hasNext() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
hasNext() - Method in class ambit2.core.io.IteratingFileReader
 
hasNext() - Method in class ambit2.core.io.IteratingFolderReader
 
hasNext() - Method in class ambit2.core.io.IteratingXLSReader
 
hasNext() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
hasNext() - Method in class ambit2.core.io.RawIteratingCSVReader
 
hasNext() - Method in class ambit2.core.io.RawIteratingReader
 
hasNext() - Method in class ambit2.core.io.RawIteratingWrapper
 
hasNext() - Method in class ambit2.core.io.ToXMLReaderSimple
 
hasNext() - Method in class ambit2.db.RepositoryReader
 
hasNext() - Method in class ambit2.db.results.RowsModel
 
hasNext() - Method in class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
hasNext() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
hasNext() - Method in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
hasNext() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
hasNext() - Method in class ambit2.rest.rdf.RDFObjectIterator
Verifies if there are more objects of the type
hasNext() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
hasNext() - Method in class ambit2.rest.task.FilteredTasksIterator
 
hasNext() - Method in class ambit2.rest.task.SingleTaskIterator
 
hasNext() - Method in class ambit2.smarts.BinaryCombinations
 
hasNext() - Method in class ambit2.some.SOMERawReader
 
hasNext() - Method in class ambit2.ui.jmol.CdkJmolAdapter.StructureIterator
 
hasPreconditionAtom(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
hasPreconditionAtomDefined() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
hasPreconditionAtomtype(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
hasPreconditionAtomTypeDefined() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
hasRecursiveSmarts - Variable in class ambit2.smarts.SmartsFlags
 
hasRecursiveSmarts - Variable in class ambit2.smarts.SmartsParser
 
hasRecursiveSmarts - Variable in class ambit2.tautomers.RuleStateFlags
 
hasSetting(String) - Method in class ambit2.core.io.IteratingFileReader
 
hasSetting(String) - Method in class ambit2.core.io.RawIteratingWrapper
 
hasSetting(String) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
hasSMARTSPattern(IAtomContainer) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
hasSMARTSPattern(T) - Method in interface ambit2.smarts.query.ISmartsPattern
 
hasSMARTSPattern(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
hasSMARTSPattern(IAtomContainer) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
hasType(AlgorithmType) - Method in class ambit2.core.data.model.Algorithm
 
hasType(String) - Method in class ambit2.core.data.model.Algorithm
 
hat - Variable in class ambit2.model.numeric.DataCoverageLeverage
 
hat - Variable in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
HAtomEnvironment - Class in ambit2.groupcontribution.nmr.nmr_1h
 
HAtomEnvironment() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
HAtomEnvironment.ShiftAssociation - Enum in ambit2.groupcontribution.nmr.nmr_1h
 
HAtomEnvironmentInstance - Class in ambit2.groupcontribution.nmr.nmr_1h
 
HAtomEnvironmentInstance() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironmentInstance
 
HAtomEnvironmentInstance(IAtom[], HAtomEnvironment) - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironmentInstance
 
hAtomEnvironments - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
HAtomManager - Class in ambit2.smarts.smirks
 
HAtomManager() - Constructor for class ambit2.smarts.smirks.HAtomManager
 
HAtomMode - Variable in class ambit2.tautomers.Rule
 
hAtomsFlag - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
header(Output, ItemList) - Method in class ambit2.base.processors.batch.BatchReporter
 
header - Variable in class ambit2.core.io.FilesWithHeaderWriter
 
header - Variable in class ambit2.core.io.FileWithHeaderWriter
 
header - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
header - Variable in class ambit2.core.io.StringArrayHeader
 
header(Result, IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
header(Writer, Q) - Method in class ambit2.db.reporters.ARFFReporter
 
header(Writer, Q) - Method in class ambit2.db.reporters.CMLReporter
 
header(Writer, Q) - Method in class ambit2.db.reporters.CSVReporter
 
header(StringWriter, Q) - Method in class ambit2.db.reporters.ImageAreaReporter
 
header(BufferedImage, Q) - Method in class ambit2.db.reporters.ImageReporter
 
header(Document, Q) - Method in class ambit2.db.reporters.PDFReporter
 
header - Variable in class ambit2.db.reporters.QueryHeaderReporter
 
header(Output, Q) - Method in class ambit2.db.reporters.QueryPacketReporter
 
header(Output, Q) - Method in class ambit2.db.reporters.QueryProperyReporter
 
header(Document, Q) - Method in class ambit2.db.reporters.RTFReporter
 
header(Writer, Q) - Method in class ambit2.db.reporters.SDFReporter
 
header(Writer, Q) - Method in class ambit2.db.reporters.SmilesReporter
 
header(OutputStream, Q) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
header(OutputStream, Q) - Method in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
header - Variable in class ambit2.ml.io.OutputARFF
 
header(XMLStreamWriter) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
xmlns:ac="http://apps.ideaconsult.net:8080/ambit2/compound/" xmlns:ot="http://www.opentox.org/api/1.1#" xmlns:bx="http://purl.org/net/nknouf/ns/bibtex#" xmlns:otee="http://www.opentox.org/echaEndpoints.owl#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:ar="http://apps.ideaconsult.net:8080/ambit2/reference/" xmlns="http://apps.ideaconsult.net:8080/ambit2/" xmlns:am="http://apps.ideaconsult.net:8080/ambit2/model/" xmlns:af="http://apps.ideaconsult.net:8080/ambit2/feature/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:ad="http://apps.ideaconsult.net:8080/ambit2/dataset/" xmlns:ag="http://apps.ideaconsult.net:8080/ambit2/algorithm/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:ota="http://www.opentox.org/algorithmTypes.owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xml:base="http://apps.ideaconsult.net:8080/ambit2/">
header - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
header(XMLStreamWriter) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
header(Writer, Q) - Method in class ambit2.rest.dataset.DatasetURIReporter
 
header - Variable in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
header(ResultSet) - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
header - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
header(XMLStreamWriter, Q) - Method in class ambit2.rest.QueryStaXReporter
 
header(Writer, Iterator<T>) - Method in class ambit2.rest.reporters.CatalogRDFReporter
 
header(Writer, Iterator<T>) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
header(Writer, Iterator<UUID>) - Method in class ambit2.rest.reporters.TaskRDFReporter
 
header(Model, Q) - Method in class ambit2.rest.substance.SubstanceRDFReporter
 
header(XMLStreamWriter) - Method in class ambit2.rest.substance.SubstanceRecordStaxWriter
 
header() - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
header - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
header() - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
header() - Method in class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
header() - Method in class ambit2.rest.task.dsl.OTDatasetTableReport
 
header(Writer, Iterator<UUID>) - Method in class ambit2.rest.task.TaskJSONReporter
 
header - Variable in class ambit2.ui.EditableHeaderUI.MouseInputHandler
 
HEADER_ROW - Variable in class ambit2.ui.EditableHeader
 
headerActions - Variable in class ambit2.ui.QueryBrowser
 
HeaderComboBoxModel - Class in ambit2.ui
JTable header as a combobox, allowing sorting and filtering
HeaderComboBoxModel(JTable, int, IHeaderAction[]) - Constructor for class ambit2.ui.HeaderComboBoxModel
 
headerEditor - Variable in class ambit2.ui.EditableHeaderTableColumn
 
headers - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
headings - Variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
headings - Variable in class ambit2.similarity.stats.PredictionModelStatistics
 
height - Variable in class ambit2.db.chart.ChartGenerator
 
height - Variable in class ambit2.pubchem.rest.PUGRestImageRequest
 
height - Variable in class ambit2.search.csls.CSLSImageRequest
 
hellinger(AtomEnvironmentList) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
Hellinger distance between two discrete probability distributions pi and qi.
hellinger(Histogram) - Method in class ambit2.domain.stats.datastructures.Histogram
Hellinger distance between two discrete probability distributions pi and qi * @param hist
hellinger(Histogram) - Method in class ambit2.similarity.stats.Histogram
Hellinger distance between two discrete probability distributions pi and qi * @param hist
help - Variable in class ambit2.ui.editors.SelectFieldsPanel
 
helper - Variable in class ambit2.db.processors.DbDescriptorValuesWriter
 
hEnvironment - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironmentInstance
 
HeteroAtomCountDescriptor - Class in ambit2.descriptors.constitutional
Number of atoms which are not hydrogens and carbons .
HeteroAtomCountDescriptor() - Constructor for class ambit2.descriptors.constitutional.HeteroAtomCountDescriptor
 
hidden - Variable in class ambit2.base.relation.composition.CompositionRelation
 
hidden - Variable in class ambit2.core.data.model.ModelQueryResults
 
high - Variable in class ambit2.similarity.stats.Bin
 
higherPriorityEnvironments - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
HighestDensityRegions - Interface in ambit2.domain.stats.transforms.densityestimation
Highest Density Regions calculations
hint - Variable in class ambit2.smarts.query.AbstractSmartsPattern
 
Histogram<T extends Comparable> - Class in ambit2.domain.stats.datastructures
A histogram.
Histogram() - Constructor for class ambit2.domain.stats.datastructures.Histogram
 
histogram - Variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
histogram - Variable in class ambit2.similarity.stats.ConfusionMatrix
 
Histogram<T extends Comparable> - Class in ambit2.similarity.stats
A histogram.
Histogram() - Constructor for class ambit2.similarity.stats.Histogram
 
histogram2file(TDigest, String, String) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
histogram2string(TDigest) - Static method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
histogram2string(TDigest, int, boolean, boolean) - Static method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
histogram_dataset - Static variable in class ambit2.db.chart.HistogramChartGenerator
 
histogram_query - Static variable in class ambit2.db.chart.HistogramChartGenerator
 
HistogramChartGenerator - Class in ambit2.db.chart
 
HistogramChartGenerator() - Constructor for class ambit2.db.chart.HistogramChartGenerator
 
histToString(double[][]) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
hitListSize - Variable in class ambit2.smarts.StructureSetAnalyzer
 
hits - Variable in class ambit2.db.DbReaderStructure
 
HLC - Static variable in class ambit2.base.ro.I5CONSTANTS
 
HNMRKnowledgeBase - Class in ambit2.groupcontribution.nmr.nmr_1h
 
HNMRKnowledgeBase() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
HNMRPredefinedKnowledgeBase - Class in ambit2.groupcontribution.nmr.nmr_1h
 
HNMRPredefinedKnowledgeBase() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
HNMRPredictCli - Class in ambit2.groupcontribution.cli
 
HNMRPredictCli() - Constructor for class ambit2.groupcontribution.cli.HNMRPredictCli
 
HNMRShifts - Class in ambit2.groupcontribution.nmr
 
HNMRShifts() - Constructor for class ambit2.groupcontribution.nmr.HNMRShifts
 
HNMRShifts(File) - Constructor for class ambit2.groupcontribution.nmr.HNMRShifts
 
hns(double[], int, Kernel) - Static method in class ambit2.domain.stats.transforms.densityestimation.Bandwidth
 
HOST - Static variable in class ambit2.base.config.Preferences
 
host - Variable in class ambit2.db.LoginInfo
 
host - Variable in class ambit2.pubchem.NCISearchProcessor
 
hp - Variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
HPDBySorting(Matrix) - Method in interface ambit2.domain.stats.transforms.densityestimation.HighestDensityRegions
 
HPDBySorting(Matrix) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
HighestDensityRegions interface
HRM_Explicit - Static variable in class ambit2.tautomers.TautomerConst
 
HRM_Implicit - Static variable in class ambit2.tautomers.TautomerConst
 
HRM_Undefined - Static variable in class ambit2.tautomers.TautomerConst
 
HShift - Class in ambit2.groupcontribution.nmr.nmr_1h
 
HShift() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
hssf - Variable in class ambit2.core.io.IteratingXLSReader
 
hstyle - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
hstyle - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
htmlbyTemplate - Variable in class ambit2.rest.freemarker.FreeMarkerSupport
 
HttpException - Exception in ambit2.base.exceptions
 
HttpException(String, int, String) - Constructor for exception ambit2.base.exceptions.HttpException
 
httpMethod - Variable in class ambit2.pubchem.HTTPRequest
 
HTTPRequest<Target,Result> - Class in ambit2.pubchem
 
HTTPRequest() - Constructor for class ambit2.pubchem.HTTPRequest
 
HybridizationFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
Wrapper for HybridizationFingerprinter, implementing IMolecularDescriptor
HybridizationFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.HybridizationFingerprinterWrapper
 
HydrogenAdderProcessor - Class in ambit2.core.processors.structure
 
HydrogenAdderProcessor() - Constructor for class ambit2.core.processors.structure.HydrogenAdderProcessor
 
hydrogens - Variable in class ambit2.balloon.ShellBalloon
 
hydrogens - Variable in class ambit2.core.processors.structure.FingerprintGenerator
 
hydrogens - Variable in class ambit2.core.smiles.OpenBabelAbstractShell
 

I

I5_REFERENCE - Static variable in class ambit2.core.io.I5ReaderSimple
 
I5_STUDY_SECTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
I5_URL - Static variable in class ambit2.core.io.I5ReaderSimple
 
I5CONSTANTS - Class in ambit2.base.ro
 
I5CONSTANTS() - Constructor for class ambit2.base.ro.I5CONSTANTS
 
i5mode - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
I5ReaderSimple - Class in ambit2.core.io
IUCLID5 .i5d files support http://iuclid.eu/ Reads ReferenceSubstances only.
I5ReaderSimple(InputStreamReader) - Constructor for class ambit2.core.io.I5ReaderSimple
 
I5ReaderSimple(InputStream) - Constructor for class ambit2.core.io.I5ReaderSimple
 
I5ReaderSimple.i5_refs_attr - Enum in ambit2.core.io
 
I5ReaderSimple.i5_tags - Enum in ambit2.core.io
 
I5Utils - Class in ambit2.base.data
 
IAcceptable - Interface in ambit2.smarts
 
IAcidicCenter - Interface in ambit2.tautomers.zwitterion
 
IAcidicCenter.State - Enum in ambit2.tautomers.zwitterion
 
IAction<RESULT> - Interface in ambit2.rules.actions
 
IActionRule - Interface in ambit2.rules
 
IAmbitEditor<T> - Interface in ambit2.base.interfaces
A class implementing this interface provides common means of visualisation.
IAmbitResult - Interface in ambit2.base.processors
Provides means of accumulating results from processing multiple compounds by ambit2.processors.IAmbitProcessor TODO verify whether we need all of the methods here.
IAtomContainerAction - Interface in ambit2.core.i
 
IAtomContainerHighlights - Interface in ambit2.rendering
Expected to set selection for image highlights
IAttributeSelection<T> - Interface in ambit2.featureselection
 
IBasicCenter - Interface in ambit2.tautomers.zwitterion
 
IBasicCenter.State - Enum in ambit2.tautomers.zwitterion
 
IBasicRule - Interface in ambit2.rules
 
IBatchProcessor<Target,ItemInput,Result> - Interface in ambit2.base.interfaces
 
IBrowserMode - Interface in ambit2.ui.table
 
IBrowserMode.BrowserMode - Enum in ambit2.ui.table
 
ICategory - Interface in ambit2.base.interfaces
Interface to set the semantic interpretation of a property value
ICategory.CategoryType - Enum in ambit2.base.interfaces
Assigns whether the category denotes toxicity or not.
ICenter - Interface in ambit2.tautomers.zwitterion
 
IChemical - Interface in ambit2.base.interfaces
 
ICiteable - Interface in ambit2.base.interfaces
 
ICommand - Interface in ambit2.db.processors
 
ICommand.COMMAND - Enum in ambit2.db.processors
 
ICompoundImageTools - Interface in ambit2.core.io
 
icon - Variable in class ambit2.base.data.ClassHolder
 
ICondition - Interface in ambit2.rules.conditions
 
ICondition.CondType - Enum in ambit2.rules.conditions
 
ICorrectionFactor - Interface in ambit2.groupcontribution.correctionfactors
 
ICorrectionFactor.Type - Enum in ambit2.groupcontribution.correctionfactors
 
ID - Variable in class ambit2.base.data.AbstractDataset
 
id - Variable in class ambit2.base.data.LiteratureEntry
 
id - Variable in class ambit2.base.data.Property
 
id - Variable in class ambit2.base.data.SourceDataset
 
id - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
id - Variable in class ambit2.base.data.Template
 
id - Variable in class ambit2.core.data.model.Algorithm
 
id - Variable in class ambit2.core.data.model.ModelWrapper
 
id - Variable in class ambit2.core.io.fp.MultiFingerprintsWriter
 
id - Variable in class ambit2.db.search.AbstractQuery
 
id - Variable in class ambit2.db.search.property.FilteredCount
 
id - Variable in class ambit2.db.search.QueryCombined
 
id - Variable in class ambit2.db.search.StoredQuery
 
id - Variable in class ambit2.db.SessionID
 
id - Variable in class ambit2.descriptors.PKANode
 
id - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
id - Variable in class ambit2.export.isa.v1_0.objects.Comment
 
id - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
id - Variable in class ambit2.export.isa.v1_0.objects.Data
 
id - Variable in class ambit2.export.isa.v1_0.objects.Factor
 
id - Variable in class ambit2.export.isa.v1_0.objects.FactorValue
 
id - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
id - Variable in class ambit2.export.isa.v1_0.objects.Material
 
id - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttribute
 
id - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttributeValue
 
id - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
id - Variable in class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
id - Variable in class ambit2.export.isa.v1_0.objects.Person
 
id - Variable in class ambit2.export.isa.v1_0.objects.Process
 
id - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
id - Variable in class ambit2.export.isa.v1_0.objects.ProtocolParameter
 
id - Variable in class ambit2.export.isa.v1_0.objects.Sample
 
id - Variable in class ambit2.export.isa.v1_0.objects.Source
 
id - Variable in class ambit2.export.isa.v1_0.objects.Study
 
id - Variable in class ambit2.reactions.GenericReaction
 
id - Variable in class ambit2.reactions.Reaction
 
id - Variable in class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialData
 
id - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
id - Variable in class ambit2.tautomers.rules.EnergyRule
 
ID - Variable in class ambit2.tautomers.TautomerIncrementStep
 
id_srcdataset - Variable in class ambit2.base.data.StructureRecord
 
IDataCoverage<DATA> - Interface in ambit2.model.numeric
 
IDataset<ID,Features,ResultType extends Comparable<?>> - Interface in ambit2.model
 
idchemical - Variable in class ambit2.base.data.StructureRecord
 
idchemical_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
idchemical_tag - Variable in class ambit2.db.processors.RepositoryWriter
 
idColumn - Variable in class ambit2.ui.table.BrowsableTableModel
 
idcompound - Variable in class ambit2.db.reporters.QueryPacketReporter
 
idcompound_resource - Static variable in class ambit2.rest.DataResources
 
idconformer_resource - Static variable in class ambit2.rest.DataResources
 
identifier - Variable in class ambit2.base.data.substance.SubstanceProperty
 
identifier - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
identifier - Variable in class ambit2.export.isa.v1_0.objects.Study
 
identifier1 - Variable in class ambit2.db.search.QueryInfo
 
identifier2 - Variable in class ambit2.db.search.QueryInfo
 
identifier3 - Variable in class ambit2.db.search.QueryInfo
 
identifierKey - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
identifierPass - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
identifiers - Variable in class ambit2.rest.legacy.OTCompound
Deprecated.
 
IDescriptorSolver - Interface in ambit2.rules.conditions
 
IDescriptorValueCondition - Interface in ambit2.rules.conditions
 
IDistanceFunction<T> - Interface in ambit2.similarity.measure
 
idproperty - Variable in class ambit2.base.data.PropertyAnnotation
 
idresult - Variable in class ambit2.base.data.study.EffectRecord
 
idresult - Variable in class ambit2.base.data.study.ValueAnnotated
 
idstructure - Variable in class ambit2.base.data.StructureRecord
 
idstructure - Variable in class ambit2.db.reporters.QueryPacketReporter
 
idstructure_SNLAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
idsubstance - Variable in class ambit2.base.data.SubstanceRecord
 
IEvaluation<Content> - Interface in ambit2.core.data.model
 
IEvaluation.EVStatsType - Enum in ambit2.core.data.model
 
IEvaluation.EVType - Enum in ambit2.core.data.model
 
IExpandable - Interface in ambit2.core.groups
 
iFFT1(int, double[], double[], double[], double[]) - Method in class ambit2.domain.stats.transforms.FFT
inverse FFT transform
IFiltered<T> - Interface in ambit2.core.groups
 
IFilteredColumns - Interface in ambit2.base.data
 
IFindNavigator<E> - Interface in ambit2.ui.table
 
IFingerprint<Type,Content> - Interface in ambit2.db.update.fp
 
IFunc - Interface in ambit2.domain.stats
IFunc
IFunction - Interface in ambit2.rules.functions
 
igf - Variable in class ambit2.reactions.reactor.Reactor
 
igf - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
IGNORED - Static variable in class ambit2.similarity.stats.PredictionModelStatistics
 
IGroup - Interface in ambit2.groupcontribution.groups
 
IGroup.Type - Enum in ambit2.groupcontribution.groups
 
IGroupRule - Interface in ambit2.groupcontribution.rules
 
IGroupSet - Interface in ambit2.groupcontribution.groups
 
IHA_INDEX - Static variable in class ambit2.tautomers.TautomerConst
 
IHasValueTransformation - Interface in ambit2.groupcontribution.transformations
 
IHeaderAction - Interface in ambit2.ui.table
 
IInputOutputState - Interface in ambit2.base.interfaces
Status of the input reader/ output writer.
IInputState - Interface in ambit2.core.io
Status of the input reader.
IISADataMapper - Interface in ambit2.export.isa.base
 
IISAExport - Interface in ambit2.export.isa
 
IIUPACComponent - Interface in ambit2.structure2name.components
 
IIUPACComponent.CompState - Enum in ambit2.structure2name.components
 
IIUPACComponent.CompType - Enum in ambit2.structure2name.components
 
ILiteratureEntry - Interface in ambit2.base.data
 
ILiteratureEntry._type - Enum in ambit2.base.data
 
ILocalDescriptor - Interface in ambit2.groupcontribution.descriptors
 
ILocalDescriptor.Type - Enum in ambit2.groupcontribution.descriptors
 
ILocalDescriptorRule - Interface in ambit2.groupcontribution.rules
 
ILocalDescriptorRule.RuleType - Enum in ambit2.groupcontribution.rules
 
image - Variable in class ambit2.base.data.ClassHolder
 
image - Variable in class ambit2.rendering.CachedImage
 
image - Variable in class ambit2.ui.Panel2D
 
ImageAreaReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
ImageAreaReporter(String, String, String) - Constructor for class ambit2.db.reporters.ImageAreaReporter
 
ImageAreaReporter(String, String, Dimension, String) - Constructor for class ambit2.db.reporters.ImageAreaReporter
 
ImageCellRenderer - Class in ambit2.ui
Table cell renderer for Image and IAtomconainer.
ImageCellRenderer(Dimension) - Constructor for class ambit2.ui.ImageCellRenderer
 
ImageCellRenderer() - Constructor for class ambit2.ui.ImageCellRenderer
 
imageMap(ImageMapAreaElement, Rectangle2D) - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
 
imageMap - Variable in class ambit2.rendering.CachedImage
 
imageMap - Variable in class ambit2.rendering.CompoundImageTools
 
ImageMapAreaElement - Class in ambit2.rendering
 
ImageMapAreaElement(double, double, String, Color) - Constructor for class ambit2.rendering.ImageMapAreaElement
 
ImageMapGenerator - Class in ambit2.rendering
 
ImageMapGenerator() - Constructor for class ambit2.rendering.ImageMapGenerator
 
imageRenderers - Variable in class ambit2.ui.QueryBrowser
 
ImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
SELECT idchemical,idstructure,text,title FROM structure left join query_results using(idchemical,idstructure) left join `query` using(idquery) left join sessions using(idsessions) where sessions.title="SMARTS" and idchemical=460 and idstructure=100664 union SELECT idchemical,idstructure,null,"SMARTS" FROM structure where idchemical=460 and idstructure=100664
ImageReporter(String, String) - Constructor for class ambit2.db.reporters.ImageReporter
 
ImageReporter(String, String, Dimension) - Constructor for class ambit2.db.reporters.ImageReporter
 
imageReporter - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
IMAGES - Static variable in class ambit2.db.cache.RetrieveStructureImagePath
 
imageSize - Variable in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
imageSize - Variable in class ambit2.pubchem.rest.PUGRestImageRequest
 
imageSize - Variable in class ambit2.rendering.CompoundImageTools
 
imageSize - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
imageSize - Variable in class ambit2.some.SOMEVisualizer
 
imagesrc - Variable in class ambit2.pubchem.DepictRequest
 
imageTools - Variable in class ambit2.core.io.PDFWriter
 
imageTools - Variable in class ambit2.ui.ImageCellRenderer
 
ImageTools3D - Class in ambit2.ui.jmol
JMol wrapper, used in Panel3D
ImageTools3D(Component, Dimension) - Constructor for class ambit2.ui.jmol.ImageTools3D
 
imageWrapper - Variable in class ambit2.db.reporters.AbstractImageReporter
 
IMetaRule - Interface in ambit2.reactions.rules
 
img - Variable in class ambit2.db.reporters.AbstractImageReporter
 
imgHelper - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
imlicitHAtomsNumbers - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
IMLOutput<V> - Interface in ambit2.ml.io
 
IModel - Interface in ambit2.base.data
Moved here for compatibility, since qsar package is removed from CDK > 1.3.4 Classes that implement this interface will build statistical models.
IModelDefinition<ID,Features,ResultType extends Comparable<?>> - Interface in ambit2.model
Defines a model, derived from objects of type FeatureType
IModelHistogram<U extends Bin> - Interface in ambit2.similarity.stats
 
IModelStatistics<ResultType> - Interface in ambit2.model
 
IModelStatistics.ModelStatus - Enum in ambit2.model
 
IMoleculeEditAction - Interface in ambit2.ui
 
IMoleculeFilterCondition - Interface in ambit2.core.filter
 
implementationOf - Variable in class ambit2.core.data.model.Algorithm
 
implicitHAtomsNumber - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
implicitHAtomsVector(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
implicitHydrogens - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
importBundles - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
importBundles(SubstanceRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
importedRecord - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
ImportSubstanceException - Exception in ambit2.rest.exception
 
ImportSubstanceException(Status, String) - Constructor for exception ambit2.rest.exception.ImportSubstanceException
 
importSubstanceMeasurements(SubstanceRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
importSubstanceRecord(SubstanceRecord) - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
importSubstanceRecord(SubstanceRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
Impurity - Class in ambit2.base.relation.composition
Substance composition: impurities
Impurity(SubstanceRecord, IStructureRecord, Proportion) - Constructor for class ambit2.base.relation.composition.Impurity
 
in - Variable in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
incFrequency() - Method in class ambit2.descriptors.AtomEnvironment
 
inchi - Variable in class ambit2.base.data.StructureRecord
 
INCHI - Static variable in class ambit2.core.config.AmbitCONSTANTS
Inchi
inchi - Variable in class ambit2.core.processors.structure.key.InchiKey
 
inchi - Variable in class ambit2.core.processors.structure.key.InchiPropertyKey
 
inchi - Variable in class ambit2.db.search.QueryInfo
 
InChI - Class in ambit2.descriptors
 
InChI() - Constructor for class ambit2.descriptors.InChI
 
inchi - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
inchi - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
InChI2SMILES(String) - Method in class ambit2.tautomers.processor.StructureStandardizer
This is last resort, when creating SMILES from structure fails for whatever reason
InChIChemicalsWriter - Class in ambit2.db.update.chemical
 
InChIChemicalsWriter() - Constructor for class ambit2.db.update.chemical.InChIChemicalsWriter
 
InchiEntry() - Constructor for class ambit2.reactions.retrosynth.ReactionSequence.InchiEntry
 
inchiFactory - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
inchiFactory - Variable in class ambit2.core.processors.structure.MoleculeReader
 
inchiIndex - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
inchiKey - Variable in class ambit2.base.data.StructureRecord
 
InchiKey - Class in ambit2.core.processors.structure.key
Returns inchi
InchiKey() - Constructor for class ambit2.core.processors.structure.key.InchiKey
 
inchiKey - Variable in class ambit2.core.processors.StructureNormalizer
 
inchiKey - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
inchiKey - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
inchiKey_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
InchiProcessor - Class in ambit2.core.processors.structure
 
InchiProcessor() - Constructor for class ambit2.core.processors.structure.InchiProcessor
 
inchiProcessor - Variable in class ambit2.core.processors.StructureNormalizer
 
inchiProperty - Variable in class ambit2.core.io.ToXMLReaderSimple
 
InchiPropertyKey - Class in ambit2.core.processors.structure.key
 
InchiPropertyKey() - Constructor for class ambit2.core.processors.structure.key.InchiPropertyKey
 
inchitag - Static variable in class ambit2.core.processors.structure.key.InchiPropertyKey
 
includeImplicitHAtoms - Variable in class ambit2.reactions.rules.scores.AtomComplexity
 
includeMol - Variable in class ambit2.db.reporters.QueryHeaderReporter
 
includeParent - Variable in class ambit2.db.search.property.QueryOntology
 
increment() - Method in class ambit2.similarity.stats.MutableInt
 
independentVariables - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
index - Static variable in class ambit2.core.data.EINECS
 
index - Variable in class ambit2.core.io.IteratingFolderReader
 
index - Variable in class ambit2.core.io.json.SubstanceStudyParser
 
index - Variable in class ambit2.db.reporters.QueryPacketReporter
 
index - Variable in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
index - Variable in class ambit2.descriptors.processors.DescriptorResultFormatter
 
index - Variable in class ambit2.smarts.ClosureBond
 
indexes - Variable in class ambit2.smarts.AtomSmartsNode
 
indexOf(Object) - Method in class ambit2.core.groups.FilteredList
 
indexOf(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
indexOf(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
indexOf(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer
 
indexOf(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer
 
indexOf(String) - Static method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
indicesToAtoms(int[], IAtomContainer) - Static method in class ambit2.groupcontribution.dataset.LocalProperties
 
indicesToChemLocPropObject(int[], IAtomContainer, LocalProperties.Type) - Static method in class ambit2.groupcontribution.dataset.LocalProperties
 
INearestNeighborsSearch<T> - Interface in ambit2.similarity.knn
 
INearestNeighborsSearch<T> - Interface in ambit2.similarity.stats
 
INeedsDescriptorSolver - Interface in ambit2.rules.conditions
 
inFile - Variable in class ambit2.dragon.DragonShell
 
inFile - Variable in class ambit2.mopac.AbstractMopacShell
 
inFile - Variable in class ambit2.some.SOMEShell
 
inFile - Variable in class ambit2.vega.VegaShell
 
info - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
info - Variable in class ambit2.groupcontribution.nmr.Substituent
 
info - Variable in class ambit2.reactions.GenericReaction
 
info - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
info - Variable in class ambit2.reactions.Reaction
 
init() - Method in class ambit2.core.groups.SuppleAtomContainer
 
init(SubstanceEndpointsBundle) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
init() - Method in class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
init() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
init() - Method in class ambit2.rest.substance.SubstanceRDFReporter
 
init() - Method in class ambit2.structure2name.IUPACNameGenerator
 
initAtomTypes(AtomTypeFactory, IAtomTypeMatcher) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
initBatch(Connection) - Method in class ambit2.db.PreparedStatementBatchExecutor
 
initColumns(int) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
initComponents(L, String[], String[]) - Method in class ambit2.ui.editors.BeanEditor
 
initComponents() - Method in class ambit2.ui.editors.FileSelector
 
initCondition() - Method in class ambit2.db.simiparity.space.QueryQMap
 
initCondition() - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
initFreeMarkerConfiguration() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
initialConnections - Variable in class ambit2.structure2name.IUPACNameGenerator
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.InChI
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.MolecularWeight
Returns a Map which specifies which descriptor is implemented by this class.
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.PKASmartsDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.SizeDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.SpherosityDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
initialise(IChemObjectBuilder) - Method in class ambit2.dragon.DescriptorDragonShell
 
initialise(IChemObjectBuilder) - Method in class ambit2.mopac.DescriptorMopacShell
 
initialise(IChemObjectBuilder) - Method in class ambit2.some.DescriptorSOMEShell
 
initialize() - Method in class ambit2.balloon.ShellBalloon
 
initialize() - Method in class ambit2.base.external.CommandShell
 
initialize() - Method in class ambit2.core.external.ShellSDFoutput
 
initialize() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
initialize() - Method in class ambit2.descriptors.PKASmartsDescriptor
 
initialize() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
initialize() - Method in class ambit2.dragon.DragonShell
 
initialize() - Method in class ambit2.groupcontribution.utils.math.ArrayUtils
 
initialize() - Method in class ambit2.mopac.AbstractMopacShell
 
initialize(IAtom) - Method in class ambit2.smarts.AtomEquivalenceInfo
 
initialize(IAtom, int, IAtomContainer) - Method in class ambit2.smarts.AtomEquivalenceInfo
 
initialize() - Method in class ambit2.smi23d.ShellMengine
 
initialize() - Method in class ambit2.smi23d.ShellSmi2SDF
 
initialize() - Method in class ambit2.some.SOMEShell
 
initialize() - Method in class ambit2.vega.VegaShell
 
InitializeFilter(Matrix, int, int) - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
InitializeFilter(Matrix, int, int) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
InitializeFilter(Matrix, int, int, int[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
initializeReactor(IAtomContainer) - Method in class ambit2.reactions.reactor.Reactor
 
initilize() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
initKDE(int) - Method in class ambit2.model.numeric.DataCoverageDensity
 
initProcessors() - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
initProcessors() - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
initProperties(InputStream) - Static method in class ambit2.base.config.Preferences
 
initQuery(String, String) - Method in class ambit2.db.reporters.AbstractImageReporter
 
initQuery(String, String) - Method in class ambit2.db.reporters.ImageAreaReporter
 
initRows() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
initVariables() - Method in class ambit2.groupcontribution.Learner
 
inMatrix(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
input - Variable in class ambit2.core.data.model.Algorithm
 
input - Variable in class ambit2.core.io.IteratingXLSReader
 
input - Variable in class ambit2.core.io.RawIteratingReader
 
input - Variable in class ambit2.pubchem.rest.PUGRestRequest
 
input - Variable in class ambit2.rest.task.CallableDatasetCreator
 
input - Variable in class ambit2.rest.task.CallablePOST
 
input - Variable in class ambit2.rest.task.LauncherResource
 
inputArg - Variable in class ambit2.reactions.cli.AmbitSmirksCli
 
inputFile - Variable in class ambit2.base.external.CommandShell
 
inputFile - Variable in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
inputFileName - Variable in class ambit2.groupcontribution.cli.GCMPredictCli
 
inputFileName - Variable in class ambit2.groupcontribution.cli.HNMRPredictCli
 
inputFileName - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
inputs - Variable in class ambit2.export.isa.v1_0.objects.Process
 
inputSmiles - Variable in class ambit2.groupcontribution.cli.GCMPredictCli
 
inputSmiles - Variable in class ambit2.groupcontribution.cli.HNMRPredictCli
 
inputSmiles - Variable in class ambit2.reactions.cli.ReactorCli
 
insert_bitset - Static variable in class ambit2.db.processors.FP1024Writer
 
insert_descriptorvalue - Static variable in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
insert_string - Static variable in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
insertProfile(IStoredQuery, Template) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
insertResults(IStoredQuery) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
insertRow() - Method in class ambit2.db.results.AmbitRows
 
insertScreenedResults(IStoredQuery, IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
insertValue(double, Property, int, AbstractPropertyWriter.mode) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
insertValue(String, Property, int, AbstractPropertyWriter.mode) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
insertValue(String, Property, int, AbstractPropertyWriter.mode) - Method in class ambit2.db.processors.ValueWriter
 
insertValue(double, Property, int, AbstractPropertyWriter.mode) - Method in class ambit2.db.processors.ValueWriter
 
insertValueNaN(Property, int, AbstractPropertyWriter.mode) - Method in class ambit2.db.processors.ValueWriter
 
inset - Variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
 
instance - Variable in class ambit2.reactions.retrosynth.RetroSynthStep
 
instanceAtomIndices - Variable in class ambit2.tautomers.TautomerRelation
 
instanceAtoms - Variable in class ambit2.reactions.GenericReactionInstance
 
instances - Variable in class ambit2.core.data.model.ModelWrapper
 
instances - Variable in class ambit2.rest.rdf.RDFInstancesIterator
 
IntArrayResult - Class in ambit2.core.data
Array of integers implementing IDescriptorResult.
IntArrayResult() - Constructor for class ambit2.core.data.IntArrayResult
 
integer_nf - Variable in class ambit2.similarity.stats.AbstractModelStatistics
 
IntendedApplication - Class in ambit2.export.isa.v1_0.objects
 
IntendedApplication() - Constructor for class ambit2.export.isa.v1_0.objects.IntendedApplication
 
intendedApplication - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
InteractiveIteratingMDLReader - Class in ambit2.core.io
A descendant of IteratingMDLReader able to ask for type of each SDF property
InteractiveIteratingMDLReader(Reader, IChemObjectBuilder) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader
 
InteractiveIteratingMDLReader(Reader, IChemObjectBuilder, boolean) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader
 
InteractiveIteratingMDLReader(InputStream, IChemObjectBuilder) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader
 
InteractiveIteratingMDLReader(InputStream, IChemObjectBuilder, boolean) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader
 
internal - Variable in class ambit2.rest.task.Task
 
internalName - Variable in class ambit2.base.data.SubstanceRecord
 
internalUUID - Variable in class ambit2.base.data.SubstanceRecord
 
interpretation_result - Variable in class ambit2.base.facet.SubstanceStudyFacet
 
interpretation_result - Variable in class ambit2.db.substance.QueryCountInterpretationResults
 
interpretation_result - Variable in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
interpretationCriteria - Variable in class ambit2.base.data.study.ProtocolApplication
 
interpretationResult - Variable in class ambit2.base.data.study.ProtocolApplication
 
interpretationResult - Variable in class ambit2.base.data.study.ProtocolEffectRecord
 
intervalAdded(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel
 
intervalRemoved(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel
 
intervalSep - Static variable in class ambit2.core.filter.MoleculeFilter
 
IntPropertyIntervalCondition - Class in ambit2.core.filter
 
IntPropertyIntervalCondition() - Constructor for class ambit2.core.filter.IntPropertyIntervalCondition
 
IntPropertyIntervalCondition.PropertyType - Enum in ambit2.core.filter
 
inverse(double) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
inverseOf() - Method in enum ambit2.base.relation.STRUCTURE_RELATION
 
inverseTransform(Matrix) - Method in class ambit2.model.numeric.DataCoverageDescriptors
perform an inverse transformation of points
the result is stored in the second argument
InverseTransformPoints(Matrix) - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
InverseTransformPoints
InverseTransformPoints(Matrix) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
Inverse transformation
investigation - Variable in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
Investigation - Class in ambit2.export.isa.v1_0.objects
ISA investigation schema JSON-schema representing an investigation in the ISA model
Investigation() - Constructor for class ambit2.export.isa.v1_0.objects.Investigation
 
investigationFilePrefix - Static variable in class ambit2.export.isa.base.ISAConst
 
investigationToFile(File) - Static method in class ambit2.export.isa.tab.TabFileUtils
 
investigationUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
IObject2Properties<D> - Interface in ambit2.core.data
 
IOTAlgorithm - Interface in ambit2.rest.legacy
Deprecated.
IOTCompound - Interface in ambit2.rest.legacy
Deprecated.
IOTDataset - Interface in ambit2.rest.legacy
Deprecated.
IOTDataset.dataset_size - Enum in ambit2.rest.legacy
Deprecated.
 
IOTFeature - Interface in ambit2.rest.legacy
Deprecated.
IOTModel - Interface in ambit2.rest.legacy
Deprecated.
IOTObject - Interface in ambit2.rest.legacy
Deprecated.
IOTPageable<T extends IOTObject> - Interface in ambit2.rest.legacy
Deprecated.
IOutputState - Interface in ambit2.core.io
Status of the output writer.
IPageNavigator - Interface in ambit2.ui.table
 
IParams<VALUE> - Interface in ambit2.base.data.study
 
IProgress - Interface in ambit2.rules.miscellaneous
 
IRandomAccessChemObjectReader - Interface in ambit2.base.interfaces
Extension of ListIterator
IRawReader<T> - Interface in ambit2.core.io
 
IReactionSequenceHandler - Interface in ambit2.reactions.retrosynth
 
IReactionSequenceHandler.EventType - Enum in ambit2.reactions.retrosynth
 
IReactionSequenceHandler.RSEvent - Class in ambit2.reactions.retrosynth
 
IRecordNavigator - Interface in ambit2.ui.table
 
IRetroSynthRule - Interface in ambit2.reactions.rules
 
IRetroSynthRule.Type - Enum in ambit2.reactions.rules
 
IRetroSynthRuleInstance - Interface in ambit2.reactions.rules
 
IRuleInstance - Interface in ambit2.tautomers
 
isAccepted() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
ISAConst - Class in ambit2.export.isa.base
 
ISAConst() - Constructor for class ambit2.export.isa.base.ISAConst
 
ISAConst.DataFileFormat - Enum in ambit2.export.isa.base
 
ISAConst.ISAFormat - Enum in ambit2.export.isa.base
 
ISAConst.ISAVersion - Enum in ambit2.export.isa.base
 
isAddEexplicitHydrogens() - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor
 
isAddGenericTypes() - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
isAddNew() - Method in class ambit2.db.readers.RetrieveField
 
isAddNew() - Method in class ambit2.db.readers.RetrieveProfileValues
 
isAddNew() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
isAddSMILEScolumn() - Method in class ambit2.core.io.FilesWithHeaderWriter
 
ISAExportConfig - Class in ambit2.export.isa
 
ISAExportConfig() - Constructor for class ambit2.export.isa.ISAExportConfig
 
isaFormat - Variable in class ambit2.export.isa.ISAExportConfig
 
isAfterLast() - Method in class ambit2.db.results.AmbitRows
 
ISAJsonConst - Class in ambit2.export.isa.json
 
ISAJsonConst() - Constructor for class ambit2.export.isa.json.ISAJsonConst
 
ISAJsonExportConfig - Class in ambit2.export.isa.json
 
ISAJsonExportConfig() - Constructor for class ambit2.export.isa.json.ISAJsonExportConfig
 
ISAJsonExporter - Class in ambit2.export.isa.json
 
ISAJsonExporter() - Constructor for class ambit2.export.isa.json.ISAJsonExporter
 
ISAJsonExporter(ISAConst.ISAVersion, Iterator<SubstanceRecord>, File, File, SubstanceEndpointsBundle) - Constructor for class ambit2.export.isa.json.ISAJsonExporter
 
ISAJsonExporter(Iterator<SubstanceRecord>, File, File, SubstanceEndpointsBundle) - Constructor for class ambit2.export.isa.json.ISAJsonExporter
 
ISAJsonExporter1_0 - Class in ambit2.export.isa.v1_0
 
ISAJsonExporter1_0() - Constructor for class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
ISAJsonExporter1_0(File, File) - Constructor for class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
ISAJsonExporter1_0(File, ISAJsonExportConfig) - Constructor for class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
ISAJsonExporter1_0(File, ISAJsonExportConfig, File) - Constructor for class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
ISAJsonMapper1_0 - Class in ambit2.export.isa.v1_0
 
ISAJsonMapper1_0() - Constructor for class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
ISAJsonUtils1_0 - Class in ambit2.export.isa.v1_0
 
ISAJsonUtils1_0() - Constructor for class ambit2.export.isa.v1_0.ISAJsonUtils1_0
 
isAllowed(CompositionRelation) - Method in class ambit2.db.substance.ids.ReadChemIdentifiersByComposition
 
isAllowed(CompositionRelation) - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
isAllowGroupRegistration() - Method in class ambit2.groupcontribution.GroupContributionModel
 
ISALocation - Class in ambit2.export.isa.base
 
ISALocation() - Constructor for class ambit2.export.isa.base.ISALocation
 
ISALocation.Layer - Enum in ambit2.export.isa.base
 
isANDOperation() - Method in class ambit2.rules.conditions.ConditionExpression
 
isAnyField() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
isApplicable() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
isAromaticityInfoNeeded() - Method in class ambit2.core.filter.MoleculeFilter
 
isAromaticityInfoNeeded(IMoleculeFilterCondition) - Static method in class ambit2.core.filter.MoleculeFilter
 
isAssignProperties() - Method in class ambit2.db.processors.AbstractDescriptorCalculator
 
ISATABConst - Class in ambit2.export.isa.tab
 
ISATABConst() - Constructor for class ambit2.export.isa.tab.ISATABConst
 
isAtomNumbers() - Method in class ambit2.ui.Panel2D
 
isAtomtypeasproperties() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
isAtomtypingonsmiles() - Method in class ambit2.core.processors.structure.MoleculeReader
 
isAutosizeColumns() - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
isaVersion - Variable in class ambit2.export.isa.ISAExportConfig
 
isaVersion - Variable in class ambit2.export.isa.json.ISAJsonExporter
 
isBeforeFirst() - Method in class ambit2.db.results.AmbitRows
 
isBoxcox() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
isBuild2D() - Method in class ambit2.core.processors.StructureNormalizer
 
isBuild2D() - Method in class ambit2.db.processors.RepositoryWriter
 
isBuilt() - Method in class ambit2.model.AbstractModel
 
isBuilt() - Method in interface ambit2.model.IModelDefinition
 
isCancelled() - Method in class ambit2.pubchem.HTTPRequest
 
isCancelled() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
isCAS() - Method in class ambit2.base.data.Property
 
isCaseSensitive() - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
isCellEditable(int, int) - Method in class ambit2.base.data.PropertiesTableModel
 
isCellEditable(int, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
isCellEditable(int, int) - Method in class ambit2.dbui.CachedRowSetTableModel
 
isCellEditable(int) - Method in class ambit2.ui.EditableHeader
 
isCellEditable(int, int) - Method in class ambit2.ui.table.BrowsableTableModel
 
isCellEditable(int, int) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
isChangeLineSeparators() - Method in class ambit2.db.reporters.SDFReporter
 
isChemicalsOnly() - Method in class ambit2.db.readers.RetrieveField
 
isChemicalsOnly() - Method in class ambit2.db.readers.RetrieveModelTemplates
 
isChemicalsOnly() - Method in class ambit2.db.readers.RetrieveProfileValues
 
isChemicalsOnly() - Method in class ambit2.db.readers.RetrieveTemplate
 
isChemicalsOnly() - Method in class ambit2.db.results.StoredQueryTableModel
 
isChemicalsOnly() - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
isChemicalsOnly() - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
isChemicalsOnly() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
isChemicalsOnly() - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
isClassUnknown() - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
isCleanKekuleBonds() - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
isClearComposition() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isClearIsotopes() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isClearMeasurements() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isCloseModel() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
isCollapsed() - Method in enum ambit2.rest.DisplayMode
 
isColumnSelectionAllowed() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
isCombine_as_and() - Method in class ambit2.db.search.QueryCombined
 
isCompleted() - Method in class ambit2.ui.table.BrowsableTableModel
 
isCompleted() - Method in interface ambit2.ui.table.IFindNavigator
 
isCompletedOK() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
isConvertToString() - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
 
isCopied() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
isCopied() - Method in class ambit2.base.data.study.ValueAnnotated
 
isCopy() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
IScoreComponent - Interface in ambit2.reactions.generator.score
 
isCreateSubLevels() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
isDataProcessing() - Method in class ambit2.core.data.model.Algorithm
 
isDatasetMembersPrefix() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
isDBAAEnabled() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
isDefined(QueryDatasetByFeatures) - Method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
 
isDelete() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
isDeleted() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
isDeleted() - Method in class ambit2.base.data.study.ValueAnnotated
 
isDeleteMatrix() - Method in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
isDescriptorSupported(String) - Method in class ambit2.rules.conditions.AbstractDescriptorSolver
 
isDescriptorSupported(String) - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
isDescriptorSupported(String) - Method in interface ambit2.rules.conditions.IDescriptorSolver
 
isDistance() - Method in enum ambit2.model.numeric.ADomainMethodType
 
isDone() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
isDone() - Method in class ambit2.rest.task.Task
 
isDropHydrogens() - Method in class ambit2.smi23d.ShellSmi2SDF
 
isEditable() - Method in interface ambit2.base.interfaces.IAmbitEditor
 
isEditable() - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
isEditable() - Method in class ambit2.dbui.dictionary.OntologyEditor
 
isEditable() - Method in class ambit2.dbui.ProfileEditor
 
isEditable() - Method in class ambit2.dbui.QueryCombinedEditor
 
isEditable() - Method in class ambit2.dbui.QueryEditor
 
isEditable() - Method in class ambit2.dbui.QueryInfoEditor
 
isEditable() - Method in class ambit2.dbui.QueryScopeEditor
 
isEditable() - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
isEditable() - Method in class ambit2.ui.editors.BeanEditor
 
isEditable() - Method in class ambit2.ui.editors.FileSelector
 
isEditable() - Method in class ambit2.ui.editors.ListEditor
 
isEditable() - Method in class ambit2.ui.editors.PreferencesPanel
 
isEditable() - Method in class ambit2.ui.editors.SelectFieldsPanel
 
isEditable() - Method in class ambit2.ui.editors.TemplateEditor
 
isEditable() - Method in class ambit2.ui.jmol.Panel3D
 
isEditable() - Method in class ambit2.ui.Panel2D
 
isEditable() - Method in class ambit2.ui.QueryBrowser
 
isEditing() - Method in class ambit2.ui.EditableHeader
 
isEINECS() - Method in class ambit2.base.data.Property
 
ISelectableRecords - Interface in ambit2.base.data
 
ISelectableRecords.SELECTION_MODE - Enum in ambit2.base.data
 
isElement(String) - Method in class ambit2.descriptors.IsotopeFactory
Checks whether the given element exists.
isEmpty() - Method in class ambit2.base.data.study.EffectRecord
 
isEmpty() - Method in class ambit2.base.data.study.Params
 
isEmpty() - Method in class ambit2.core.groups.FilteredList
 
isEmpty() - Method in class ambit2.core.groups.SuppleAtomContainer
 
isEmpty() - Method in class ambit2.model.numeric.DataCoverage
 
isEmpty() - Method in class ambit2.model.numeric.DataCoverageDensity
 
isEmpty() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
isEmpty() - Method in class ambit2.model.numeric.DataCoverageDistance
 
isEmpty() - Method in interface ambit2.model.numeric.IDataCoverage
 
isEmpty() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
isEmpty() - Method in class ambit2.rendering.CachedImage
 
isEmpty() - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Tries to GET the URI and returns true if the dataset is empty, false otherwise.
isEmpty - Variable in class ambit2.rest.legacy.OTDataset
Deprecated.
 
isEmpty() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
isEmpty(boolean) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
isEnabled() - Method in class ambit2.base.data.Property
 
isEnabled() - Method in class ambit2.base.external.CommandShell
 
isEnabled() - Method in enum ambit2.base.processors.search.AbstractFinder.SITE
 
isEnabled() - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
isEnabled() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
isEnabled(ModelQueryResults, String) - Method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
 
isEnabled(ReadStoredQuery) - Method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
 
isEnabled() - Method in class ambit2.descriptors.FunctionalGroup
 
isEnabled() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
isEnabled()
isEnabled() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
isEnabled() - Method in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
isEnabled() - Method in class ambit2.rest.model.predictor.ExternalModel
 
isEnabled() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
isEnabled() - Method in class ambit2.some.SOMEVisualizer
 
isEnableEmailVerification() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
isEnableFeatures() - Method in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
isEnableFeatures() - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
isEndOfRecord(String) - Method in class ambit2.core.io.pdb.RawIteratingPDBReader
 
isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingMOLReader
 
isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingReader
 
isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingSDFReader
 
isEndOfRecord(String) - Method in class ambit2.some.SOMERawReader
 
isERROR() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
isErrorIfDisconnected() - Method in class ambit2.mopac.AbstractMopacShell
 
isErrorIfDisconnected() - Method in class ambit2.mopac.DescriptorMopacShell
 
isEvaluated() - Method in class ambit2.featureselection.AbstractAttributeSelection
 
isEvaluated() - Method in interface ambit2.featureselection.IAttributeSelection
 
isExcludeAromaticSystems() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isExcludeAzideGroups() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isExcludeHidden() - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
isExcludeNitroGroup() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isexcludeNitroGroupPartially() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isExcludeNitroxides() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isExcludeSulfonylGroups() - Method in class ambit2.tautomers.rules.TautomerRegion
 
isExpanded(IBond) - Method in class ambit2.core.groups.AbstractGroup
 
isExpanded() - Method in interface ambit2.core.groups.IExpandable
 
isExpanded() - Method in class ambit2.core.groups.MultipleGroup
 
isExpanded(IBond) - Method in class ambit2.core.groups.SuperAtom
 
isExpanded() - Method in class ambit2.core.groups.SuperAtom
 
isExpired(long) - Method in class ambit2.rest.task.Task
 
isExplicitH() - Method in class ambit2.ui.Panel2D
 
isExtendedURI() - Method in class ambit2.base.data.substance.SubstanceProperty
 
isFeatureSource(Resource) - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
isFiltered() - Method in class ambit2.core.groups.FilteredList
 
isFiltered(T) - Method in class ambit2.core.groups.FilteredList
 
isFiltered(T) - Method in interface ambit2.core.groups.IFiltered
 
isFiltered() - Method in interface ambit2.core.groups.IFiltered
 
isFiltered(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
isFiltered(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
isFiltered() - Method in class ambit2.core.groups.SuppleAtomContainer
 
isFirst() - Method in class ambit2.db.results.AmbitRows
 
isFixErrors() - Method in class ambit2.base.data.study.StructureRecordValidator
 
isFlag() - Method in class ambit2.similarity.stats.MutableInt
 
isFlagAddImplicitHAtomsOnResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagApplyDuplicationCheckInChI() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagApplyDuplicationCheckIsomorphism() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagApplyDuplicationFilter() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagApplyExcludeFilter() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagApplyStereoTransformation() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagApplyWarningFilter() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagAromaticityTransformation() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagCheckAromaticityOnResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagCheckResultStereo() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagCheckStereoElements() - Method in class ambit2.smarts.IsomorphismTester
 
isFlagCheckStereoElements() - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
isFlagClearAromaticityBeforeResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagClearExcplicitHAtomsBeforeResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagClearHybridizationBeforeResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagClearImplicitHAtomsBeforeResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagConvertAddedImplicitHToExplicitOnResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagConvertExplicitHToImplicitOnResultProcess() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagExcludeWarningTautomers() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagExplicitHAtoms() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
isFlagFilterEquivalentMappings() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagFilterIncorrectHAtomsStructures() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagFilterIncorrectValencySumStructures() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagHAtomsTransformation() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagPrepareTarget() - Method in class ambit2.smarts.groups.GroupMatch
 
isFlagProcessResultStructures() - Method in class ambit2.smarts.SMIRKSManager
 
isFlagReactRecursively() - Method in class ambit2.reactions.reactor.Reactor
 
isFlagStoreCACTVSRank() - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
isFlagStoreRemovedByFilterTautomers() - Method in class ambit2.tautomers.FilterTautomers
 
isFlagUse() - Method in class ambit2.reactions.GenericReaction
 
isFlagUse() - Method in class ambit2.reactions.Reaction
 
isFlagUseAbsolutePathForFileLocation() - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
isFlagUseCDKIsomorphismTester() - Method in class ambit2.smarts.SmartsManager
 
isFocusable() - Method in class ambit2.ui.editors.EditorPanel
 
isForbidden() - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
isForbidden() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
isForceOrdering() - Method in class ambit2.db.search.structure.QuerySimilarity
 
isForceOrdering() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
isForceReadRDFLocalObjects() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
isForceStructureDelete() - Method in class ambit2.db.update.chemical.DeleteChemical
 
isFound(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
isFound(int) - Method in interface ambit2.ui.table.IFindNavigator
 
isFp1024_screening() - Method in class ambit2.db.search.structure.QuerySMARTS
 
isGenerate2D() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateInChI() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateSmiles() - Method in class ambit2.smi23d.ShellSmi2SDF
 
isGenerateSMILES() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateSMILES_Aromatic() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateSMILES_Canonical() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateStereofrom2D() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isGenerateTautomers() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
ISGroup - Interface in ambit2.core.groups
 
isGroupByInterpretationResult() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
isGroupVisible(IChemObject) - Static method in class ambit2.core.groups.AbstractGroup
 
isHandlePrescreen() - Method in class ambit2.db.DbReader
 
isHeaderEditable - Variable in class ambit2.ui.EditableHeaderTableColumn
 
isHeaderEditable() - Method in class ambit2.ui.EditableHeaderTableColumn
 
isHeaderEmpty() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
isHidden() - Method in class ambit2.base.relation.composition.CompositionRelation
 
isHidden() - Method in class ambit2.core.data.model.ModelQueryResults
 
isHigherPriority(HAtomEnvironment) - Method in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
isHtmlbyTemplate() - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
isHtmlbyTemplate() - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
isHtmlbyTemplate() - Method in class ambit2.rest.freemarker.FreeMarkerSupport
 
isHydrogens() - Method in class ambit2.balloon.ShellBalloon
 
isHydrogens() - Method in class ambit2.core.processors.structure.FingerprintGenerator
 
isHydrogens() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
isI5mode() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isI5UUID() - Method in class ambit2.base.data.Property
 
isIdenticalTo(SLNBondExpression) - Method in class ambit2.sln.SLNBondExpression
 
isIdenticalTo(SmartsBondExpression) - Method in class ambit2.smarts.SmartsBondExpression
 
ISimilarityResultType - Interface in ambit2.similarity
 
isImplicitHydrogens() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isImportBundles() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isIncludeImplicitHAtoms() - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
isIncludeLicenseInTextFiles() - Method in class ambit2.db.reporters.QueryStructureReporter
 
isIncludeMol() - Method in class ambit2.db.reporters.QueryHeaderReporter
 
isIncludeParent() - Method in class ambit2.db.search.property.QueryOntology
 
isInternal() - Method in class ambit2.rest.task.Task
 
isInvalidated(DoubleBondStereochemistry) - Static method in class ambit2.smarts.StereoChemUtils
 
isInvalidated(TetrahedralChirality) - Static method in class ambit2.smarts.StereoChemUtils
 
isInvalidated(ExtendedTetrahedral) - Static method in class ambit2.smarts.StereoChemUtils
 
isIterateSubjects() - Method in class ambit2.rest.rdf.RDFObjectIterator
 
isJSONP() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
isKeepEffectRecordsForDocUUID() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isKeeprawrecord() - Method in class ambit2.core.io.RawIteratingCSVReader
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.CASKey
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.EINECSKey
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.NameKey
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.NoneKey
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.PropertyKey
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
isKeyValid(Property) - Method in class ambit2.core.processors.structure.key.SampleKey
 
isLast() - Method in class ambit2.db.results.AmbitRows
 
ISLNDictionaryObject - Interface in ambit2.sln.dictionary
 
ISLNDictionaryObject.Type - Enum in ambit2.sln.dictionary
 
isLoadExamples() - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
isLocalPropertyModel() - Method in class ambit2.groupcontribution.GroupContributionModel
 
isLogicalOperation() - Method in class ambit2.sln.SLNExpressionToken
 
isLogicalOperation() - Method in class ambit2.smarts.SmartsExpressionToken
 
isLogX() - Method in class ambit2.db.chart.ChartGenerator
 
isLogY() - Method in class ambit2.db.chart.ChartGenerator
 
isLowestDistanceIsClosest() - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
isLowestDistanceIsClosest() - Method in class ambit2.similarity.measure.DistanceComparable
 
isMandatory() - Method in enum ambit2.rest.OpenTox.params
 
ISmartsPattern<T> - Interface in ambit2.smarts.query
Generic interface for a SMARTS pattern.
ISmartsPatternFactory - Interface in ambit2.smarts.query
An interface for smarts pattern factory.
isMissing() - Method in class ambit2.groupcontribution.groups.AtomGroup
 
isMissing() - Method in class ambit2.groupcontribution.groups.BondGroup
 
isMissing() - Method in class ambit2.groupcontribution.groups.DGroup
 
isMissing() - Method in class ambit2.groupcontribution.groups.GGroup
 
isMissing() - Method in interface ambit2.groupcontribution.groups.IGroup
 
isMobileH - Variable in class ambit2.tautomers.Rule
 
isModal() - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
isMOLONLY() - Method in class ambit2.db.reporters.SDFReporter
 
isName() - Method in class ambit2.base.data.Property
 
isNanomaterial() - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
isNegate() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
isNegate() - Method in interface ambit2.smarts.query.ISmartsPattern
 
isNegated() - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
isNegated() - Method in class ambit2.rules.conditions.ConditionExpression
 
isNegated() - Method in class ambit2.rules.conditions.DescriptorExpression
 
isNegated() - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
isNegated() - Method in interface ambit2.rules.conditions.ICondition
 
isNegated() - Method in class ambit2.rules.conditions.ValueCondition
 
isNeutralise() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isNewResource() - Method in class ambit2.rest.task.TaskResult
 
isNoDuplicates() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
isNoDuplicates() - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
isNominal - Variable in class ambit2.base.data.Property
 
isNominal() - Method in class ambit2.base.data.Property
 
isNominal() - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
isNominal - Variable in class ambit2.rest.legacy.OTFeature
Deprecated.
 
isNumeric() - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
isNumeric - Variable in class ambit2.rest.legacy.OTFeature
Deprecated.
 
isomorphismFound - Variable in class ambit2.smarts.IsomorphismTester
 
isomorphismFound - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
isomorphismNodes - Variable in class ambit2.smarts.IsomorphismTester
 
isomorphismNodes - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
IsomorphismTester - Class in ambit2.smarts
 
IsomorphismTester() - Constructor for class ambit2.smarts.IsomorphismTester
 
isOpenToxAAEnabled() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
isOptimize() - Method in class ambit2.mopac.AbstractMopacShell
 
isOptimize() - Method in class ambit2.mopac.Mopac7Writer
 
isOrder_descendant() - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
ISortableColumns - Interface in ambit2.base.data
 
isoTester - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
isoTester - Variable in class ambit2.reactions.fragmentation.FragmentationRule
 
isoTester - Variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
isoTester - Variable in class ambit2.smarts.query.FastSmartsMatcher
 
isoTester - Variable in class ambit2.smarts.SMIRKSManager
 
IsotopeFactory - Class in ambit2.descriptors
Used to store and return data of a particular isotope.
isotopesFactory - Variable in class ambit2.core.processors.IsotopesProcessor
 
IsotopesProcessor - Class in ambit2.core.processors
Sets the mass number to the most abundant isotope
IsotopesProcessor(Logger) - Constructor for class ambit2.core.processors.IsotopesProcessor
 
isotopesProcessor - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
ISourceDataset - Interface in ambit2.base.data
 
ISourceDataset.fields - Enum in ambit2.base.data
 
ISourceDataset.license - Enum in ambit2.base.data
 
ISparseFingerprint<T> - Interface in ambit2.descriptors.fingerprints
 
isPca() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
isPredicted() - Method in enum ambit2.base.data.study.ReliabilityParams._r_flags
 
isPredicting() - Method in interface ambit2.model.IModelStatistics
 
isPredicting() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
isPreferedStructure() - Method in class ambit2.db.readers.RetrieveStructure
 
isPreferredStructure() - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
isPreferredStructure() - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
isPreferredStructure() - Method in class ambit2.db.search.structure.QueryStructureByID
 
isPrescreen() - Method in class ambit2.db.cache.QueryCachedResults
 
isPrescreen() - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
isPrescreen() - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
isPrescreen() - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
isPrescreen() - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
isPrescreen() - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
isPrescreen() - Method in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
isPrescreen() - Method in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
isPrescreen() - Method in class ambit2.db.facets.compounds.CollectionsByChemical
 
isPrescreen() - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
isPrescreen() - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
isPrescreen() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
isPrescreen() - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
isPrescreen() - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
isPrescreen() - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
isPrescreen() - Method in class ambit2.db.readers.AbstractStructureRetrieval
 
isPrescreen() - Method in class ambit2.db.readers.ReadChemicalIds
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveDatasets
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveDescriptor
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveField
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveModelTemplates
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveProfileValues
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
isPrescreen() - Method in class ambit2.db.readers.RetrieveTemplate
 
isPrescreen() - Method in class ambit2.db.search.DictionaryQuery
 
isPrescreen() - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
isPrescreen() - Method in class ambit2.db.search.property.FilteredCount
 
isPrescreen() - Method in class ambit2.db.search.property.PropertyCount
 
isPrescreen() - Method in class ambit2.db.search.property.PropertyRange
 
isPrescreen() - Method in class ambit2.db.search.property.PropertyStatsNumeric
 
isPrescreen() - Method in class ambit2.db.search.property.PropertyStatsString
 
isPrescreen() - Method in class ambit2.db.search.property.QueryMetricRange
 
isPrescreen() - Method in class ambit2.db.search.property.QueryOntology
 
isPrescreen() - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
isPrescreen() - Method in class ambit2.db.search.qlabel.QueryConsensus
 
isPrescreen() - Method in class ambit2.db.search.qlabel.QueryQLabel
 
isPrescreen() - Method in class ambit2.db.search.QueryCombined
 
isPrescreen() - Method in class ambit2.db.search.QuerySmilesByID
 
isPrescreen() - Method in class ambit2.db.search.QueryUser
 
isPrescreen() - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
isPrescreen() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
isPrescreen() - Method in class ambit2.db.search.structure.pairwise.QueryStructurePairs
 
isPrescreen() - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
isPrescreen() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
isPrescreen() - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
isPrescreen() - Method in class ambit2.db.search.structure.QuerySimilarityBitset
 
isPrescreen() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
isPrescreen() - Method in class ambit2.db.search.structure.QuerySMARTS
 
isPrescreen() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
isPrescreen() - Method in class ambit2.db.search.structure.ScopeQuery
 
isPrescreen() - Method in class ambit2.db.simiparity.space.QueryQMap
 
isPrescreen() - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
isPrescreen() - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
isPrescreen() - Method in class ambit2.db.substance.AbstractReadSubstance
 
isPrescreen() - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
isPrescreen() - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
isPrescreen() - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
isPrescreen() - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
isPrescreen() - Method in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
isPrescreen() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
isPrescreen() - Method in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
isPrescreen() - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
isPrescreen() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
isPrescreen() - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
isPrescreen() - Method in class ambit2.db.update.bookmark.ReadBookmark
 
isPrescreen() - Method in class ambit2.db.update.bundle.BundleOwnerByNumber
 
isPrescreen() - Method in class ambit2.db.update.bundle.effects.BundleStudyFacetQuery
 
isPrescreen() - Method in class ambit2.db.update.dataset.AbstractReadDataset
 
isPrescreen() - Method in class ambit2.db.update.dataset.QueryCount
 
isPrescreen() - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
isPrescreen() - Method in class ambit2.db.update.fp.QueryFingerprints
 
isPrescreen() - Method in class ambit2.db.update.model.QueryModel
 
isPrescreen() - Method in class ambit2.db.update.model.ReadModel
 
isPrescreen() - Method in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
isPrescreen() - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
isPrescreen() - Method in class ambit2.db.update.reference.ReadReference
 
isPrescreen() - Method in class ambit2.db.update.storedquery.ReadStoredQuery
 
isPrescreen() - Method in class ambit2.db.update.storedquery.SearchStoredQueries
 
isPrescreen() - Method in class ambit2.db.version.DBVersionQuery
 
isPresent() - Method in class ambit2.descriptors.PKANode
 
isProperty() - Method in enum ambit2.rest.substance.RDFTermsSubstance
 
isProtocolapp_copied() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
isProtocolapp_deleted() - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
isQueryDoubleBond(IBond) - Static method in class ambit2.smarts.SmartsHelper
 
isQueryExpansion() - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
isRange() - Method in enum ambit2.model.numeric.ADomainMethodType
 
isReadOnly() - Method in class ambit2.db.results.AmbitRows
 
isReadOutput() - Method in class ambit2.core.external.ShellSDFoutput
 
isReady() - Method in class ambit2.db.results.AmbitRows
 
isRemoveCDKTitle() - Method in class ambit2.core.processors.structure.MoleculeReader
 
isRequiresDataset() - Method in class ambit2.core.data.model.Algorithm
 
isRetrieve_conformers() - Method in class ambit2.pubchem.EntrezSearchProcessor
 
isRetrieve_sdf() - Method in class ambit2.pubchem.EntrezSearchProcessor
 
isRetrieveConformers() - Method in class ambit2.pubchem.PUGProcessor
 
isRetrieveProperties() - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
isReuseRecord() - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
isRingBond(IBond) - Static method in class ambit2.smarts.RingQueryBond
 
isRowSelectionAllowed() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
isRuleActive() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
isRuleActive() - Method in class ambit2.reactions.rules.RetroSynthRule
 
isRuleActive - Variable in class ambit2.tautomers.Rule
 
isRuleInstanceInRegion(IRuleInstance, IAtomContainer) - Method in class ambit2.tautomers.rules.TautomerRegion
 
isSameRecord(QuerySolution) - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
isScale() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
isSearchByAlias() - Method in class ambit2.db.readers.RetrieveField
 
isSearchByAlias() - Method in class ambit2.db.readers.RetrieveProfileValues
 
isSearchByAlias() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
isSearchByAlias() - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
isSearchByAlias() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
isSearchByID() - Method in class ambit2.db.readers.RetrieveField
 
isSearchByID() - Method in class ambit2.db.readers.RetrieveProfileValues
 
isSelected() - Method in class ambit2.base.data.StructureRecord
 
isSelected() - Method in interface ambit2.base.interfaces.IStructureRecord
 
isSelected() - Method in class ambit2.base.relation.composition.CompositionRelation
 
isSelected() - Method in class ambit2.db.search.AbstractQuery
 
isSelected() - Method in class ambit2.db.update.storedquery.SelectStoredQuery
 
isSelected() - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
isSelected() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
isSendTokenAsCookie() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
isSgroupLine(String) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
isSimilarityOrder() - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
isSimpleGuardEnabled() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
isSimpleSecretAAEnabled() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
isSingleBondOrExpression(IBond) - Static method in class ambit2.smarts.SmartsHelper
 
isSk1024_screening() - Method in class ambit2.db.search.structure.QuerySMARTS
 
isSparse(String) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
isSparseproperties() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
isSplitFragments() - Method in class ambit2.tautomers.processor.StructureStandardizer
 
isSplitRecord() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
isStandardRule - Variable in class ambit2.tautomers.Rule
 
isStartingMaterial(String) - Method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
isStartingMaterial(IAtomContainer) - Method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
isStoredProcedure() - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
isStoredProcedure() - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
isStoredProcedure() - Method in class ambit2.db.update.dataset.DeleteDataset
 
isStoredProcedure() - Method in class ambit2.db.update.fpae.CreateAtomEnvironment
 
isStructureRequired() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
isSummary() - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
isSupervised() - Method in class ambit2.core.data.model.Algorithm
 
isSupported(Object) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
isSupported(Object) - Method in class ambit2.rest.model.predictor.FingerprintsPredictor
 
isSupported(Object) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
isSupported(Object) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
isSupported(Object) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
isSupported(Object) - Method in class ambit2.rest.task.weka.WekaPredictor
 
isSupportsPredictedVarURI() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
isTerminal() - Method in class ambit2.descriptors.PKANode
 
isThumbnail() - Method in class ambit2.db.chart.ChartGenerator
 
IStoredQuery - Interface in ambit2.db.search
 
isToxCastAssayFile - Variable in class ambit2.core.io.ToxcastAssayReader
 
isTransformationasproperties() - Method in class ambit2.smarts.processors.SMIRKSProcessor
assigns performed transformations as atomcontainer properties
IStrategyRule - Interface in ambit2.reactions.rules
 
IStrategyRule.Type - Enum in ambit2.reactions.rules
 
IStringAction - Interface in ambit2.rules.actions
 
IStructureDiagramDepiction<OUTPUT> - Interface in ambit2.core.data
 
IStructureDiagramHighlights - Interface in ambit2.core.data
 
IStructureDiagramSelection<P> - Interface in ambit2.rendering
 
IStructureKey<Target,Result> - Interface in ambit2.core.processors.structure.key
 
IStructureKey.Matcher - Enum in ambit2.core.processors.structure.key
 
IStructureRecord - Interface in ambit2.base.interfaces
 
IStructureRecord.MOL_TYPE - Enum in ambit2.base.interfaces
 
IStructureRecord.STRUC_TYPE - Enum in ambit2.base.interfaces
 
IStructureRelation<RELATION_TYPE,RELATION_METRIC,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord> - Interface in ambit2.base.interfaces
 
isTrue(Object) - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
isTrue(Object) - Method in class ambit2.rules.conditions.ConditionExpression
 
isTrue(Object) - Method in class ambit2.rules.conditions.DescriptorExpression
 
isTrue(Object) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
isTrue(Double) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
isTrue(Object) - Method in interface ambit2.rules.conditions.ICondition
 
isTrue(Object) - Method in interface ambit2.rules.conditions.IDescriptorValueCondition
 
isTrue(Double) - Method in interface ambit2.rules.conditions.IValueCondition
 
isTrue(Double) - Method in interface ambit2.rules.conditions.IValueIntervalCondition
 
isTrue(Object) - Method in class ambit2.rules.conditions.ValueCondition
 
isTrue(Double) - Method in class ambit2.rules.conditions.ValueCondition
 
IStudyPrinter - Interface in ambit2.core.io.study
 
isUseCache() - Method in class ambit2.db.StatementExecutor
Deprecated.
isUseCDKIsomorphism() - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
isUsed() - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
isUsed() - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
isUseExistingDatabase() - Method in class ambit2.db.processors.DbCreateDatabase
 
isUseExistingStructure() - Method in class ambit2.db.processors.RepositoryWriter
 
isUseHydrogens() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
isUseOriginalStructure() - Method in class ambit2.mopac.AbstractMopacShell
 
isUseOriginalStructure() - Method in class ambit2.some.SOMEShell
 
isUsePrecalculatedAtomProperties() - Method in class ambit2.db.search.structure.QuerySMARTS
 
isValid(String) - Static method in class ambit2.core.data.EINECS
200-002-3 200-006-5 EINECS:abc-def-g
g=(a+2b+3c+4d+5e+6f)mod11
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.CASKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.ChEMBLCompoundURI
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.DSSToxID
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.EINECSKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.InchiPropertyKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.NameKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.NoneKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PropertyKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PropertyNameKey
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PubchemCID
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PubchemSID
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.SampleKey
 
isValidFormat(String) - Static method in class ambit2.base.processors.CASProcessor
 
isValidFormat(String) - Static method in class ambit2.core.data.EINECS
 
isValidStereoElement() - Method in class ambit2.smarts.StereoChange
 
isValuesRequired() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
isVerbose() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
isVerboseMatch() - Method in class ambit2.descriptors.FunctionalGroup
 
isVisible(T) - Method in class ambit2.core.groups.FilteredList
 
isVisible(T) - Method in interface ambit2.core.groups.IFiltered
 
isVisible(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
isVisible(ObjectNode) - Method in class ambit2.core.io.study.StudyFormatter
 
isWarmupEnabled() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
isWriteCompoundURI() - Method in class ambit2.db.reporters.CSVReporter
 
isXMLBased() - Method in class ambit2.core.io.DelimitedFileFormat
 
isXMLBased() - Method in class ambit2.core.io.XLSFileFormat
 
item - Variable in class ambit2.ml.io.OutputARFF
 
items - Variable in class ambit2.rest.legacy.OTContainers
Deprecated.
 
itemStateChanged(ItemEvent) - Method in class ambit2.ui.DelimitersPanel
 
iterateLevelMolecules(ReactionSequenceLevel) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
iterateLevelMoleculesRandomly(ReactionSequenceLevel) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
iterateSubjects - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
IteratingChemObjectReaderWrapper - Class in ambit2.core.io
A wrapper for DefaultChemObjectReader.
IteratingChemObjectReaderWrapper(DefaultChemObjectReader) - Constructor for class ambit2.core.io.IteratingChemObjectReaderWrapper
 
IteratingDelimitedFileReader - Class in ambit2.core.io
Iterating reader for delimited files.
IteratingDelimitedFileReader(Reader) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader
 
IteratingDelimitedFileReader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader
 
IteratingDelimitedFileReader(InputStream) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader
 
IteratingDelimitedFileReader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader
 
IteratingDelimitedFileReaderComplexHeader<COLUMN> - Class in ambit2.core.io
 
IteratingDelimitedFileReaderComplexHeader(Reader) - Constructor for class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
IteratingDelimitedFileReaderComplexHeader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
IteratingDelimitedFileReaderComplexHeader(InputStream) - Constructor for class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
IteratingDelimitedFileReaderComplexHeader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
IteratingFileReader - Class in ambit2.core.io
A wrapper for all file readers.
IteratingFileReader(File) - Constructor for class ambit2.core.io.IteratingFileReader
 
IteratingFileReader(File, IChemFormat) - Constructor for class ambit2.core.io.IteratingFileReader
 
IteratingFilesWithHeaderReader<COLUMN> - Class in ambit2.core.io
 
IteratingFilesWithHeaderReader() - Constructor for class ambit2.core.io.IteratingFilesWithHeaderReader
 
IteratingFolderReader<T,ItemReader extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader> - Class in ambit2.core.io
 
IteratingFolderReader(File[]) - Constructor for class ambit2.core.io.IteratingFolderReader
 
IteratingMolFolderReader - Class in ambit2.core.io
 
IteratingMolFolderReader() - Constructor for class ambit2.core.io.IteratingMolFolderReader
 
IteratingMolFolderReader(File[]) - Constructor for class ambit2.core.io.IteratingMolFolderReader
 
IteratingXLSReader - Class in ambit2.core.io
Reads XLS files.
IteratingXLSReader(InputStream, int) - Constructor for class ambit2.core.io.IteratingXLSReader
 
IteratingXLSReader(InputStream, Integer, Boolean) - Constructor for class ambit2.core.io.IteratingXLSReader
 
iterator() - Method in class ambit2.base.data.Profile
 
iterator() - Method in class ambit2.core.groups.AbstractGroup.SelfIterable
 
iterator() - Method in class ambit2.core.groups.FilteredList
 
iterator - Variable in class ambit2.core.io.IteratingXLSReader
 
iterator - Variable in class ambit2.core.io.RawIteratingCSVReader
 
iterator - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
IUCLID5_UUID - Static variable in class ambit2.base.data.LiteratureEntry
 
IUCLID5_UUID - Static variable in class ambit2.base.data.Property
 
IUPAC_name - Static variable in class ambit2.base.data.LiteratureEntry
 
IUPACNameGenerator - Class in ambit2.structure2name
 
IUPACNameGenerator() - Constructor for class ambit2.structure2name.IUPACNameGenerator
 
IUPACRuleDataBase - Class in ambit2.structure2name.rules
 
IUPACRuleDataBase() - Constructor for class ambit2.structure2name.rules.IUPACRuleDataBase
 
IValue<VALUE,QUALIFIER,UNITS> - Interface in ambit2.base.data.study
 
IValue - Interface in ambit2.rules.conditions.value
 
IValue.Relation - Enum in ambit2.rules.conditions.value
 
IValueCondition - Interface in ambit2.rules.conditions
 
IValueInterval - Interface in ambit2.rules.conditions.value
 
IValueIntervalCondition - Interface in ambit2.rules.conditions
 
IValueTransformation - Interface in ambit2.groupcontribution.transformations
 

J

JAVA_BIN - Static variable in class ambit2.vega.VegaShell
 
JAVA_EXE - Static variable in class ambit2.vega.VegaShell
 
JAVA_HOME - Static variable in class ambit2.vega.VegaShell
 
JChemPaintDialog - Class in ambit2.jchempaint.editor
A JDialog containing a JChemPaintEditorPanel.
JChemPaintDialog(IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Dialog, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Dialog, boolean, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Frame, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Frame, boolean, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Dialog, String, boolean, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Frame, String, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
JChemPaintDialog(Frame, String, boolean, IChemModel) - Constructor for class ambit2.jchempaint.editor.JChemPaintDialog
 
jcpDialog - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
jcpep - Variable in class ambit2.jchempaint.editor.JChemPaintDialog
 
jcpep - Variable in class ambit2.jchempaint.editor.StructureDiagramEditor
 
jcpModel - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
jcpModel - Variable in class ambit2.jchempaint.editor.StructureDiagramEditor
 
jenaModel - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
jenaModel - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
jenaModel - Variable in class ambit2.rest.reporters.CatalogRDFReporter
 
jenaModel - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
jobs - Variable in class ambit2.rest.task.CallableDatasetCreator
 
join - Static variable in class ambit2.db.search.property.PropertiesByDataset
 
join - Static variable in class ambit2.db.search.property.PropertiesByQuery
 
join - Static variable in class ambit2.db.search.QueryCombined
 
join(IQueryObject<T>, String, StringBuffer) - Method in class ambit2.db.search.QueryCombined
 
join - Static variable in class ambit2.db.search.structure.QueryStoredResults
 
join_struc_dataset - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
join_struc_dataset - Static variable in class ambit2.db.search.structure.QueryStructureType
 
join_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
join_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
join_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureType
 
joinOn() - Method in class ambit2.db.search.QueryCombined
 
joinOn() - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
json2params(String) - Method in class ambit2.db.substance.study.SubstanceStudyFlatQuery
{ "params": { ":id": { "mandatory": false, "type": "Integer", "value": 123 } } }
jsonDate(Date) - Static method in class ambit2.base.json.JSONUtils
 
jsonEscape(String) - Static method in class ambit2.base.json.JSONUtils
 
jsonExpNumber(Double) - Static method in class ambit2.base.json.JSONUtils
 
jsonFlags - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
JsonFlags() - Constructor for class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
jsonFormat(List) - Static method in class ambit2.base.json.JSONUtils
 
jsonname() - Method in enum ambit2.base.data.SubstanceRecord.jsonSubstance
 
jsonname() - Method in enum ambit2.base.relation.composition.CompositionRelation.jsonFeature
 
jsonNodeToJavaField(JsonNode, Object, String, boolean) - Static method in class ambit2.rules.json.JSONParsingUtils
 
jsonNumber(Number) - Static method in class ambit2.base.json.JSONUtils
 
jsonNumber(Double) - Static method in class ambit2.base.json.JSONUtils
 
jsonNumber(Integer) - Static method in class ambit2.base.json.JSONUtils
 
jsonp - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
jsonParams - Variable in class ambit2.db.search.SQLFileQueryParams
 
JSONParserUtils - Class in ambit2.core.json
 
JSONParserUtils() - Constructor for class ambit2.core.json.JSONParserUtils
 
JSONParsingUtils - Class in ambit2.rules.json
 
JSONParsingUtils() - Constructor for class ambit2.rules.json.JSONParsingUtils
 
JSONParsingUtils.STRUCTURE_RECORD_INPUT_INFO - Enum in ambit2.rules.json
 
jsonQuote(String) - Static method in class ambit2.base.json.JSONUtils
Returns null, if the value is null, or a quoted string otherwise
JSONRuleParser - Class in ambit2.structure2name.rules.parser
 
JSONRuleParser() - Constructor for class ambit2.structure2name.rules.parser.JSONRuleParser
 
JsonRuleParser - Class in ambit2.tautomers.rules
 
JsonRuleParser() - Constructor for class ambit2.tautomers.rules.JsonRuleParser
 
jsonSanitizeCallback(String) - Static method in class ambit2.base.json.JSONUtils
Used for JSONP callbacks TODO: full name validation
JSONUtils - Class in ambit2.base.json
http://www.ietf.org/rfc/rfc4627.txt
JSONUtils() - Constructor for class ambit2.base.json.JSONUtils
 

K

k - Variable in class ambit2.similarity.measure.BinaryKernelDistance
 
kB - Static variable in class ambit2.tautomers.TautomerRanking
 
KCEpanechnikov - Class in ambit2.domain.stats.transforms.densityestimation
Canonical Epanechnikov kernel
KCEpanechnikov() - Constructor for class ambit2.domain.stats.transforms.densityestimation.KCEpanechnikov
 
KDensity1D - Class in ambit2.domain.stats.transforms.densityestimation
Kernel Density Estimation Package
KDensity1D() - Constructor for class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
KDensityMD - Class in ambit2.domain.stats.transforms.densityestimation
Multivariate kernel density estimation
KDensityMD(int) - Constructor for class ambit2.domain.stats.transforms.densityestimation.KDensityMD
MVDE class constructor
KDensityMDProduct - Class in ambit2.domain.stats.transforms.densityestimation
Multivariate density estimation by product of 1D Kernel Density Estimates Up to now not used in Ambit
KDensityMDProduct(int) - Constructor for class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
keepEffectRecordsForDocUUID - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
keeprawrecord - Variable in class ambit2.core.io.RawIteratingCSVReader
 
Kernel - Class in ambit2.domain.stats.transforms.densityestimation
Abstract kernel
Kernel() - Constructor for class ambit2.domain.stats.transforms.densityestimation.Kernel
 
KernelName - Variable in class ambit2.domain.stats.transforms.densityestimation.Kernel
 
KeVtoJ - Static variable in class ambit2.tautomers.TautomerRanking
 
key - Variable in class ambit2.core.processors.structure.key.CASKey
 
key - Variable in class ambit2.core.processors.structure.key.InchiKey
 
key - Variable in class ambit2.core.processors.structure.key.PropertyKey
 
key - Variable in class ambit2.core.processors.structure.key.SmilesKey
 
key - Variable in class ambit2.db.reporters.SmilesReporter
 
KeyResult - Static variable in class ambit2.base.ro.I5CONSTANTS
 
keys - Static variable in class ambit2.db.update.fp.Fingerprint
 
keys - Variable in class ambit2.rest.task.FilteredTasksIterator
 
keys2String(int) - Method in class ambit2.core.data.HashIntDescriptorResult
 
keySet() - Method in class ambit2.base.data.study.Params
 
keyWord - Variable in class ambit2.reactions.rules.GenericRuleMetaInfo
 
KeyWordElementSeparator - Static variable in class ambit2.reactions.ReactionConst
 
KeyWordElementSeparator - Variable in class ambit2.reactions.rules.GenericParserUtils
 
KeyWordElementSeparator - Static variable in class ambit2.tautomers.TautomerConst
 
keyWordPrefix - Static variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
KeyWordPrefix - Static variable in class ambit2.reactions.ReactionConst
 
KeyWordPrefix - Variable in class ambit2.reactions.rules.GenericParserUtils
 
KeyWordPrefix - Static variable in class ambit2.tautomers.TautomerConst
 
keyWordRequired - Variable in class ambit2.reactions.rules.GenericRuleMetaInfo
 
keyWordSeparator - Static variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
KeyWordSeparator - Static variable in class ambit2.reactions.ReactionConst
 
KeyWordSeparator - Variable in class ambit2.reactions.rules.GenericParserUtils
 
KeyWordSeparator - Static variable in class ambit2.tautomers.TautomerConst
 
KLaplacian - Class in ambit2.domain.stats.transforms.densityestimation
Laplacian kernel
KLaplacian() - Constructor for class ambit2.domain.stats.transforms.densityestimation.KLaplacian
 
KlekotaRothFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
 
KlekotaRothFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.KlekotaRothFingerprinterWrapper
 
KnimeWorkflowScore - Class in ambit2.reactions.generator.score.components
 
KnimeWorkflowScore() - Constructor for class ambit2.reactions.generator.score.components.KnimeWorkflowScore
 
kNN - Variable in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
KNormal - Class in ambit2.domain.stats.transforms.densityestimation
NorGaussian (normal) mal kernel
KNormal() - Constructor for class ambit2.domain.stats.transforms.densityestimation.KNormal
 
KnowledgeBase - Class in ambit2.tautomers
 

L

label - Variable in class ambit2.base.data.AbstractLabel
 
label - Variable in class ambit2.base.data.Property
 
label - Variable in class ambit2.ui.table.FindNavigator
 
label - Variable in class ambit2.ui.table.PageNavigator
 
label - Variable in class ambit2.ui.table.RecordNavigator
 
labels - Static variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
lambda - Variable in class ambit2.similarity.measure.BinaryKernelDistance
 
LaplasMatrix(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
last() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader
 
last() - Method in class ambit2.db.results.AmbitRows
 
last() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
last() - Method in interface ambit2.model.IDataset
 
LAST - Static variable in class ambit2.similarity.stats.ClassificationModelStatistics
 
LAST - Static variable in class ambit2.similarity.stats.PredictionModelStatistics
 
lastIndexOf(Object) - Method in class ambit2.core.groups.FilteredList
 
lastModified - Variable in class ambit2.core.io.FileState
 
lastName - Variable in class ambit2.base.data.AmbitUser
 
lastName - Variable in class ambit2.export.isa.v1_0.objects.Person
 
lastName - Variable in class ambit2.ui.editors.AmbitUserEditor
 
launchEditor(Component) - Method in class ambit2.ui.Panel2D
 
LauncherResource - Class in ambit2.rest.task
 
LauncherResource() - Constructor for class ambit2.rest.task.LauncherResource
 
launchFeaturesCalculations(Model, String) - Method in class ambit2.rest.task.CallableDatasetCreator
 
launchUI() - Method in class ambit2.ui.AmbitSettingsListener
 
layer - Variable in class ambit2.export.isa.base.ISALocation
 
layerPos2ID - Variable in class ambit2.export.isa.base.ISALocation
 
layerPos2Index - Variable in class ambit2.export.isa.base.ISALocation
 
layerPosID - Variable in class ambit2.export.isa.base.ISALocation
 
layerPosIndex - Variable in class ambit2.export.isa.base.ISALocation
 
LDAtomFormalCharge - Class in ambit2.groupcontribution.descriptors
 
LDAtomFormalCharge() - Constructor for class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
LDAtomHeavyNeighbours - Class in ambit2.groupcontribution.descriptors
 
LDAtomHeavyNeighbours() - Constructor for class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
LDAtomHybridization - Class in ambit2.groupcontribution.descriptors
 
LDAtomHybridization() - Constructor for class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
LDAtomSymbol - Class in ambit2.groupcontribution.descriptors
 
LDAtomSymbol() - Constructor for class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
LDAtomValency - Class in ambit2.groupcontribution.descriptors
 
LDAtomValency() - Constructor for class ambit2.groupcontribution.descriptors.LDAtomValency
 
LDHNum - Class in ambit2.groupcontribution.descriptors
 
LDHNum() - Constructor for class ambit2.groupcontribution.descriptors.LDHNum
 
learn(IDataset<ID, Features, ResultType>) - Method in interface ambit2.model.IModelDefinition
 
learn(ID, Features, ResultType, ResultType) - Method in interface ambit2.model.IModelDefinition
 
learn(IDataset<ID, Features, ResultType>) - Method in class ambit2.similarity.AbstractSimilarityModel
 
learn(ID, Features, Double, Double) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
Learner - Class in ambit2.groupcontribution
 
Learner() - Constructor for class ambit2.groupcontribution.Learner
 
leaveOneOut - Variable in class ambit2.groupcontribution.GCMTestConfig
 
leaveOneOutValidation - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
left - Variable in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
legend - Variable in class ambit2.db.chart.ChartGenerator
 
length() - Method in class ambit2.core.data.AbstractDescriptorResultType
 
length() - Method in class ambit2.core.data.ArrayResult
 
length() - Method in class ambit2.core.data.HashDescriptorResult
 
length - Variable in class ambit2.core.io.FileState
 
length() - Method in class ambit2.descriptors.VerboseDescriptorResult
 
level - Variable in class ambit2.core.io.SimpleIOListener
 
level - Variable in class ambit2.reactions.reactor.ReactorNode
 
level - Variable in class ambit2.reactions.retrosynth.IReactionSequenceHandler.RSEvent
 
level - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScore
 
level - Variable in class ambit2.ui.AmbitSettingsListener
 
levelIndex - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
levels - Variable in class ambit2.descriptors.AtomEnvironment
 
levels - Variable in class ambit2.reactions.retrosynth.ReactionSequence.InchiEntry
 
levelWeight - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
LevensteinDistance - Class in ambit2.similarity.measure
Levenstein (edit) distance between strings.
LevensteinDistance() - Constructor for class ambit2.similarity.measure.LevensteinDistance
 
license - Variable in class ambit2.rest.legacy.OTDataset
Deprecated.
 
licenseColumn - Variable in class ambit2.db.reporters.CSVReporter
 
licenseURI - Variable in class ambit2.base.data.SourceDataset
 
licenseURI - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
licenseURI - Variable in class ambit2.base.processors.batch.BatchReporter
 
licenseURI - Variable in class ambit2.core.processors.ProcessorFileExport
 
licenseURI - Variable in class ambit2.db.search.StoredQuery
 
licenseURI - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
ligand0Deleted - Variable in class ambit2.smarts.StereoChange
 
ligand1 - Variable in class ambit2.smarts.DoubleBondStereoInfo
 
ligand1Deleted - Variable in class ambit2.smarts.StereoChange
 
ligand2 - Variable in class ambit2.smarts.DoubleBondStereoInfo
 
ligandAtomDeleted - Variable in class ambit2.smarts.StereoChange
 
LIMIT - Variable in class ambit2.db.search.QueryExecutor
 
limitDiffForSwitchToCombinatorial - Variable in class ambit2.tautomers.RuleSelector
 
limitFuzziness - Variable in class ambit2.tautomers.RuleSelector
 
LinearFunction - Class in ambit2.rules.functions
 
LinearFunction(double[]) - Constructor for class ambit2.rules.functions.LinearFunction
 
LinearNotationType - Enum in ambit2.sln.io
 
lines - Variable in class ambit2.core.io.StringArrayHeader
 
lineseparator - Variable in class ambit2.db.reporters.CSVReporter
 
link_WikiPathway - Static variable in class ambit2.base.data.Property
 
Linkage - Class in ambit2.export.isa.v1_0.objects
 
Linkage() - Constructor for class ambit2.export.isa.v1_0.objects.Linkage
 
linkages - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
linkageType - Variable in class ambit2.export.isa.v1_0.objects.Linkage
 
linkStepToNextLevel(ReactionSequenceStep) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
linspace(double, double, int, double[]) - Method in class ambit2.domain.stats.transforms.Misc
 
list - Variable in class ambit2.ui.editors.ListEditor
 
listEditor - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
listEditor - Variable in class ambit2.dbui.QueryCombinedEditor
 
ListEditor - Class in ambit2.ui.editors
 
ListEditor() - Constructor for class ambit2.ui.editors.ListEditor
 
ListEditor(ListModel) - Constructor for class ambit2.ui.editors.ListEditor
 
listIterator() - Method in class ambit2.core.groups.FilteredList
 
listIterator(int) - Method in class ambit2.core.groups.FilteredList
 
ListReporter<Item,Output> - Class in ambit2.base.processors.batch
 
ListReporter() - Constructor for class ambit2.base.processors.batch.ListReporter
 
LiteratureEntry - Class in ambit2.base.data
A Literature entry:
title, URL
LiteratureEntry(String, String) - Constructor for class ambit2.base.data.LiteratureEntry
We need separate instances for web services
ln2_1 - Static variable in class ambit2.domain.stats.datastructures.Histogram
 
ln2_1 - Static variable in class ambit2.similarity.stats.Histogram
 
LO - Static variable in class ambit2.sln.SLNConst
 
LO - Static variable in class ambit2.smarts.SmartsConst
 
LO_AND - Static variable in class ambit2.sln.SLNConst
 
LO_AND - Static variable in class ambit2.smarts.SmartsConst
 
LO_ANDLO - Static variable in class ambit2.sln.SLNConst
 
LO_ANDLO - Static variable in class ambit2.smarts.SmartsConst
 
LO_NOT - Static variable in class ambit2.sln.SLNConst
 
LO_NOT - Static variable in class ambit2.smarts.SmartsConst
 
LO_OR - Static variable in class ambit2.sln.SLNConst
 
LO_OR - Static variable in class ambit2.smarts.SmartsConst
 
LO_UNDEFINED - Static variable in class ambit2.smarts.SmartsConst
 
load(InputStream) - Static method in class ambit2.base.data.ClassHolder
 
load(InputStream) - Method in class ambit2.base.data.Template
 
load(Reader) - Method in class ambit2.base.data.Template
 
load() - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
load(OT.OTProperty[], String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
Reads RDF and initializes variables
loadDataFromFile(File) - Method in class ambit2.groupcontribution.dataset.DataSet
 
loadDefaultEnergyRules() - Method in class ambit2.tautomers.ranking.EnergyRanking
 
loadExamples - Variable in class ambit2.smarts.processors.SMIRKSProcessor
 
loadFromJSON(File) - Static method in class ambit2.export.isa.json.ISAJsonExportConfig
 
loadFromJSON(File) - Method in class ambit2.groupcontribution.io.GCM2Json
 
loadFromJSON(File) - Method in class ambit2.reactions.retrosynth.SyntheticStrategy
 
loadFromProperties(String) - Method in class ambit2.groupcontribution.io.GCM2Properties
 
loadIUPACRuleDataBase(String) - Method in class ambit2.structure2name.rules.parser.JSONRuleParser
 
loadKnowledgeBaseFromTextFile(String) - Method in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
loadPredefinedBase() - Method in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
loadPredefinedBase() - Method in class ambit2.tautomers.KnowledgeBase
 
loadProperties() - Static method in class ambit2.base.config.Preferences
 
loadProperties() - Static method in class ambit2.ui.EditorPreferences
 
loadProperties() - Method in class ambit2.vega.VegaShell
 
loadReactionsFromJSON(File, boolean) - Method in class ambit2.reactions.ReactionDataBase
 
loadReactionsFromJSON(File) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
loadReactionsFromJSON(InputStream) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
loadReactionsFromRuleFormat(String) - Method in class ambit2.reactions.io.ReactionReadUtils
 
loadReactionsFromTabDelimitedFile(File, boolean) - Method in class ambit2.reactions.ReactionDataBase
 
loadReactionsFromTabDelimitedFile(File, boolean, Map<String, Integer>, int) - Method in class ambit2.reactions.ReactionDataBase
 
loadReactionsFromTabulatedText(String) - Method in class ambit2.reactions.io.ReactionReadUtils
 
loadSmilesStringsFromFile(String) - Method in class ambit2.smarts.ChemObjectFactory
 
loadSmilesTuplesFromFile(String) - Method in class ambit2.smarts.ChemObjectFactory
 
loadSQL(InputStream) - Method in class ambit2.db.search.SQLFileQueryParams
 
LOCAL_AA_ENABLED - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
LocalDescriptorManager - Class in ambit2.groupcontribution.descriptors
 
LocalDescriptorManager() - Constructor for class ambit2.groupcontribution.descriptors.LocalDescriptorManager
 
localDescriptors - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
localDescriptors - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
localDescriptorsString - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
LocalDictOffseet - Static variable in class ambit2.sln.SLNConst
 
LocalProperties - Class in ambit2.groupcontribution.dataset
 
LocalProperties() - Constructor for class ambit2.groupcontribution.dataset.LocalProperties
 
LocalProperties.Type - Enum in ambit2.groupcontribution.dataset
 
LocalPropertiesIterator - Class in ambit2.groupcontribution.dataset
 
LocalPropertiesIterator(File) - Constructor for class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
LocalPropertiesIterator(File, LocalProperties.Type) - Constructor for class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
LocalPropertiesIterator(File, CSVFormat, LocalProperties.Type) - Constructor for class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
locPropType - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
log(SubstanceRecord, String) - Method in class ambit2.base.data.study.StructureRecordValidator
 
log2(double) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
log_2 - Static variable in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
logfile - Variable in class ambit2.pubchem.BatchRetrievePubChem
 
logFile - Variable in class ambit2.rest.task.CallableProtectedTask
 
loggedFromHost - Variable in class ambit2.base.data.AmbitUser
 
loggedFromHost - Variable in class ambit2.ui.editors.AmbitUserEditor
 
logger - Variable in class ambit2.base.external.CommandShell
 
logger - Static variable in class ambit2.base.io.SimpleErrorHandler
 
logger - Static variable in class ambit2.chebi.ChEBIClient
 
logger - Static variable in class ambit2.core.data.MoleculeTools
 
logger - Static variable in class ambit2.core.io.ECHAPreregistrationListReader
 
logger - Static variable in class ambit2.core.io.FilesWithHeaderWriter
 
logger - Static variable in class ambit2.core.io.FileWithHeaderWriter
 
logger - Static variable in class ambit2.core.io.I5ReaderSimple
 
logger - Static variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
logger - Static variable in class ambit2.core.io.IteratingFolderReader
 
logger - Static variable in class ambit2.core.io.json.SubstanceStudyParser
 
logger - Static variable in class ambit2.core.io.RawIteratingReader
 
logger - Static variable in class ambit2.core.io.SGroupMDL2000Helper
 
logger - Variable in class ambit2.core.io.study.StudyFormatter
 
logger - Static variable in class ambit2.core.io.ToXMLReaderSimple
 
logger - Variable in class ambit2.core.processors.AbstractStructureProcessor
 
logger - Static variable in class ambit2.core.smiles.SmilesParserWrapper
 
logger - Static variable in class ambit2.db.search.AbstractQuery
 
logger - Static variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
logger - Static variable in class ambit2.descriptors.PKASmartsDescriptor
 
logger - Static variable in class ambit2.descriptors.processors.AtomEnvironmentList
 
logger - Variable in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
logger - Variable in class ambit2.dragon.DescriptorDragonShell
 
logger - Static variable in class ambit2.dragon.DragonDescriptorDictionary
 
logger - Static variable in class ambit2.export.isa.ISAExportConfig
 
logger - Static variable in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
logger - Static variable in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
logger - Variable in class ambit2.model.AbstractModel
 
logger - Static variable in class ambit2.model.numeric.DataCoverage
 
logger - Static variable in class ambit2.mopac.Mopac7Reader
 
logger - Static variable in class ambit2.reactions.reactor.Reactor
 
logger - Static variable in class ambit2.rendering.CompoundImageTools
 
logger - Variable in class ambit2.rest.freemarker.FreeMarkerStatusService
 
logger - Static variable in class ambit2.rest.task.CallableProtectedTask
 
logger - Variable in class ambit2.rest.task.TaskStorage
 
logger - Static variable in class ambit2.similarity.knn.NearestNeighborsSearch
 
logger - Static variable in class ambit2.similarity.stats.Histogram
 
logger - Static variable in class ambit2.smarts.query.AbstractSmartsPattern
 
logger - Static variable in class ambit2.some.DescriptorSOMEShell
 
logger - Static variable in class ambit2.tautomers.RuleInstance
 
logger - Static variable in class ambit2.tautomers.RuleManager
 
logger - Static variable in class ambit2.tautomers.Tautomer2DescriptorUtils
 
logger - Static variable in class ambit2.tautomers.TautomerManager
 
logger - Static variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
loggingProperties - Static variable in class ambit2.base.config.AMBITConfigProperties
 
LoginInfo - Class in ambit2.db
 
LoginInfo() - Constructor for class ambit2.db.LoginInfo
 
loginInfo - Variable in class ambit2.dbui.LoginInfoBean
 
LoginInfoBean - Class in ambit2.dbui
 
LoginInfoBean() - Constructor for class ambit2.dbui.LoginInfoBean
 
LoginPanel - Class in ambit2.dbui
Editor for LoginInfo
LoginPanel() - Constructor for class ambit2.dbui.LoginPanel
 
LogOperationChars - Static variable in class ambit2.smarts.SmartsConst
 
logStep - Variable in class ambit2.reactions.reactor.ReactorResult
 
logX - Variable in class ambit2.db.chart.ChartGenerator
 
logY - Variable in class ambit2.db.chart.ChartGenerator
 
lonePairs - Variable in class ambit2.core.groups.SuppleAtomContainer
 
lonePairs() - Method in class ambit2.core.groups.SuppleAtomContainer
 
lookup - Variable in class ambit2.base.ro.AbstractAnnotator
 
lookup - Variable in class ambit2.db.DbReaderStructure
 
lookup(Target, IProcessor<Target, Result>, ResultListener<Result>) - Method in class ambit2.pubchem.QuerySupport
Executes a query.
lookup - Variable in class ambit2.rest.rdf.RDFStructuresIterator
 
lookup - Variable in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
lookup(ArrayNode, String, String) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
loQualifier - Variable in class ambit2.base.data.study.EffectRecord
 
loQualifier - Variable in class ambit2.base.data.study.Value
 
lotIdentifier - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
loValue - Variable in class ambit2.base.data.study.EffectRecord
 
loValue - Variable in class ambit2.base.data.study.Value
 
low - Variable in class ambit2.similarity.stats.Bin
 
lowestDistanceIsClosest - Variable in class ambit2.similarity.knn.NearestNeighborsSearch
 
lowestDistanceIsClosest - Variable in class ambit2.similarity.measure.DistanceComparable
 

M

MACCSFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
Wrapper for MACCSFingerprinter, implementing IMolecularDescriptor
MACCSFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.MACCSFingerprinterWrapper
 
MAE - Static variable in class ambit2.similarity.stats.PredictionModelStatistics
 
main(String[]) - Static method in class ambit2.core.io.QuotedTokenizer
 
main(String[]) - Static method in class ambit2.groupcontribution.cli.GCMPredictCli
 
main(String[]) - Static method in class ambit2.groupcontribution.cli.GroupContributionCli
 
main(String[]) - Static method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
main(String[]) - Static method in class ambit2.ml.io.app.AmbitML
 
main(String[]) - Static method in class ambit2.ml.mlib.ClusteringApp
 
main(String[]) - Static method in class ambit2.pubchem.SearchApplication
 
main(String[]) - Static method in class ambit2.reactions.cli.AmbitSmirksCli
 
main(String[]) - Static method in class ambit2.reactions.cli.ComplexityCli
 
main(String[]) - Static method in class ambit2.reactions.cli.ReactorCli
 
main(String[]) - Static method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
main(String[]) - Static method in class ambit2.smarts.smirks.Transformations
CC1CN(CC(O1)C)C2=NC3=CC=CC=C3N=C2C(C#N)S(=O)(=O)C4=CC=CC(=C4)C
main(String[]) - Static method in class ambit2.ui.DelimitersPanel
 
mainPanel - Variable in class ambit2.dbui.QueryEditor
 
mainsubscript - Static variable in class ambit2.core.groups.ComponentGroup
 
maintainer - Variable in class ambit2.base.data.SourceDataset
 
maintainer - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
maintainer - Variable in class ambit2.db.search.StoredQuery
 
mainType - Variable in class ambit2.db.reporters.AbstractImageReporter
 
major - Variable in class ambit2.db.version.AmbitDBVersion
 
makeAtomDesignation(int[], List<ILocalDescriptor>) - Static method in class ambit2.groupcontribution.GroupContributionModel
 
makeAtomicFragmenation(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeBondBasedFragmenation(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeCustomGroupFragmenation(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeDataSet(List<String>, List<Double>, String) - Static method in class ambit2.groupcontribution.dataset.DataSet
 
makeFragmentation(DataSet, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeFragmentation(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeMatrixFromRows(int[]) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
makeRindData() - Method in class ambit2.structure2name.IUPACNameGenerator
 
makeSecondOrderFragmenation(DataSetObject, GroupContributionModel) - Static method in class ambit2.groupcontribution.fragmentation.Fragmentation
 
makeSmartsQueries() - Method in class ambit2.tautomers.rules.AtomCondition
 
makeSmartsQueries(SmartsParser) - Method in class ambit2.tautomers.rules.AtomCondition
 
makeValidationModelMatrices(int[], MatrixDouble, MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.CrossValidation
 
makeValidationTestMatrices(int[], MatrixDouble, MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.CrossValidation
 
MalariaHTSDataDelimitedReader - Class in ambit2.core.io.sj
XLS file SAMPLE batch SJ000001054 1 SJ000001111 1 SJ000001119 1 SDF file SJ000001054-1
MalariaHTSDataDelimitedReader(InputStream) - Constructor for class ambit2.core.io.sj.MalariaHTSDataDelimitedReader
 
map - Variable in class ambit2.descriptors.AtomEnvironentMatrix
 
map - Variable in class ambit2.descriptors.AtomEnvironmentDescriptor
 
map_folder - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
mapErrors - Variable in class ambit2.smarts.SMIRKSReaction
 
mapper - Variable in class ambit2.core.io.study.StudyFormatter
 
MappingUtils - Class in ambit2.smarts
 
MappingUtils() - Constructor for class ambit2.smarts.MappingUtils
 
mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression>, IAtomContainer) - Method in class ambit2.smarts.groups.GroupMatch
 
mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression>, IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
markAtomGroups(IAtomContainer, List<IQueryAtomContainer>) - Method in class ambit2.smarts.SmartsManager
Calculates for each atom a bit set which describes the participation of this atom in each of the predefined groups.
markAtomGroups(IAtomContainer, List<IQueryAtomContainer>, SmartsConst.SSM_MODE) - Method in class ambit2.smarts.SmartsManager
 
markProperty - Static variable in class ambit2.smarts.SmartsToChemObject
 
Markush2Smarts - Class in ambit2.markush
 
Markush2Smarts() - Constructor for class ambit2.markush.Markush2Smarts
 
MarkushException - Exception in ambit2.markush
 
MarkushException(String) - Constructor for exception ambit2.markush.MarkushException
 
MarkushException(String, Exception) - Constructor for exception ambit2.markush.MarkushException
 
MarkushHelpers - Class in ambit2.markush
 
MarkushHelpers() - Constructor for class ambit2.markush.MarkushHelpers
 
mAromaticity - Variable in class ambit2.smarts.ChemObjectToSmiles
 
match() - Method in class ambit2.core.io.FileState
 
match(File) - Method in class ambit2.core.io.FileState
 
match(IAtom) - Method in interface ambit2.sln.dictionary.ISLNDictionaryObject
 
match(IBond) - Method in interface ambit2.sln.dictionary.ISLNDictionaryObject
 
match(IAtomContainer) - Method in class ambit2.smarts.groups.GroupMatch
 
match(IAtomContainer) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
match(IAtomContainer) - Method in interface ambit2.smarts.query.ISmartsPattern
 
match(IQueryAtom, IAtom) - Method in class ambit2.smarts.smirks.SmartsMatch
 
match(IQueryBond, IBond) - Method in class ambit2.smarts.smirks.SmartsMatch
 
match_GMOE(int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_iMOE(int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_NMOE(IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_OB_Hybr(int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_R(int[], int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_r(int[], int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_rbc(int[], int, IAtom) - Method in class ambit2.sln.SLNAtomExpression
 
match_src(int[], int, IAtom) - Method in class ambit2.sln.SLNAtomExpression
 
match_vMOE(int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_x(int, IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
match_XMOE(IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
matchAtPosition(IAtomContainer, int) - Method in class ambit2.smarts.groups.GroupMatch
 
matchCLG(List<IQueryAtomContainer>, List<Integer>, IAtomContainerSet) - Method in class ambit2.smarts.SMIRKSManager
 
matchCount(IAtomContainer) - Method in class ambit2.smarts.groups.GroupMatch
 
matches(List<String>) - Method in class ambit2.core.io.DelimitedFileFormat
 
matches(int, String) - Method in class ambit2.core.io.XLSFileFormat
 
matches(List<String>) - Method in class ambit2.core.io.XLSFileFormat
 
matches(IAtom) - Method in class ambit2.sln.SLNAtom
 
matches(IAtom) - Method in class ambit2.sln.SLNAtomExpression
 
matches(IBond) - Method in class ambit2.sln.SLNBond
 
matches(IBond) - Method in class ambit2.sln.SLNBondExpression
 
matches(IAtom) - Method in class ambit2.smarts.AliphaticSymbolQueryAtom
 
matches(IAtom) - Method in class ambit2.smarts.AromaticSymbolQueryAtom
 
matches(IBond) - Method in class ambit2.smarts.DoubleBondAromaticityNotSpecified
 
matches(IBond) - Method in class ambit2.smarts.DoubleNonAromaticBond
 
matches(IBond) - Method in class ambit2.smarts.RingQueryBond
 
matches(IBond) - Method in class ambit2.smarts.SingleBondAromaticityNotSpecified
 
matches(IBond) - Method in class ambit2.smarts.SingleNonAromaticBond
 
matches(IBond) - Method in class ambit2.smarts.SingleOrAromaticBond
 
matches(IAtom) - Method in class ambit2.smarts.SmartsAtomExpression
 
matches(IBond) - Method in class ambit2.smarts.SmartsBondExpression
 
matches(IAtom) - Method in class ambit2.smarts.SymbolQueryAtomAromaticityNotSpecified
 
matches(IBond) - Method in class ambit2.smarts.TripleBondAromaticityNotSpecified
 
matchesToString(IAtomContainer, List<IAtom>) - Method in class ambit2.smarts.SmartsManager
 
matchReaction(String) - Method in class ambit2.smarts.smirks.ReactionSearch
 
matchReaction(SMIRKSReaction) - Method in class ambit2.smarts.smirks.ReactionSearch
 
matchReaction(List<IAtomContainer>, List<IAtomContainer>) - Method in class ambit2.smarts.smirks.ReactionSearch
 
matchReaction(SMIRKSReaction, IAtomContainer, IAtomContainer, IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
matchReaction(SMIRKSReaction, IAtomContainerSet, IAtomContainerSet, IAtomContainerSet) - Method in class ambit2.smarts.SMIRKSManager
 
Material - Class in ambit2.export.isa.v1_0.objects
ISA material node schema JSON-schema representing a material node in the ISA model, which is not a source or a sample (as they have specific schemas) - this will correspond to 'Extract Name', 'Labeled Extract Name'
Material() - Constructor for class ambit2.export.isa.v1_0.objects.Material
 
Material.Type - Enum in ambit2.export.isa.v1_0.objects
 
MaterialAttribute - Class in ambit2.export.isa.v1_0.objects
ISA material attribute schema JSON-schema representing a characteristics category (what appears between the brackets in Charactersitics[]) in the ISA model
MaterialAttribute() - Constructor for class ambit2.export.isa.v1_0.objects.MaterialAttribute
 
MaterialAttributeValue - Class in ambit2.export.isa.v1_0.objects
ISA material attribute schema JSON-schema representing a material attribute (or characteristic) value in the ISA model
MaterialAttributeValue() - Constructor for class ambit2.export.isa.v1_0.objects.MaterialAttributeValue
 
materials - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
Materials - Class in ambit2.export.isa.v1_0.objects
 
Materials() - Constructor for class ambit2.export.isa.v1_0.objects.Materials
 
materials - Variable in class ambit2.export.isa.v1_0.objects.Study
 
Materials_ - Class in ambit2.export.isa.v1_0.objects
 
Materials_() - Constructor for class ambit2.export.isa.v1_0.objects.Materials_
 
MathUtilities - Class in ambit2.groupcontribution.utils.math
 
MathUtilities() - Constructor for class ambit2.groupcontribution.utils.math.MathUtilities
 
matrix - Variable in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
matrix - Variable in class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
matrix - Variable in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
MatrixDouble - Class in ambit2.groupcontribution.utils.math
 
MatrixDouble() - Constructor for class ambit2.groupcontribution.utils.math.MatrixDouble
 
MatrixDouble(int, int) - Constructor for class ambit2.groupcontribution.utils.math.MatrixDouble
 
MatrixDouble(MatrixDouble) - Constructor for class ambit2.groupcontribution.utils.math.MatrixDouble
 
MatrixDouble(List<Double>) - Constructor for class ambit2.groupcontribution.utils.math.MatrixDouble
 
MatrixMarketReaderAbstract<T,V> - Class in ambit2.base.io.format
 
MatrixMarketReaderAbstract() - Constructor for class ambit2.base.io.format.MatrixMarketReaderAbstract
 
matrixOutputFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
max(int[]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
max(double[]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
max(double[], int) - Static method in class ambit2.domain.stats.Tools
 
max(double[][]) - Static method in class ambit2.domain.stats.Tools
 
max(Vector) - Static method in class ambit2.domain.stats.Tools
 
max - Variable in class ambit2.rest.SimpleTaskResource
 
MAX_DIAMETER - Static variable in class ambit2.descriptors.CrossSectionalDiameterDescriptor
Cross sectional diameter
max_hits - Static variable in class ambit2.rest.AbstractResource
 
MAX_LENGTH - Static variable in class ambit2.descriptors.CrossSectionalDiameterDescriptor
Maximum length of the molecule
maxAllAtoms - Variable in class ambit2.mopac.AbstractMopacShell
 
maxAmplitude() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
 
maxAmplitude() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
MaxAmplitude
maxAmplitude() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
maxCompNumber - Variable in class ambit2.sln.SLNParser
 
maxCompNumber - Variable in class ambit2.smarts.SmartsParser
 
maxCyclicBonds - Static variable in class ambit2.core.config.AmbitCONSTANTS
max cyclic bonds for skipping huge compounds
maxdata - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
maxElement() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
maxHAtoms - Static variable in class ambit2.core.config.AmbitCONSTANTS
max H atoms for skipping huge compounds
maxHeavyAtoms - Static variable in class ambit2.core.config.AmbitCONSTANTS
max heavy atoms for skipping huge compounds
maxHeavyAtoms - Variable in class ambit2.mopac.AbstractMopacShell
 
maxHitStructSize - Variable in class ambit2.smarts.StructureSetAnalyzer
 
MaximumDiameterDescriptor - Class in ambit2.descriptors
Maximum cross sectional diameter.
MaximumDiameterDescriptor() - Constructor for class ambit2.descriptors.MaximumDiameterDescriptor
 
maxLevel - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
maxLevels - Variable in class ambit2.core.data.HashIntDescriptorResult
 
maxLevels - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
maxNominalValues - Variable in class ambit2.rest.rdf.RDFInstancesIterator
 
MaxNumberOfRegisteredZwitterions - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
MaxNumberOfZwitterionicPairs - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
maxNumOfBackTracks - Variable in class ambit2.tautomers.TautomerManager
 
maxNumOfFailedNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
maxNumOfNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
maxNumOfReactions - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
maxNumOfSubCombinations - Variable in class ambit2.tautomers.TautomerManager
 
maxNumOfSuccessNodes - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
maxNumOfTautomerRegistrations - Variable in class ambit2.tautomers.TautomerManager
 
maxPoints - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
maxProperty - Variable in class ambit2.featureselection.RRelieFFAttributeSelection
 
MAXRECORDS - Static variable in class ambit2.base.config.Preferences
 
maxRecords - Variable in class ambit2.db.results.ResultSetTableModel
 
maxRecords - Variable in class ambit2.db.search.AbstractQuery
 
maxRecords - Variable in class ambit2.db.search.structure.ProcessorMissingDescriptorsQuery
 
maxRecords - Variable in class ambit2.db.search.structure.QueryCombinedStructure
 
maxretry - Variable in class ambit2.pubchem.HTTPRequest
 
MAXRINGS - Static variable in class ambit2.smarts.CMLUtilities
 
maxSizeOfSequence - Variable in class ambit2.smarts.StructureSetAnalyzer
 
maxValue - Variable in class ambit2.base.data.Range
 
maxValue - Variable in class ambit2.db.search.QuerySmilesByID
 
maxValue - Variable in class ambit2.db.search.structure.NumberQuery
 
maxValue - Variable in class ambit2.db.search.structure.QueryDistance
 
maxValue - Variable in class ambit2.db.search.structure.QueryFieldNumeric
 
maxValue - Variable in class ambit2.db.search.structure.QueryStructureByID
 
maxX - Variable in class ambit2.db.chart.BarChartGenerator
 
mcmMaterial - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
McmMaterial - Class in ambit2.export.isa.v1_0.objects
Material Definition of Material (or Substance)
McmMaterial() - Constructor for class ambit2.export.isa.v1_0.objects.McmMaterial
 
mcmType - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
McmType - Class in ambit2.export.isa.v1_0.objects
 
McmType() - Constructor for class ambit2.export.isa.v1_0.objects.McmType
 
mcsAnalysis() - Method in class ambit2.smarts.StructureSetAnalyzer
 
MCSSDistance - Class in ambit2.similarity.measure
The MCSS of two compounds is the largest possible substructure that is present in both structures.
MCSSDistance() - Constructor for class ambit2.similarity.measure.MCSSDistance
 
MDLReader - Class in ambit2.core.io
Reads a molecule from the original MDL MOL or SDF file .
MDLReader() - Constructor for class ambit2.core.io.MDLReader
 
MDLReader(InputStream) - Constructor for class ambit2.core.io.MDLReader
Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLReader
 
MDLReader(Reader) - Constructor for class ambit2.core.io.MDLReader
Constructs a new MDLReader that can read Molecule from a given Reader.
MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLReader
 
mean(double[], int) - Static method in class ambit2.domain.stats.Tools
 
mean(double[][]) - Static method in class ambit2.domain.stats.Tools
 
mean(Vector) - Static method in class ambit2.domain.stats.Tools
 
mean(double[]) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
mean(MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
mean(List<Double>) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
MEAN_DIAMETER - Static variable in class ambit2.base.ro.I5CONSTANTS
 
meanAbsoluteError(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
meanAbsoluteError(List<Double>, List<Double>) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
meandata - Variable in class ambit2.model.numeric.DataCoverageDistance
 
measurements - Variable in class ambit2.base.data.SubstanceRecord
 
measurements - Variable in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
measurementType - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
media - Variable in class ambit2.rest.task.CallablePOST
 
mediaType - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
mediaType - Variable in class ambit2.rest.RDFBatchParser
 
mediaType - Variable in class ambit2.rest.reporters.CatalogRDFReporter
 
mElementSymbol - Static variable in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
MemoryRowsModel<T> - Class in ambit2.db.results
 
MemoryRowsModel(AmbitRows<T>) - Constructor for class ambit2.db.results.MemoryRowsModel
 
mengine - Variable in class ambit2.mopac.MopacShell
 
MENGINE_LINUX - Static variable in class ambit2.base.config.Preferences
 
MENGINE_WIN - Static variable in class ambit2.base.config.Preferences
 
merge() - Method in class ambit2.rest.legacy.OTDatasets
Deprecated.
 
mergedProperties - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
MESSAGE - Static variable in exception ambit2.base.exceptions.PropertyNotInTemplateException
 
message - Variable in class ambit2.sln.SLNParserError
 
message - Variable in class ambit2.smarts.SmartsParserError
 
MESSAGE_UNSUPPORTED_TYPE - Static variable in class ambit2.mopac.AbstractMopacShell
 
metadata - Variable in class ambit2.db.processors.ConnectionStatisticsProcessor
 
method - Variable in class ambit2.db.search.QueryInfo
 
method - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
method - Variable in class ambit2.dbui.QueryInfoEditor
 
method - Variable in class ambit2.rest.RemoteStreamConvertor
 
METHOD_EXACT - Static variable in class ambit2.db.search.QueryInfo
 
method_options - Static variable in class ambit2.db.search.QueryInfo
 
METHOD_SIMILARITY - Static variable in class ambit2.db.search.QueryInfo
 
METHOD_SMARTS - Static variable in class ambit2.db.search.QueryInfo
 
METHOD_SUBSTRUCTURE - Static variable in class ambit2.db.search.QueryInfo
 
methods - Static variable in class ambit2.db.search.structure.QuerySimilarityStructure
 
methodType - Static variable in class ambit2.base.ro.I5CONSTANTS
 
metric - Variable in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
metric - Variable in class ambit2.db.search.property.FilteredCount
 
metric - Variable in class ambit2.db.search.structure.QueryStructureByID
 
metric - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
mGenerateSubQueries - Variable in class ambit2.smarts.SmartsManager
 
midInitials - Variable in class ambit2.export.isa.v1_0.objects.Person
 
millimetres2WidthUnits(double) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
Convert into millimetres Excels width units..
mimeType - Variable in class ambit2.db.cache.RetrieveStructureImagePath
 
min(int[]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
min(double[]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
min(double[], int) - Static method in class ambit2.domain.stats.Tools
 
min(double[][]) - Static method in class ambit2.domain.stats.Tools
 
min(Vector) - Static method in class ambit2.domain.stats.Tools
 
MIN_DIAMETER - Static variable in class ambit2.descriptors.CrossSectionalDiameterDescriptor
minimum diameter
mindata - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
minor - Variable in class ambit2.db.version.AmbitDBVersion
 
minProperty - Variable in class ambit2.featureselection.RRelieFFAttributeSelection
 
minValue - Variable in class ambit2.base.data.Range
 
minX - Variable in class ambit2.db.chart.BarChartGenerator
 
Misc - Class in ambit2.domain.stats.transforms
Miscelaneous routines for the ambit2.stats.transforms.FFT
Misc() - Constructor for class ambit2.domain.stats.transforms.Misc
 
MISSING_DESCRIPTOR - Static variable in class ambit2.db.search.structure.QueryMissingDescriptor
 
MISSING_DESCRIPTOR - Static variable in class ambit2.db.search.structure.QueryMissingProperty
 
MISSING_DISTANCES - Static variable in class ambit2.db.search.structure.QueryMissingDistances
 
MissingFingerprintsQuery - Class in ambit2.db.search.structure
 
MissingFingerprintsQuery(FPTable) - Constructor for class ambit2.db.search.structure.MissingFingerprintsQuery
 
MissingFingerprintsQuery() - Constructor for class ambit2.db.search.structure.MissingFingerprintsQuery
 
MissingInChIsQuery - Class in ambit2.db.search.structure
 
MissingInChIsQuery(String) - Constructor for class ambit2.db.search.structure.MissingInChIsQuery
TODO identify potential errors update chemicals,(SELECT inchi,count(*) c FROM chemicals where inchi is not null group by inchi ) a set label='ERROR' where chemicals.inchi=a.inchi and a.c>1; update chemicals set label="ERROR" where inchi is null;
MissingInChIsQuery() - Constructor for class ambit2.db.search.structure.MissingInChIsQuery
 
MLResources - Class in ambit2.rest.algorithm
 
MMPAnalysis - Class in ambit2.reactions.mmp.analysis
 
MMPAnalysis() - Constructor for class ambit2.reactions.mmp.analysis.MMPAnalysis
 
mNeedExplicitHData - Variable in class ambit2.smarts.SmartsFlags
 
mNeedExplicitHData - Variable in class ambit2.tautomers.RuleStateFlags
 
mNeedNeighbourData - Variable in class ambit2.smarts.SmartsFlags
 
mNeedNeighbourData - Variable in class ambit2.tautomers.RuleStateFlags
 
mNeedParentMoleculeData - Variable in class ambit2.smarts.SmartsFlags
 
mNeedParentMoleculeData - Variable in class ambit2.tautomers.RuleStateFlags
 
mNeedRingData - Variable in class ambit2.smarts.SmartsFlags
 
mNeedRingData - Variable in class ambit2.tautomers.RuleStateFlags
 
mNeedRingData2 - Variable in class ambit2.smarts.SmartsFlags
 
mNeedRingData2 - Variable in class ambit2.tautomers.RuleStateFlags
 
mNeedValenceData - Variable in class ambit2.smarts.SmartsFlags
 
mNeedValenceData - Variable in class ambit2.tautomers.RuleStateFlags
 
mobileAtom - Variable in class ambit2.tautomers.RuleInstance
 
mobileGroup - Variable in class ambit2.tautomers.Rule
 
mobileGroupPos - Variable in class ambit2.tautomers.Rule
 
modal - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
mode - Variable in class ambit2.base.processors.search.AbstractFinder
 
mode - Variable in class ambit2.core.io.RawIteratingFolderReader
 
mode - Variable in class ambit2.db.reporters.SmilesReporter
 
mode - Variable in class ambit2.db.search.structure.QuerySimilarityBitset
 
mode - Variable in class ambit2.db.substance.QueryCountProtocolApplications
 
mode - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
mode - Variable in class ambit2.smarts.smirks.SmartsMatch
 
mode - Variable in class ambit2.ui.BrowserModeCellRenderer
 
modeArg - Variable in class ambit2.reactions.cli.AmbitSmirksCli
 
model - Variable in class ambit2.dbui.QueryCombinedEditor
 
model - Variable in class ambit2.dbui.QueryScopeEditor
 
model(String, String) - Static method in class ambit2.rest.legacy.OTModel
Deprecated.
 
model(String, String) - Static method in class ambit2.rest.legacy.OTSuperModel
Deprecated.
 
model - Variable in class ambit2.rest.model.predictor.ExternalModel
 
model - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
model - Variable in class ambit2.rest.model.task.CallableModelCreator
 
model_reporter - Variable in class ambit2.rest.model.builder.ModelBuilder
 
model_resource - Static variable in class ambit2.rest.algorithm.MLResources
 
model_resourceID - Static variable in class ambit2.rest.algorithm.MLResources
 
model_resourcekey - Static variable in class ambit2.rest.algorithm.MLResources
 
model_uri - Variable in class ambit2.rest.task.LauncherResource
 
modelAAEnabled - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
ModelBuilder<DATA,A extends Algorithm,Model extends ModelQueryResults> - Class in ambit2.rest.model.builder
Abstract class for model building
ModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String) - Constructor for class ambit2.rest.model.builder.ModelBuilder
 
ModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String[], String[], String) - Constructor for class ambit2.rest.model.builder.ModelBuilder
 
modelHidden - Variable in class ambit2.rest.model.builder.ExpertModelBuilder
 
modelHidden - Variable in class ambit2.rest.model.builder.SimpleModelBuilder
 
ModelParams - Class in ambit2.base.data.study
 
ModelParams() - Constructor for class ambit2.base.data.study.ModelParams
 
ModelParams(String) - Constructor for class ambit2.base.data.study.ModelParams
 
ModelPredictor<Predictor,NativeTypeItem> - Class in ambit2.rest.model.predictor
Abstract class for all predictive models TODO - refactor to avoid weka dependence! weka models should be subclassed
ModelPredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.ModelPredictor
 
ModelQueryResults - Class in ambit2.core.data.model
Training and test instances are available via IQueryRetrieval Content: base64 encoded string
ModelQueryResults() - Constructor for class ambit2.core.data.model.ModelQueryResults
 
ModelReader - Class in ambit2.groupcontribution.io
 
ModelReader() - Constructor for class ambit2.groupcontribution.io.ModelReader
 
modelReporter - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
ModelTemplates - Class in ambit2.db.search.property
 
ModelTemplates() - Constructor for class ambit2.db.search.property.ModelTemplates
 
ModelTemplates._ModelTemplates - Enum in ambit2.db.search.property
 
modelURI - Variable in class ambit2.rest.task.CallableDatasetCreator
 
ModelURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<ModelQueryResults>> - Class in ambit2.rest.model
 
ModelURIReporter(Request, ResourceDoc) - Constructor for class ambit2.rest.model.ModelURIReporter
 
ModelURIReporter(Request) - Constructor for class ambit2.rest.model.ModelURIReporter
 
ModelURIReporter() - Constructor for class ambit2.rest.model.ModelURIReporter
 
ModelValuesHistogram<T extends Comparable,U extends Bin> - Class in ambit2.similarity.stats
 
ModelValuesHistogram(String) - Constructor for class ambit2.similarity.stats.ModelValuesHistogram
 
ModelWrapper<T,TrainingInstances extends T,TestInstances extends T,Content,EVCONTENT> - Class in ambit2.core.data.model
Encapsulated a Model, defined by Template predictors, Template dependent variables and instances.
ModelWrapper() - Constructor for class ambit2.core.data.model.ModelWrapper
 
ModelWriter - Class in ambit2.groupcontribution.io
 
ModelWriter() - Constructor for class ambit2.groupcontribution.io.ModelWriter
 
mol - Variable in class ambit2.some.SOMEVisualizer
 
mol0 - Variable in class ambit2.tautomers.TautomerUtils.TautomerPair
 
mol1 - Variable in class ambit2.tautomers.TautomerUtils.TautomerPair
 
mol2record(Object[], String, Object) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
MolecularComplexity - Class in ambit2.reactions.rules.scores
 
MolecularComplexity() - Constructor for class ambit2.reactions.rules.scores.MolecularComplexity
 
molecularFilter - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
MolecularWeight - Class in ambit2.descriptors
Temporary copied from CDK in order to specify the Carbon 12 atomic mass with the right precision (see CDK bug ID ID: 2794591) IDescriptor based on the weight of atoms of a certain element type.
MolecularWeight() - Constructor for class ambit2.descriptors.MolecularWeight
Constructor for the WeightDescriptor object.
molecule - Variable in class ambit2.db.search.QueryInfo
 
molecule - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
molecule - Variable in class ambit2.jchempaint.editor.AbstractMoleculeAction
 
molecule - Variable in class ambit2.structure2name.IUPACNameGenerator
 
molecule - Variable in class ambit2.tautomers.RuleInstance
 
MoleculeAnalysis - Class in ambit2.structure2name.components
 
MoleculeAnalysis() - Constructor for class ambit2.structure2name.components.MoleculeAnalysis
 
moleculeComplexity - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScore
 
moleculeComplexityWeight - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
MoleculeEditAction - Class in ambit2.jchempaint.editor
Launches JChemPaint structure diagram editor for a preset molecule
MoleculeEditAction() - Constructor for class ambit2.jchempaint.editor.MoleculeEditAction
 
MoleculeEditAction(IAtomContainer) - Constructor for class ambit2.jchempaint.editor.MoleculeEditAction
 
MoleculeEditAction(IAtomContainer, String) - Constructor for class ambit2.jchempaint.editor.MoleculeEditAction
 
MoleculeEditAction(IAtomContainer, String, Icon) - Constructor for class ambit2.jchempaint.editor.MoleculeEditAction
 
MoleculeFilter - Class in ambit2.core.filter
 
MoleculeFilter() - Constructor for class ambit2.core.filter.MoleculeFilter
 
MoleculeInChIKeyProperty - Static variable in class ambit2.reactions.retrosynth.ReactionSequence
 
MoleculePairProcessor - Class in ambit2.core.processors.structure
Reads pair of structures
MoleculePairProcessor() - Constructor for class ambit2.core.processors.structure.MoleculePairProcessor
 
moleculeProperty - Static variable in class ambit2.descriptors.utils.RingInfo
 
MoleculeReader - Class in ambit2.core.processors.structure
 
MoleculeReader() - Constructor for class ambit2.core.processors.structure.MoleculeReader
 
MoleculeReader(boolean, boolean) - Constructor for class ambit2.core.processors.structure.MoleculeReader
 
molecules - Variable in class ambit2.core.processors.structure.MoleculePairProcessor
 
molecules - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
molecules - Variable in class ambit2.reactions.retrosynth.ReactionSequence.InchiEntry
 
molecules - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
moleculeSimilarity - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScore
 
moleculeSimilarityWeight - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
MoleculeStatusProperty - Static variable in class ambit2.reactions.retrosynth.ReactionSequence
 
MoleculeTools - Class in ambit2.core.data
Various structure processing.
MoleculeTools() - Constructor for class ambit2.core.data.MoleculeTools
 
moleculeToSMILES(IAtomContainer, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
MoleculeUtils - Class in ambit2.groupcontribution.utils
 
MoleculeUtils() - Constructor for class ambit2.groupcontribution.utils.MoleculeUtils
 
MoleculeWriter - Class in ambit2.core.processors.structure
 
MoleculeWriter() - Constructor for class ambit2.core.processors.structure.MoleculeWriter
 
MolFileFilter - Class in ambit2.base.io
 
MolFileFilter() - Constructor for class ambit2.base.io.MolFileFilter
 
MolFileFilter(String, String) - Constructor for class ambit2.base.io.MolFileFilter
 
molFilterString - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
molIdColIndex - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
molNotation - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
MOLONLY - Variable in class ambit2.db.reporters.SDFReporter
 
MolPropertiesIOSetting - Class in ambit2.core.io
An IOSetting descendant to provide means for transforming property names.
MolPropertiesIOSetting(String, IOSetting.Importance, String, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting
 
MolPropertiesIOSetting(ArrayList, IOSetting.Importance, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting
 
MolPropertiesIOSetting(Map, IOSetting.Importance, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting
 
molReader - Variable in class ambit2.core.io.RawIteratingCSVReader
 
molReader - Variable in class ambit2.core.processors.StructureNormalizer
 
molReader - Variable in class ambit2.db.processors.quality.FPStructureWriter
 
molReader - Variable in class ambit2.db.processors.quality.QualityLabelWriter
 
molReader - Variable in class ambit2.db.search.structure.QuerySimilarityStructure
 
molToSmiles(IAtomContainer) - Method in class ambit2.reactions.reactor.Reactor
 
MOLWEIGHT - Static variable in class ambit2.core.config.AmbitCONSTANTS
Molecular weight
MonomerGroup - Class in ambit2.core.groups
 
MonomerGroup(String, int) - Constructor for class ambit2.core.groups.MonomerGroup
 
Mopac7Reader - Class in ambit2.mopac
Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
parameters "NO.
Mopac7Reader(Reader) - Constructor for class ambit2.mopac.Mopac7Reader
Contructs a new Mopac7reader that can read Molecule from a given Reader.
Mopac7Reader(InputStream) - Constructor for class ambit2.mopac.Mopac7Reader
 
Mopac7Writer - Class in ambit2.mopac
Prepares input file for running MOPAC by AbstractMopacShell
Optimization is switched on if there are no coordinates.
Mopac7Writer(OutputStream) - Constructor for class ambit2.mopac.Mopac7Writer
 
Mopac7Writer(Writer) - Constructor for class ambit2.mopac.Mopac7Writer
 
mopac_commands - Variable in class ambit2.mopac.AbstractMopacShell
 
mopac_commands - Variable in class ambit2.mopac.Mopac7Writer
 
mopac_commands - Variable in class ambit2.rest.model.predictor.DescriptorPredictor
 
MOPAC_DIR - Static variable in class ambit2.base.config.Preferences
 
MOPAC_EXE - Static variable in class ambit2.base.config.Preferences
 
mopac_shell - Variable in class ambit2.mopac.DescriptorMopacShell
 
MopacOriginalStructure - Class in ambit2.mopac
Same as DescriptorMopacShell, but with default options to use the original structure and skip optimisation.
MopacOriginalStructure() - Constructor for class ambit2.mopac.MopacOriginalStructure
 
MopacShell - Class in ambit2.mopac
Runs MOPAC and smi2sdf + mengine as means to generate the starting 3D structure
MopacShell() - Constructor for class ambit2.mopac.MopacShell
 
mopacshell - Variable in class ambit2.rest.model.predictor.StructureProcessor
 
MopacShellBalloon - Class in ambit2.mopac
 
MopacShellBalloon() - Constructor for class ambit2.mopac.MopacShellBalloon
 
MopacShellBalloon(ShellBalloon) - Constructor for class ambit2.mopac.MopacShellBalloon
 
MopacShellOB - Class in ambit2.mopac
 
MopacShellOB() - Constructor for class ambit2.mopac.MopacShellOB
 
MopacShellOB(OpenBabelGen3D) - Constructor for class ambit2.mopac.MopacShellOB
 
MopacUtilities - Class in ambit2.mopac
Some utilities and helper functions for the work with MOPAC
MopacUtilities() - Constructor for class ambit2.mopac.MopacUtilities
 
moreHeaders - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
MostImportantDescriptors() - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
MostImportantDescriptors
MostImportantDescriptors() - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
MostImportantDescriptors
MouseInputHandler(EditableHeader) - Constructor for class ambit2.ui.EditableHeaderUI.MouseInputHandler
 
mousePressed(MouseEvent) - Method in class ambit2.ui.EditableHeaderUI.MouseInputHandler
 
mouseReleased(MouseEvent) - Method in class ambit2.ui.EditableHeaderUI.MouseInputHandler
 
move(int, int, int[]) - Static method in class ambit2.smarts.ChiralPermutations
 
move(TypedListModel<Property>, JList[], TypedListModel<Property>[]) - Method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
 
moveAll() - Method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
 
moveProperty(Property, ProcessorOntology.SIDE, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
moveTemplate(Dictionary, ProcessorOntology.SIDE, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
moveToCurrentRow() - Method in class ambit2.db.results.AmbitRows
 
moveToInsertRow() - Method in class ambit2.db.results.AmbitRows
 
MP_ATOM_TOP_DEGREES - Static variable in class ambit2.descriptors.utils.TopologicalUtilities
 
MRV_MULTICENTER - Static variable in class ambit2.core.groups.DataGroup
 
MSG_CANTCREATEFILE - Static variable in class ambit2.core.io.FileState
 
MSG_EMPTY - Static variable in class ambit2.db.update.dataset.UpdateDataset
 
MSG_EMPTYFILE - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_EMPTYFILE - Static variable in class ambit2.core.config.Resources
Empty file
MSG_ERRORONOPEN - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_ERRORONOPEN - Static variable in class ambit2.core.config.Resources
error on file open
MSG_ERRORONSAVE - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_ERRORONSAVE - Static variable in class ambit2.core.config.Resources
Error on file save
MSG_ERRORSAVE - Static variable in class ambit2.core.io.FileState
 
msg_exit - Static variable in class ambit2.core.config.Resources
Exit
MSG_FILEDONOTEXISTS - Static variable in class ambit2.core.io.FileState
 
msg_notallowed - Static variable in class ambit2.core.config.Resources
not allowed
MSG_NOTFOUND - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_OPEN - Static variable in class ambit2.core.io.FileState
 
MSG_OPENSUCCESS - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_OPENSUCCESS - Static variable in class ambit2.core.config.Resources
successful file open
MSG_SAVESUCCESS - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_SAVESUCCESS - Static variable in class ambit2.core.config.Resources
Successful file save
MSG_UNSUPPORTEDFORMAT - Static variable in exception ambit2.base.exceptions.AmbitIOException
 
MSG_UNSUPPORTEDFORMAT - Static variable in class ambit2.core.config.Resources
unsupported format
MSG_UNSUPPORTEDFORMAT - Static variable in class ambit2.core.io.FileState
 
mSTCO - Variable in class ambit2.smarts.SMIRKSReaction
 
mSupportDoubleBondAromaticityNotSpecified - Variable in class ambit2.smarts.SmartsParser
 
mSupportMOEExtension - Variable in class ambit2.smarts.SmartsParser
 
mSupportOpenBabelExtension - Variable in class ambit2.smarts.SmartsParser
 
mSupportOpenEyeExtension - Variable in class ambit2.smarts.SmartsParser
 
mSupportSingleBondAromaticityNotSpecified - Variable in class ambit2.smarts.SmartsParser
 
mSupportSmirksSyntax - Variable in class ambit2.smarts.SmartsParser
 
multicenter - Variable in class ambit2.core.groups.DataGroup
 
MultiFingerprintsWriter - Class in ambit2.core.io.fp
 
MultiFingerprintsWriter(File, List<IFingerprinter>, String[]) - Constructor for class ambit2.core.io.fp.MultiFingerprintsWriter
 
MultiNewlineFilterReader - Class in ambit2.core.io
 
MultiNewlineFilterReader(Reader) - Constructor for class ambit2.core.io.MultiNewlineFilterReader
 
MultipleGroup - Class in ambit2.core.groups
 
MultipleGroup(String, int) - Constructor for class ambit2.core.groups.MultipleGroup
 
multiplier - Variable in class ambit2.core.groups.MultipleGroup
 
multiplier - Variable in class ambit2.domain.stats.transforms.densityestimation.Kernel
 
Multiply(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.MathUtilities
 
MultiValue<V extends IValue> - Class in ambit2.base.data.study
 
MultiValue() - Constructor for class ambit2.base.data.study.MultiValue
 
MultiValue(V) - Constructor for class ambit2.base.data.study.MultiValue
 
mUseMOEvPrimitive - Variable in class ambit2.smarts.SmartsParser
 
MutableInt - Class in ambit2.similarity.stats
A mutable integer object.
MutableInt(int) - Constructor for class ambit2.similarity.stats.MutableInt
 
MyIOUtilities - Class in ambit2.base.io
This class is to simplify OpenFile / SaveFile dialogs calls
MyIOUtilities() - Constructor for class ambit2.base.io.MyIOUtilities
 
mysqlPassword() - Method in class ambit2.base.data.AmbitUser
 

N

n - Variable in class ambit2.rest.legacy.OTFibonacciSequence
Deprecated.
 
n_error - Static variable in class ambit2.db.processors.ValueWriter
 
n_idchemical - Static variable in class ambit2.db.processors.ValueWriter
 
n_idproperty - Static variable in class ambit2.db.processors.ValueWriter
 
n_idstructure - Static variable in class ambit2.db.processors.ValueWriter
 
n_text - Static variable in class ambit2.db.processors.ValueWriter
 
n_value - Static variable in class ambit2.db.processors.ValueWriter
 
n_value_num - Static variable in class ambit2.db.processors.ValueWriter
 
name - Variable in class ambit2.base.data.AmbitUser
 
name - Variable in class ambit2.base.data.Profile
 
name - Variable in class ambit2.base.data.Property
 
name - Variable in class ambit2.base.data.SourceDataset
 
name - Variable in class ambit2.base.data.StringBean
 
name - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
name - Variable in class ambit2.base.relation.AbstractRelation
 
name - Variable in class ambit2.core.data.model.Algorithm
 
name - Variable in class ambit2.core.data.model.ModelWrapper
 
name - Variable in class ambit2.core.data.model.Parameter
 
name - Variable in class ambit2.db.search.AbstractQuery
 
name - Variable in class ambit2.db.search.StoredQuery
 
name - Variable in class ambit2.db.SessionID
 
name - Variable in class ambit2.db.substance.study.facet.OwnerFacet
 
name - Variable in class ambit2.export.isa.v1_0.objects.ChemicalName
 
name - Variable in class ambit2.export.isa.v1_0.objects.Comment
 
name - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
name - Variable in class ambit2.export.isa.v1_0.objects.Data
 
name - Variable in class ambit2.export.isa.v1_0.objects.DataFile
 
name - Variable in class ambit2.export.isa.v1_0.objects.IntendedApplication
 
name - Variable in class ambit2.export.isa.v1_0.objects.Material
 
name - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
name - Variable in class ambit2.export.isa.v1_0.objects.McmType
 
name - Variable in class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
name - Variable in class ambit2.export.isa.v1_0.objects.Organization
 
name - Variable in class ambit2.export.isa.v1_0.objects.Process
 
name - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
name - Variable in class ambit2.export.isa.v1_0.objects.Sample
 
name - Variable in class ambit2.export.isa.v1_0.objects.Source
 
name - Variable in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
name - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
name - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
name - Variable in class ambit2.groupcontribution.nmr.Substituent
 
name - Variable in class ambit2.reactions.GenericReaction
 
name - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
name - Variable in class ambit2.reactions.Reaction
 
name - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
name - Variable in class ambit2.rest.task.Task
 
name - Variable in class ambit2.rest.task.TaskStorage
 
name - Variable in class ambit2.rest.wrapper.WrappedService
 
name - Variable in class ambit2.sln.SLNContainerAttributes
 
name - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
name - Variable in class ambit2.smarts.query.AbstractSmartsPattern
 
name - Variable in class ambit2.structure2name.rules.FunctionalGroupData
 
name - Variable in class ambit2.tautomers.Rule
 
name - Variable in class ambit2.ui.editors.AmbitUserEditor
 
name2smiles(String) - Method in class ambit2.namestructure.Name2StructureProcessor
 
name2structure(String) - Method in class ambit2.namestructure.Name2StructureProcessor
 
Name2StructureFinder - Class in ambit2.namestructure
 
Name2StructureFinder(Template, AbstractFinder.MODE) - Constructor for class ambit2.namestructure.Name2StructureFinder
 
Name2StructureProcessor - Class in ambit2.namestructure
Name to structure convertor, based on OPSIN package http://sourceforge.net/projects/oscar3-chem
Name2StructureProcessor() - Constructor for class ambit2.namestructure.Name2StructureProcessor
 
name_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
nameCondition - Variable in class ambit2.db.search.structure.QueryFieldAbstract
 
namedConfig - Variable in class ambit2.rest.DBConnection
 
NameKey - Class in ambit2.core.processors.structure.key
 
NameKey() - Constructor for class ambit2.core.processors.structure.key.NameKey
 
NameOnlyProperty - Class in ambit2.core.processors.structure.key
 
NameOnlyProperty(String) - Constructor for class ambit2.core.processors.structure.key.NameOnlyProperty
 
nameProperty - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
nameProperty - Static variable in class ambit2.core.io.I5ReaderSimple
 
nameProperty - Variable in class ambit2.core.io.RawIteratingFolderReader
 
Names - Static variable in class ambit2.base.data.Property
 
names - Static variable in class ambit2.base.data.SourceDataset
 
NAMES - Static variable in class ambit2.core.config.AmbitCONSTANTS
Chemical name
names - Variable in class ambit2.db.readers.ValuesByTemplateReader
 
names - Static variable in class ambit2.descriptors.AbstractKekulizationVerifier
 
names - Variable in class ambit2.descriptors.constitutional.DerivedMolecularWeightDescriptor
 
names - Variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
names - Static variable in class ambit2.descriptors.InChI
 
NAMESPACE - Static variable in class ambit2.rest.rdf.BibTex
The namespace of the vocabulary as a resource
NAMESPACE - Static variable in class ambit2.rest.rdf.OTA
The namespace of the vocabalary as a resource
NAMESPACE - Static variable in class ambit2.rest.rdf.OTEE
The namespace of the vocabalary as a resource
nameToStructure - Variable in class ambit2.namestructure.Name2StructureProcessor
 
NameUtils - Class in ambit2.structure2name.helpers
 
NameUtils() - Constructor for class ambit2.structure2name.helpers.NameUtils
 
NaN - Static variable in class ambit2.db.readers.RetrieveProfileValues
 
NaN - Static variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
nanomaterial - Variable in class ambit2.db.search.structure.AbstractStructureQuery
 
nci_url - Variable in class ambit2.pubchem.NCISearchProcessor
 
NCISearchProcessor - Class in ambit2.pubchem
The general format of the URLS are http://cactus.nci.nih.gov/chemical/structure/{identifier}/{method} Allowed identifier values are: SMILES, Std.
NCISearchProcessor() - Constructor for class ambit2.pubchem.NCISearchProcessor
 
NCISearchProcessor.METHODS - Enum in ambit2.pubchem
 
nClasses - Variable in class ambit2.smarts.EquivalenceTester
 
nColumns - Variable in class ambit2.groupcontribution.utils.math.MatrixDouble
 
NearestNeighborsSearch<T> - Class in ambit2.similarity.knn
Brute force implementation of nearest neighbors.
NearestNeighborsSearch() - Constructor for class ambit2.similarity.knn.NearestNeighborsSearch
 
NearestNeighborsSearch(IDistanceFunction<T>) - Constructor for class ambit2.similarity.knn.NearestNeighborsSearch
 
nearestNeighborsSearch - Variable in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
NearestNeighborsSimilarity<ID,Features> - Class in ambit2.similarity.knn
Calculates average distance to kNN nearest neighbors, as defined by IDistanceFunction.
NearestNeighborsSimilarity(IDistanceFunction<Features>, int) - Constructor for class ambit2.similarity.knn.NearestNeighborsSimilarity
 
needExplicitHData() - Method in class ambit2.smarts.SmartsParser
 
needJoin() - Method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
 
needNeighbourData() - Method in class ambit2.smarts.SmartsParser
 
needParentMoleculeData() - Method in class ambit2.smarts.SmartsParser
 
needRingData() - Method in class ambit2.smarts.SmartsParser
 
needRingData2() - Method in class ambit2.smarts.SmartsParser
 
needValencyData() - Method in class ambit2.smarts.SmartsParser
 
negate - Variable in class ambit2.smarts.query.AbstractSmartsPattern
 
nErrors - Variable in class ambit2.groupcontribution.dataset.DataSet
 
NestedFunctions - Class in ambit2.rules.functions
 
NestedFunctions() - Constructor for class ambit2.rules.functions.NestedFunctions
 
neutralise - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
NeutraliseProcessor - Class in ambit2.smarts.processors
Chemical structure neutralisation via set of predefined SMIRKS /smirks/smirks.json.
NeutraliseProcessor(Logger) - Constructor for class ambit2.smarts.processors.NeutraliseProcessor
 
neutraliser - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
newAtom(IChemObjectBuilder, IElement) - Static method in class ambit2.core.data.MoleculeTools
 
newAtom(IChemObjectBuilder, IAtom) - Static method in class ambit2.core.data.MoleculeTools
 
newAtom(IChemObjectBuilder, String) - Static method in class ambit2.core.data.MoleculeTools
 
newAtom(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newAtomContainer(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newAtomContainer(IChemObjectBuilder, IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
 
newAtomContainerSet(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newBond(IChemObjectBuilder, IAtom, IAtom, IBond.Order, IBond.Stereo) - Static method in class ambit2.core.data.MoleculeTools
 
newBond(IChemObjectBuilder, IAtom, IAtom, IBond.Order) - Static method in class ambit2.core.data.MoleculeTools
 
newBond(IChemObjectBuilder, IAtom, IAtom) - Static method in class ambit2.core.data.MoleculeTools
 
newBond(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newChemFile(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newChemModel(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newChemSequence(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newCompound(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
newCompound(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
newElement(IChemObjectBuilder, String) - Static method in class ambit2.core.data.MoleculeTools
 
newLonePair(IChemObjectBuilder, IAtom) - Static method in class ambit2.core.data.MoleculeTools
 
newModel - Variable in class ambit2.rest.model.task.CallableModelCreator
 
newMolecule(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newMoleculeSet(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newProperty(RDFNode) - Method in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
newProperty(RDFNode) - Method in class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
newProperty(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
newProperty(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
newProperty(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
newProperty(RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
newPseudoAtom(IChemObjectBuilder, String) - Static method in class ambit2.core.data.MoleculeTools
 
newRecord(String, Integer, String, String) - Method in class ambit2.core.io.ToXMLReaderSimple
 
newResource - Variable in class ambit2.rest.task.TaskResult
 
newRing(IChemObjectBuilder, int) - Static method in class ambit2.core.data.MoleculeTools
 
newRingSet(IChemObjectBuilder) - Static method in class ambit2.core.data.MoleculeTools
 
newRow(int, String, String, String, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
newSingleElectron(IChemObjectBuilder, IAtom) - Static method in class ambit2.core.data.MoleculeTools
 
next() - Method in class ambit2.chebi.ChEBIClient
 
next() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator
 
next() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
next() - Method in class ambit2.core.io.I5ReaderSimple
 
next() - Method in class ambit2.core.io.InteractiveIteratingMDLReader
 
next() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
next() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
next() - Method in class ambit2.core.io.IteratingFileReader
 
next() - Method in class ambit2.core.io.IteratingFolderReader
 
next() - Method in class ambit2.core.io.IteratingMolFolderReader
 
next() - Method in class ambit2.core.io.IteratingXLSReader
 
next() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
next() - Method in class ambit2.core.io.pdb.RawIteratingPDBReader
 
next() - Method in class ambit2.core.io.RawIteratingCSVReader
 
next() - Method in class ambit2.core.io.RawIteratingFolderReader
 
next() - Method in class ambit2.core.io.RawIteratingMOLReader
 
next() - Method in class ambit2.core.io.RawIteratingReader
 
next() - Method in class ambit2.core.io.RawIteratingSDFReader
 
next() - Method in class ambit2.core.io.RawIteratingWrapper
 
next() - Method in class ambit2.core.io.sj.MalariaHTSDataDelimitedReader
 
next() - Method in class ambit2.core.io.ToXMLReaderSimple
 
next() - Method in class ambit2.db.RepositoryReader
 
next() - Method in class ambit2.db.results.AmbitRows
 
next() - Method in class ambit2.db.results.RowsModel
 
next() - Method in class ambit2.groupcontribution.dataset.DataSetObjectIterator
 
next() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
next() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
next() - Method in interface ambit2.model.IDataset
 
next() - Method in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
next() - Method in class ambit2.rest.legacy.OTFibonacciSequence
Deprecated.
 
next() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
next() - Method in class ambit2.rest.rdf.RDFObjectIterator
Returns next object
next() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
next(boolean) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
next(boolean) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
next() - Method in class ambit2.rest.task.FilteredTasksIterator
 
next() - Method in class ambit2.rest.task.SingleTaskIterator
 
next() - Method in class ambit2.smarts.BinaryCombinations
 
next() - Method in class ambit2.ui.table.BrowsableTableModel
 
next() - Method in interface ambit2.ui.table.IRecordNavigator
 
next(ActionEvent) - Method in class ambit2.ui.WizardPanel
 
nextLayer(IAtomContainer) - Method in class ambit2.smarts.AtomEquivalenceInfo
 
nextLevel - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
nextPage() - Method in class ambit2.db.results.AmbitRows
 
nextPage() - Method in class ambit2.dbui.CachedRowSetTableModel
 
nextPage() - Method in class ambit2.ui.table.BrowsableTableModel
 
nextPage - Variable in class ambit2.ui.table.FindNavigator
 
nextPage() - Method in interface ambit2.ui.table.IPageNavigator
 
nextPage - Variable in class ambit2.ui.table.PageNavigator
 
nextPage - Variable in class ambit2.ui.table.RecordNavigator
 
nextProcess - Variable in class ambit2.export.isa.v1_0.objects.Process
 
nextRecord() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
nextRecord() - Method in class ambit2.core.io.I5ReaderSimple
 
nextRecord() - Method in interface ambit2.core.io.IRawReader
 
nextRecord() - Method in class ambit2.core.io.json.SubstanceStudyParser
 
nextRecord() - Method in class ambit2.core.io.pdb.RawIteratingPDBReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingCSVReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingFolderReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingMOLReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingSDFReader
 
nextRecord() - Method in class ambit2.core.io.RawIteratingWrapper
 
nextRecord() - Method in class ambit2.core.io.ToXMLReaderSimple
 
nextRecord() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
nextRecord - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
nextRecord() - Method in class ambit2.some.SOMERawReader
 
nextRecordNode - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
nextState() - Method in class ambit2.tautomers.CombinedRuleInstance
 
nextState() - Method in interface ambit2.tautomers.IRuleInstance
 
nextState() - Method in class ambit2.tautomers.RuleInstance
 
nf - Variable in class ambit2.mopac.Mopac7Writer
 
nf - Variable in class ambit2.ui.NumberCellRenderer
 
nKeys - Static variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
nKeys - Variable in class ambit2.smarts.SmartsScreeningKeys
 
nMobileGroups - Variable in class ambit2.tautomers.Rule
 
NNAtomEnvironmentSimilarity<ID> - Class in ambit2.similarity.knn
 
NNAtomEnvironmentSimilarity(IDistanceFunction<AtomEnvironmentList>, int) - Constructor for class ambit2.similarity.knn.NNAtomEnvironmentSimilarity
 
NNAtomEnvironmentSimilarity(int) - Constructor for class ambit2.similarity.knn.NNAtomEnvironmentSimilarity
 
NNAtomEnvironmentSimilarity() - Constructor for class ambit2.similarity.knn.NNAtomEnvironmentSimilarity
 
NNFingerprintSimilarity<ID> - Class in ambit2.similarity.knn
kNN similarity on bitsets BitSet
NNFingerprintSimilarity(IDistanceFunction<BitSet>, int) - Constructor for class ambit2.similarity.knn.NNFingerprintSimilarity
 
NNFingerprintSimilarity(int) - Constructor for class ambit2.similarity.knn.NNFingerprintSimilarity
Uses FingerprintDistance.
nodatalabel - Variable in class ambit2.ui.editors.EditorPanel
 
noDataText - Variable in class ambit2.ui.editors.EditorPanel
 
node - Variable in class ambit2.reactions.reactor.ReactorInfoPack
 
Node - Class in ambit2.smarts
 
Node() - Constructor for class ambit2.smarts.Node
 
NodeComponent - Class in ambit2.reactions.retrosynth
 
NodeComponent() - Constructor for class ambit2.reactions.retrosynth.NodeComponent
 
NodeComponent(IAtomContainer) - Constructor for class ambit2.reactions.retrosynth.NodeComponent
 
NodeExplorer - Class in ambit2.smarts
 
NodeExplorer() - Constructor for class ambit2.smarts.NodeExplorer
 
nodeHashCodes - Variable in class ambit2.reactions.reactor.Reactor
 
NodeLogingFrequency - Variable in class ambit2.reactions.reactor.ReactorStrategy
 
nodeNo - Variable in class ambit2.descriptors.PKANode
 
nodeYes - Variable in class ambit2.descriptors.PKANode
 
NoDocumentUUIDException - Exception in ambit2.base.exceptions
 
NoDocumentUUIDException(ProtocolApplication) - Constructor for exception ambit2.base.exceptions.NoDocumentUUIDException
 
noDuplicates - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
noDuplicates - Variable in class ambit2.descriptors.processors.AtomEnvironmentList
 
Nominal2SimilarityChartGenerator - Class in ambit2.db.chart
Interval chart - range of similarity per nominal property (e.g.
Nominal2SimilarityChartGenerator() - Constructor for class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
NonAdditivityAnalysis - Class in ambit2.reactions.mmp.analysis
 
NonAdditivityAnalysis() - Constructor for class ambit2.reactions.mmp.analysis.NonAdditivityAnalysis
 
NoneKey - Class in ambit2.core.processors.structure.key
 
NoneKey() - Constructor for class ambit2.core.processors.structure.key.NoneKey
 
norm() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
normalize() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensity1D
normalize()
normalizeKey(String) - Method in class ambit2.core.data.HashIntDescriptorResult
 
normalizer - Variable in class ambit2.db.processors.RepositoryWriter
 
normalizeValue() - Method in class ambit2.db.search.structure.QueryStructure
 
noStructure() - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
nRows - Variable in class ambit2.groupcontribution.utils.math.MatrixDouble
 
NS - Static variable in class ambit2.rest.rdf.BibTex
 
NS - Static variable in class ambit2.rest.rdf.OTA
 
NS - Static variable in class ambit2.rest.rdf.OTEE
 
nStates - Variable in class ambit2.tautomers.Rule
 
nullify(int[][]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
nullify(double[][]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
nullify(Protocol) - Static method in class ambit2.export.isa.v1_0.ObjectUtils
 
nullify(Source) - Static method in class ambit2.export.isa.v1_0.ObjectUtils
 
nullify(Sample) - Static method in class ambit2.export.isa.v1_0.ObjectUtils
 
nullify() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
nullify() - Method in class ambit2.structure2name.IUPACNameGenerator
 
nullifyAtoms(int) - Method in class ambit2.smarts.Node
 
nullifyRegion() - Method in class ambit2.tautomers.rules.TautomerRegion
 
num - Variable in class ambit2.rest.task.FilteredTasksIterator
 
numAllowedProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
number - Variable in class ambit2.core.groups.AbstractGroup
 
number - Variable in class ambit2.core.groups.MultipleGroup
 
number - Variable in class ambit2.structure2name.rules.CarbonData
 
NUMBER_PREFIX - Static variable in class ambit2.structure2name.helpers.NameUtils
 
NUMBER_PREFIX1_10 - Static variable in class ambit2.structure2name.helpers.NameUtils
 
NumberCellRenderer - Class in ambit2.ui
 
NumberCellRenderer() - Constructor for class ambit2.ui.NumberCellRenderer
 
numberOfHeaderLines - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
numberofHeaderLines - Variable in class ambit2.db.reporters.CSVReporter
 
numberOfStereoElements(IAtomContainer) - Static method in class ambit2.reactions.rules.scores.MolecularComplexity
 
numberOfTetrahedralStereoElements(IAtomContainer) - Static method in class ambit2.reactions.rules.scores.MolecularComplexity
 
NumberQuery<F> - Class in ambit2.db.search.structure
 
NumberQuery() - Constructor for class ambit2.db.search.structure.NumberQuery
 
numberToName(int) - Static method in class ambit2.structure2name.helpers.NameUtils
 
numberToSubstituentName(int) - Static method in class ambit2.structure2name.helpers.NameUtils
 
numCycles - Variable in class ambit2.groupcontribution.utils.math.CrossValidation
 
Numeric2SimilarityChartGenerator - Class in ambit2.db.chart
 
Numeric2SimilarityChartGenerator() - Constructor for class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
NumericADPredictor - Class in ambit2.rest.model.predictor
 
NumericADPredictor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.NumericADPredictor
 
numFailedNodes - Variable in class ambit2.reactions.reactor.ReactorResult
 
numFinilizedProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
numFolds - Variable in class ambit2.groupcontribution.utils.math.CrossValidation
 
numForbiddenProducts - Variable in class ambit2.reactions.reactor.ReactorNode
 
numFragments - Variable in class ambit2.sln.SLNParser
 
numFragments - Variable in class ambit2.smarts.SmartsParser
 
numHAtom - Variable in class ambit2.sln.SLNAtom
 
numOfGeneratedZwitterions - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
numOfProperties - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
numReactions - Variable in class ambit2.reactions.reactor.ReactorResult
 
numReactorNodes - Variable in class ambit2.reactions.reactor.ReactorResult
 
numSuccessNodes - Variable in class ambit2.reactions.reactor.ReactorResult
 

O

OBABEL_EXE - Static variable in class ambit2.core.smiles.OpenBabelAbstractShell
 
OBABEL_HOME - Static variable in class ambit2.core.smiles.OpenBabelAbstractShell
 
object - Variable in class ambit2.base.data.PropertyAnnotation
 
object - Variable in class ambit2.dbui.QueryInfoEditor
 
object - Variable in class ambit2.model.numeric.DataCoverage
 
object(Reference) - Static method in class ambit2.rest.legacy.OTObject
Deprecated.
 
object(String) - Static method in class ambit2.rest.legacy.OTObject
Deprecated.
 
object - Variable in class ambit2.similarity.measure.DistanceComparable
 
object - Variable in class ambit2.ui.editors.BeanEditor
 
objectFieldName - Variable in class ambit2.reactions.rules.GenericRuleMetaInfo
 
objectToJsonField(Object) - Static method in class ambit2.rules.json.JSONParsingUtils
 
objectToParse - Variable in class ambit2.rest.RDFBatchParser
 
ObjectUtils - Class in ambit2.export.isa.v1_0
 
ObjectUtils() - Constructor for class ambit2.export.isa.v1_0.ObjectUtils
 
obo_uri - Static variable in class ambit2.rest.substance.SubstanceRecordStaxWriter
 
observed - Variable in class ambit2.model.dataset.DoubleArrayDataset
 
observed - Variable in class ambit2.similarity.stats.ConfusionMatrix
 
observed - Variable in class ambit2.similarity.stats.ValuePair
 
oddColor - Variable in class ambit2.ui.ColorTableCellRenderer
 
Odor - Static variable in class ambit2.base.ro.I5CONSTANTS
 
offset - Variable in class ambit2.core.io.FileState
 
offset - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
offset - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
OK - Static variable in class ambit2.descriptors.AbstractKekulizationVerifier
 
OK - Static variable in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
okAction() - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
onduplicate_number - Static variable in class ambit2.db.processors.ValueWriter
 
onduplicate_string - Static variable in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
onError(ItemInput, Object, Result, Exception) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
onItemProcessed(ItemInput, Object, Result) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
onItemRead(ItemInput, Result) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
onStopEvent() - Method in class ambit2.core.io.SimpleIOListener
 
ontolink2id(String) - Static method in class ambit2.base.ro.AbstractAnnotator
 
ontology_service - Variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.ChemicalName
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.DataFile
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.IntendedApplication
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.McmType
 
OntologyAnnotation - Class in ambit2.export.isa.v1_0.objects
ISA ontology reference schema JSON-schema representing an ontology reference or annotation in the ISA model (for fields that are required to be ontology annotations)
OntologyAnnotation() - Constructor for class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
ontologyAnnotation - Variable in class ambit2.export.isa.v1_0.objects.TechnologyType
 
OntologyEditor - Class in ambit2.dbui.dictionary
 
OntologyEditor() - Constructor for class ambit2.dbui.dictionary.OntologyEditor
 
OntologyManager1_0 - Class in ambit2.export.isa.v1_0
 
OntologyManager1_0() - Constructor for class ambit2.export.isa.v1_0.OntologyManager1_0
 
OntologySourceReference - Class in ambit2.export.isa.v1_0.objects
ISA ontology source reference schema JSON-schema representing an ontology reference in the ISA model
OntologySourceReference() - Constructor for class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
ontologySourceReferences - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
open() - Method in class ambit2.base.external.CommandShell
 
open() - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
open() - Method in class ambit2.core.processors.AbstractStructureProcessor
 
open() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
open() - Method in class ambit2.db.AbstractRepositoryAccess
 
open() - Method in class ambit2.db.chart.BarChartGenerator
 
open() - Method in class ambit2.db.chart.FingerprintHistogramDataset
 
open() - Method in class ambit2.db.chart.FuncGroupsChartGenerator
 
open() - Method in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
open() - Method in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
open() - Method in class ambit2.db.chart.PieChartGenerator
 
open() - Method in class ambit2.db.chart.PropertiesChartGenerator
 
open() - Method in class ambit2.db.chart.XTabChartGenerator
 
open() - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
open() - Method in class ambit2.db.processors.ConnectionStatusProcessor
 
open() - Method in class ambit2.db.processors.DBProcessorsChain
 
open() - Method in class ambit2.db.processors.DbStructureWriter
 
open() - Method in class ambit2.db.processors.DescriptorsCalculator
 
open() - Method in class ambit2.db.processors.processorCloseSession
 
open() - Method in class ambit2.db.processors.ProcessorCreateProfileQuery
 
open() - Method in class ambit2.db.processors.ProcessorCreateQuery
 
open() - Method in class ambit2.db.processors.ProcessorCreateSession
 
open() - Method in class ambit2.db.processors.ProcessorOntology
 
open() - Method in class ambit2.db.processors.ProcessorSetQueryScope
 
open() - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
open() - Method in class ambit2.db.processors.PropertyImporter
 
open() - Method in class ambit2.db.processors.QueryInfo2Query
 
open() - Method in class ambit2.db.processors.RepositoryWriter
 
open() - Method in class ambit2.db.readers.ValuesByTemplateReader
 
open() - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
open() - Method in class ambit2.db.reporters.ARFF3ColReporter
 
open() - Method in class ambit2.db.reporters.ARFFReporter
 
open() - Method in class ambit2.db.reporters.CMLReporter
 
open() - Method in class ambit2.db.reporters.CSVReporter
 
open() - Method in class ambit2.db.reporters.ImageAreaReporter
 
open() - Method in class ambit2.db.reporters.ImageReporter
 
open() - Method in class ambit2.db.reporters.PDFReporter
 
open() - Method in class ambit2.db.reporters.QueryPacketReporter
 
open() - Method in class ambit2.db.reporters.QueryProperyReporter
 
open() - Method in class ambit2.db.reporters.RTFReporter
 
open() - Method in class ambit2.db.reporters.SDFReporter
 
open() - Method in class ambit2.db.reporters.SmilesReporter
 
open() - Method in class ambit2.db.RepositoryReader
 
open() - Method in class ambit2.db.results.AmbitRows
 
open() - Method in class ambit2.db.search.QueryExecutor
 
open() - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
open() - Method in class ambit2.db.StatementExecutor
 
open() - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
open() - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
open() - Method in class ambit2.dbui.dictionary.OntologyEditor
 
open() - Method in class ambit2.dbui.ProfileEditor
 
open() - Method in class ambit2.dbui.QueryChemicalEditor
 
open() - Method in class ambit2.dbui.QueryCombinedEditor
 
open() - Method in class ambit2.dbui.QueryDatasetEditor
 
open() - Method in class ambit2.dbui.QueryFieldEditor
 
open() - Method in class ambit2.dbui.QueryFieldNumericEditor
 
open() - Method in class ambit2.dbui.QueryFunctionalGroupsEditor
 
open() - Method in class ambit2.dbui.QueryScopeEditor
 
open() - Method in class ambit2.dbui.QuerySimilarityEditor
 
open() - Method in class ambit2.dbui.QuerySmartsEditor
 
open() - Method in class ambit2.dbui.QueryStoredResultsEditor
 
open() - Method in class ambit2.dbui.QueryStructureByQualityEditor
 
open() - Method in class ambit2.dbui.QueryStructureByValueQualityEditor
 
open() - Method in class ambit2.descriptors.FunctionalGroup
 
open() - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
open() - Method in interface ambit2.ml.io.IMLOutput
 
open() - Method in class ambit2.ml.io.OutputARFF
 
open() - Method in class ambit2.ml.io.OutputVW
 
open() - Method in class ambit2.ml.io.OutputVW_LDA
 
open() - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
open() - Method in class ambit2.rest.dataset.DatasetURIReporter
 
open() - Method in class ambit2.rest.dataset.RDFFileWriter
 
open() - Method in class ambit2.rest.model.ModelURIReporter
 
open() - Method in class ambit2.rest.model.predictor.ExternalModel
 
open() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
open() - Method in class ambit2.rest.structure.CompoundURIReporter
 
open() - Method in class ambit2.some.SOMEVisualizer
 
OPENBABEL_LINUX - Static variable in class ambit2.base.config.Preferences
 
OPENBABEL_WIN - Static variable in class ambit2.base.config.Preferences
 
OpenBabelAbstractShell<X> - Class in ambit2.core.smiles
 
OpenBabelAbstractShell() - Constructor for class ambit2.core.smiles.OpenBabelAbstractShell
 
OpenBabelDepiction - Class in ambit2.core.smiles
 
OpenBabelDepiction() - Constructor for class ambit2.core.smiles.OpenBabelDepiction
 
OpenBabelGen3D - Class in ambit2.core.smiles
 
OpenBabelGen3D() - Constructor for class ambit2.core.smiles.OpenBabelGen3D
 
OpenBabelShell - Class in ambit2.core.smiles
 
OpenBabelShell() - Constructor for class ambit2.core.smiles.OpenBabelShell
 
openBracket - Static variable in class ambit2.core.filter.MoleculeFilter
 
openBufferedReader(String, BufferedReader) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
openBufferedReader(String, String, BufferedReader, Hashtable) - Method in class ambit2.ui.jmol.CdkJmolAdapter
 
openFile(Frame, String, String[], String[]) - Static method in class ambit2.base.io.MyIOUtilities
 
OpenSSOServicesConfig - Class in ambit2.rest.aa.opensso
Configuration for OpenSSO authn, authz and policy services
OpenSSOServicesConfig.CONFIG - Enum in ambit2.rest.aa.opensso
 
OpenTox - Class in ambit2.rest
 
OpenTox.params - Enum in ambit2.rest
 
OpenTox.URI - Enum in ambit2.rest
 
OPENTOX_AA_ENABLED - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
opentox_CAS - Static variable in class ambit2.base.data.Property
 
opentox_ChEBI - Static variable in class ambit2.base.data.Property
 
opentox_ChEMBL - Static variable in class ambit2.base.data.Property
 
opentox_ChemSpider - Static variable in class ambit2.base.data.Property
 
opentox_CMS - Static variable in class ambit2.base.data.Property
 
opentox_ConfidenceFeature - Static variable in class ambit2.base.data.Property
 
opentox_DrugBank - Static variable in class ambit2.base.data.Property
 
opentox_EC - Static variable in class ambit2.base.data.Property
 
opentox_InChI - Static variable in class ambit2.base.data.Property
 
opentox_InChI_std - Static variable in class ambit2.base.data.Property
 
opentox_InChIAuxInfo - Static variable in class ambit2.base.data.Property
 
opentox_InChIAuxInfo_std - Static variable in class ambit2.base.data.Property
 
opentox_InChIKey - Static variable in class ambit2.base.data.Property
 
opentox_InChIKey_std - Static variable in class ambit2.base.data.Property
 
opentox_IUCLID5_UUID - Static variable in class ambit2.base.data.Property
 
opentox_IupacName - Static variable in class ambit2.base.data.Property
 
opentox_KEGG - Static variable in class ambit2.base.data.Property
 
opentox_LS - Static variable in class ambit2.base.data.Property
 
opentox_Name - Static variable in class ambit2.base.data.Property
 
opentox_Pubchem - Static variable in class ambit2.base.data.Property
 
opentox_REACHDATE - Static variable in class ambit2.base.data.Property
 
opentox_SigmaAldrich - Static variable in class ambit2.base.data.Property
 
opentox_SMILES - Static variable in class ambit2.base.data.Property
 
opentox_SubstanceDataSource - Static variable in class ambit2.base.data.Property
 
opentox_ToxbankWiki - Static variable in class ambit2.base.data.Property
 
opentox_TradeName - Static variable in class ambit2.base.data.Property
 
opentox_TupleFeature - Static variable in class ambit2.base.data.Property
 
OpenToxRequest - Class in ambit2.search.opentox
 
OpenToxRequest(String) - Constructor for class ambit2.search.opentox.OpenToxRequest
 
opentoxservice - Variable in class ambit2.search.opentox.OpenToxRequest
 
operation - Variable in class ambit2.db.processors.AbstractRepositoryWriter
 
operation - Variable in class ambit2.db.processors.ProcessorOntology
 
operation - Variable in class ambit2.pubchem.rest.PUGRestRequest
 
opsin2cdk(OpsinResult) - Method in class ambit2.namestructure.Name2StructureProcessor
 
opsin2cml(OpsinResult, OutputStream) - Method in class ambit2.namestructure.Name2StructureProcessor
 
optimize - Variable in class ambit2.mopac.AbstractMopacShell
 
optimize - Variable in class ambit2.mopac.Mopac7Writer
 
option - Variable in class ambit2.pubchem.NCISearchProcessor
 
optionalInChIHeader - Variable in class ambit2.core.io.FileInputState
 
optionalInChIHeader - Variable in class ambit2.core.io.RawIteratingCSVReader
 
optionalInChIKeyHeader - Variable in class ambit2.core.io.FileInputState
 
optionalInChIKeyHeader - Variable in class ambit2.core.io.RawIteratingCSVReader
 
optionalSMILESHeader - Variable in class ambit2.core.io.FileInputState
 
optionalSMILESHeader - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
optionalSMILESHeader - Variable in class ambit2.core.io.RawIteratingCSVReader
 
options - Variable in class ambit2.base.data.SelectionBean
 
options - Variable in class ambit2.core.io.ZipReader
 
options - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
order - Variable in class ambit2.base.data.Property
 
order - Variable in class ambit2.core.groups.ComponentGroup
 
order - Variable in class ambit2.db.results.StoredQueryTableModel
 
order - Variable in class ambit2.db.search.structure.QuerySimilarityBitset
 
order - Variable in class ambit2.db.update.fp.QueryFingerprints
 
order - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
order_descendant - Variable in class ambit2.db.search.structure.AbstractStructureQuery
 
Organ - Static variable in class ambit2.base.ro.I5CONSTANTS
 
Organization - Class in ambit2.export.isa.v1_0.objects
ISA organization schema JSON-schema representing an organization in the ISA model v1.0
Organization() - Constructor for class ambit2.export.isa.v1_0.objects.Organization
 
originalMolecule - Variable in class ambit2.structure2name.IUPACNameGenerator
 
OriginalRuleString - Variable in class ambit2.tautomers.Rule
 
OriginFilter - Class in ambit2.rest
CORS
OriginFilter(Context, String) - Constructor for class ambit2.rest.OriginFilter
 
OriginFilter(Context, List<String>) - Constructor for class ambit2.rest.OriginFilter
 
OrthogonalTransform - Class in ambit2.domain.stats.transforms.transformfilters
Principal Component Analysis
OrthogonalTransform() - Constructor for class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
os_FreeBSD - Static variable in class ambit2.base.external.CommandShell
 
os_LINUX - Static variable in class ambit2.base.external.CommandShell
 
os_LINUX64 - Static variable in class ambit2.base.external.CommandShell
 
os_MAC - Static variable in class ambit2.base.external.CommandShell
 
os_WINDOWS - Static variable in class ambit2.base.external.CommandShell
 
os_WINDOWS7 - Static variable in class ambit2.base.external.CommandShell
 
os_WINDOWSVISTA - Static variable in class ambit2.base.external.CommandShell
 
ot - Static variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
OTA - Class in ambit2.rest.rdf
OpenTox algorithm types ontology http://www.opentox.org/algorithmTypes#
OTA() - Constructor for class ambit2.rest.rdf.OTA
 
OTA.OTAClass - Enum in ambit2.rest.rdf
 
OTA.OTAProperty - Enum in ambit2.rest.rdf
 
OTAlgorithm - Class in ambit2.rest.legacy
Deprecated.
OTAlgorithm(String, String) - Constructor for class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
OTAlgorithms - Class in ambit2.rest.legacy
Deprecated.
OTAlgorithms(String, String) - Constructor for class ambit2.rest.legacy.OTAlgorithms
Deprecated.
 
OTCompound - Class in ambit2.rest.legacy
Deprecated.
OTCompound(Reference) - Constructor for class ambit2.rest.legacy.OTCompound
Deprecated.
 
OTCompound(String) - Constructor for class ambit2.rest.legacy.OTCompound
Deprecated.
 
OTCompound._titles - Enum in ambit2.rest.legacy
Deprecated.
 
OTContainers<T extends IOTObject> - Class in ambit2.rest.legacy
Deprecated.
OTContainers(String, String) - Constructor for class ambit2.rest.legacy.OTContainers
Deprecated.
 
OTDataset - Class in ambit2.rest.legacy
Deprecated.
OTDataset(Reference) - Constructor for class ambit2.rest.legacy.OTDataset
Deprecated.
 
OTDataset(String) - Constructor for class ambit2.rest.legacy.OTDataset
Deprecated.
 
OTDataset.dataset_size - Enum in ambit2.rest.legacy
Deprecated.
 
OTDatasetComparisonReport - Class in ambit2.rest.task.dsl
 
OTDatasetComparisonReport(Reference, OTDataset) - Constructor for class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
OTDatasetRDFReport - Class in ambit2.rest.task.dsl
 
OTDatasetRDFReport(Reference) - Constructor for class ambit2.rest.task.dsl.OTDatasetRDFReport
 
OTDatasetRDFReport(OTDataset, boolean, OTFeatures, boolean, OTFeatures, String, int, int, String) - Constructor for class ambit2.rest.task.dsl.OTDatasetRDFReport
 
OTDatasetReport - Class in ambit2.rest.task.dsl
 
OTDatasetReport(Reference) - Constructor for class ambit2.rest.task.dsl.OTDatasetReport
 
OTDatasetReport(OTDataset, OTFeatures, String, int, int, String) - Constructor for class ambit2.rest.task.dsl.OTDatasetReport
 
OTDatasets - Class in ambit2.rest.legacy
Deprecated.
OTDatasets(String, String) - Constructor for class ambit2.rest.legacy.OTDatasets
Deprecated.
 
OTDatasetScrollableReport - Class in ambit2.rest.task.dsl
 
OTDatasetScrollableReport(OTDataset, OTFeatures, String, int, int) - Constructor for class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
OTDatasetTableReport - Class in ambit2.rest.task.dsl
 
OTDatasetTableReport(OTDataset, OTFeatures, String, int, int) - Constructor for class ambit2.rest.task.dsl.OTDatasetTableReport
 
OTEE - Class in ambit2.rest.rdf
Echa endpoints ontology
OTEE() - Constructor for class ambit2.rest.rdf.OTEE
 
OTEE.OTAProperty - Enum in ambit2.rest.rdf
 
OTEE.OTEEClass - Enum in ambit2.rest.rdf
 
OTFeature - Class in ambit2.rest.legacy
Deprecated.
OTFeature(String, String) - Constructor for class ambit2.rest.legacy.OTFeature
Deprecated.
 
OTFeatures - Class in ambit2.rest.legacy
Deprecated.
OTFeatures(String, String) - Constructor for class ambit2.rest.legacy.OTFeatures
Deprecated.
 
OTFibonacciSequence - Class in ambit2.rest.legacy
Deprecated.
OTFibonacciSequence() - Constructor for class ambit2.rest.legacy.OTFibonacciSequence
Deprecated.
 
otherMaterials - Variable in class ambit2.export.isa.v1_0.objects.Materials
 
otherMaterials - Variable in class ambit2.export.isa.v1_0.objects.Materials_
 
OTModel - Class in ambit2.rest.legacy
Deprecated.
OTModel(String, String) - Constructor for class ambit2.rest.legacy.OTModel
Deprecated.
 
OTObject - Class in ambit2.rest.legacy
Deprecated.
OTObject(Reference) - Constructor for class ambit2.rest.legacy.OTObject
Deprecated.
 
OTObject(String) - Constructor for class ambit2.rest.legacy.OTObject
Deprecated.
 
OTObject() - Constructor for class ambit2.rest.legacy.OTObject
Deprecated.
 
OTOntologyService<Z> - Class in ambit2.rest.legacy
Deprecated.
OTOntologyService(Reference) - Constructor for class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
OTOntologyService(String) - Constructor for class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
OTProcessingContainers<T extends OTProcessingResource> - Class in ambit2.rest.legacy
Deprecated.
OTProcessingContainers(String, String) - Constructor for class ambit2.rest.legacy.OTProcessingContainers
Deprecated.
 
OTProcessingResource - Class in ambit2.rest.legacy
Deprecated.
OTProcessingResource(String, String) - Constructor for class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
OTProcessingResource() - Constructor for class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
OTRemoteTask - Class in ambit2.rest.legacy
Deprecated.
OTRemoteTask(Reference, MediaType, Representation, Method) - Constructor for class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
OTRemoteTaskPool - Class in ambit2.rest.legacy
Deprecated.
OTRemoteTaskPool() - Constructor for class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
OTSuperModel - Class in ambit2.rest.legacy
Deprecated.
OTSuperModel(String, String) - Constructor for class ambit2.rest.legacy.OTSuperModel
Deprecated.
 
out - Variable in class ambit2.core.io.XLSFileWriter
 
out - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
out - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
outFile - Variable in class ambit2.dragon.DragonShell
 
outFile - Variable in class ambit2.some.SOMEShell
 
outFile - Variable in class ambit2.vega.VegaShell
 
outFilePath - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
outFilePrefix - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
outFiles - Variable in class ambit2.mopac.AbstractMopacShell
 
outFiles - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
outFileType - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
output - Variable in class ambit2.base.processors.batch.BatchReporter
 
output - Variable in class ambit2.core.processors.ProcessorFileExport
 
output - Variable in class ambit2.pubchem.rest.PUGRestRequest
 
output - Variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
OutputARFF - Class in ambit2.ml.io
 
OutputARFF(String, String, boolean) - Constructor for class ambit2.ml.io.OutputARFF
 
outputDir - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
outputFile - Variable in class ambit2.base.external.CommandShell
 
outputFileName - Variable in class ambit2.core.smiles.OpenBabelDepiction
 
outputFileName - Variable in class ambit2.groupcontribution.cli.GCMPredictCli
 
outputFileName - Variable in class ambit2.groupcontribution.cli.HNMRPredictCli
 
outputFileName - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
outputGCMFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
outputs - Variable in class ambit2.export.isa.v1_0.objects.Process
 
outputTautomerPair(TautomerUtils.TautomerPair) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
OutputVW - Class in ambit2.ml.io
 
OutputVW(String, String, boolean) - Constructor for class ambit2.ml.io.OutputVW
 
OutputVW_LDA - Class in ambit2.ml.io
 
OutputVW_LDA(String, String, boolean) - Constructor for class ambit2.ml.io.OutputVW_LDA
 
outWriters - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
OverallDegreeOfClustering(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
overlaps(RuleInstance, RuleInstance) - Static method in class ambit2.tautomers.RuleManager
 
overlaps(RuleInstance, List<IRuleInstance>) - Static method in class ambit2.tautomers.RuleManager
 
OVERLAY_ROW_AND_COLUMN - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage
 
owl - Static variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
OWNER_name - Static variable in class ambit2.base.data.LiteratureEntry
 
OwnerFacet - Class in ambit2.db.substance.study.facet
 
OwnerFacet() - Constructor for class ambit2.db.substance.study.facet.OwnerFacet
 
ownerName - Variable in class ambit2.base.data.SubstanceRecord
 
OwnerSubstanceStats - Class in ambit2.db.substance.study.facet
 
OwnerSubstanceStats(String) - Constructor for class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
ownerUUID - Variable in class ambit2.base.data.SubstanceRecord
 

P

p_model - Variable in class ambit2.model.AbstractModel
 
p_stats - Variable in class ambit2.model.AbstractModel
 
p_title - Static variable in class ambit2.base.data.LiteratureEntry
 
p_url - Static variable in class ambit2.base.data.LiteratureEntry
 
page - Variable in class ambit2.db.search.AbstractQuery
 
page - Variable in class ambit2.db.search.structure.QueryCombinedStructure
 
page - Variable in class ambit2.dbui.CachedRowSetTableModel
 
page - Variable in class ambit2.rest.SimpleTaskResource
 
page - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
page - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
page - Variable in class ambit2.ui.table.BrowsableTableModel
 
paged_limit - Variable in class ambit2.db.search.QueryExecutor
 
pageNavigator() - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
pageNavigator() - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
PageNavigator - Class in ambit2.ui.table
 
PageNavigator(IPageNavigator) - Constructor for class ambit2.ui.table.PageNavigator
 
pageSize - Variable in class ambit2.db.search.structure.QueryMissingProperty
SELECT structure.idchemical,s.idstructure,type_structure,p1.status,p2.status FROM structure join struc_dataset s using(idstructure) left outer join property_values p1 on s.idstructure=p1.idstructure and p1.idproperty =36 and id_srcdataset=1 left outer join property_values p2 on s.idstructure=p2.idstructure and p2.idproperty =37 and id_srcdataset=1 where type_structure != "NA" and p2.id is null and p1.id is null
pageSize - Variable in class ambit2.rest.SimpleTaskResource
 
pageSize - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
pageSize - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
pageSize - Variable in class ambit2.ui.table.BrowsableTableModel
 
pageSize - Variable in class ambit2.ui.table.PageNavigator
 
paint(IRenderer, IAtomContainerSet, boolean, Graphics2D, IAtomContainerHighlights, boolean) - Method in class ambit2.rendering.CompoundImageTools
 
paint(IRenderer, IAtomContainerSet, boolean, Graphics2D, IAtomContainerHighlights, Dimension, boolean) - Method in class ambit2.rendering.CompoundImageTools
TODO sort molecules, in order to display the largest part first
paint(Graphics) - Method in class ambit2.ui.jmol.ImageTools3D
 
paint(Graphics) - Method in class ambit2.ui.jmol.Panel3D
 
paint(Graphics) - Method in class ambit2.ui.Panel2D
 
paintBorderShadow(Graphics2D, Color, Color, int, Shape) - Static method in class ambit2.ui.Utils
TODO resolve Duplicate with CompoundImageTools method
painter3D - Variable in class ambit2.ui.jmol.Panel3D
 
PairPropertiesWriter - Class in ambit2.db.search.structure.pairwise
 
PairPropertiesWriter() - Constructor for class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
pairSQL - Static variable in class ambit2.db.search.property.FreeTextPropertyQuery
 
pairSQL - Static variable in class ambit2.db.search.structure.FreeTextQuery
 
PairwiseSimilarity - Static variable in class ambit2.core.config.AmbitCONSTANTS
Pairwise similarity
panel - Variable in class ambit2.dbui.ProfileEditor
 
panel - Variable in class ambit2.ui.editors.TemplateEditor
 
panel2d - Variable in class ambit2.dbui.QueryInfoEditor
 
Panel2D<A extends IMoleculeEditAction> - Class in ambit2.ui
2D structure diagram
Panel2D() - Constructor for class ambit2.ui.Panel2D
 
Panel2D._atomrendermode - Enum in ambit2.ui
 
Panel2D.property_name - Enum in ambit2.ui
 
Panel3D - Class in ambit2.ui.jmol
Makes use of JmolViewer to display 3D molecule.
Panel3D() - Constructor for class ambit2.ui.jmol.Panel3D
 
papp - Variable in exception ambit2.base.exceptions.NoDocumentUUIDException
 
paQuery - Variable in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
param - Variable in class ambit2.db.chart.ChartGenerator
 
param - Variable in class ambit2.sln.SLNExpressionToken
 
param - Variable in class ambit2.sln.SLNParserError
 
param - Variable in class ambit2.smarts.SmartsExpressionToken
 
param - Variable in class ambit2.smarts.SmartsParserError
 
Parameter<T> - Class in ambit2.core.data.model
 
Parameter(String, T) - Constructor for class ambit2.core.data.model.Parameter
 
Parameter.ParameterScope - Enum in ambit2.core.data.model
 
parameterName - Variable in class ambit2.export.isa.v1_0.objects.ProtocolParameter
 
parameters - Variable in class ambit2.base.data.study.ProtocolApplication
 
parameters - Variable in class ambit2.core.data.model.Algorithm
 
parameters - Variable in class ambit2.core.data.model.ModelWrapper
 
parameters - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
parameters - Variable in class ambit2.model.AbstractModel
 
parameters - Variable in class ambit2.model.builder.AbstractModelBuilder
 
parameters - Static variable in class ambit2.mopac.Mopac7Reader
 
parameters - Variable in class ambit2.rest.model.builder.SimpleModelBuilder
 
parameterValues - Variable in class ambit2.export.isa.v1_0.objects.Process
 
paramHeaders - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
paramNames - Variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
Params<VALUE> - Class in ambit2.base.data.study
 
Params() - Constructor for class ambit2.base.data.study.Params
 
Params(VALUE) - Constructor for class ambit2.base.data.study.Params
 
Params(String, VALUE) - Constructor for class ambit2.base.data.study.Params
 
params - Variable in class ambit2.mopac.DescriptorMopacShell
 
params - Variable in class ambit2.reactions.retrosynth.IReactionSequenceHandler.RSEvent
 
params - Variable in class ambit2.rules.functions.LinearFunction
 
params - Variable in class ambit2.rules.functions.ValueTransformation
 
paramSplitter - Variable in class ambit2.groupcontribution.transformations.TransformationUtils
 
parent - Variable in class ambit2.descriptors.PKANode
 
parent - Variable in class ambit2.smarts.AtomSmartsNode
 
parentAtoms - Variable in class ambit2.core.groups.MultipleGroup
 
parentBonds - Variable in class ambit2.core.groups.MultipleGroup
 
parentComponent - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
parentID - Variable in class ambit2.tautomers.TautomerIncrementStep
 
parentNode - Variable in class ambit2.reactions.reactor.ReactorNode
 
parents - Variable in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
parentTag - Variable in class ambit2.core.io.I5ReaderSimple
 
parse(String) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
parse(Document) - Method in class ambit2.pubchem.EntrezESearchParser
 
parse(QuerySolution, PROPERTY) - Method in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
parse(QuerySolution, COMPOUND) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
parse(QuerySolution, PROPERTY) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
parse(QuerySolution, Item) - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
parse(String) - Method in class ambit2.sln.SLNParser
 
parse(String) - Method in class ambit2.smarts.SmartsParser
 
parse(String) - Method in class ambit2.smarts.SMIRKSManager
 
parse(String) - Method in class ambit2.tautomers.RuleParser
 
parseAP_RecursiveSmarts() - Method in class ambit2.smarts.SmartsParser
 
parseAtomCondition(JsonNode) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
parseByPosition(String, int[]) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
parseCompany(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseComponent(String, String, SmartsFlags, List<IQueryAtomContainer>, List<Integer>) - Method in class ambit2.smarts.SMIRKSManager
 
parseComposition(JsonNode) - Method in class ambit2.core.io.json.SubstanceStudyParser
TODO
parseConditionExpression(String) - Static method in class ambit2.rules.conditions.parser.ConditionParsingUtils
 
parseConditions(ObjectMapper, Object) - Static method in class ambit2.core.io.json.SubstanceStudyParser
 
parseDecriptor(String) - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
parseDocument() - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
parseDocument() - Method in class ambit2.core.io.I5ReaderSimple
 
parseEffects(ArrayNode, Protocol) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseElement(ISALocation, String) - Static method in class ambit2.export.isa.base.ISALocation
 
parseEnergyCorrection(JsonNode) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
parseEnergyRule(JsonNode) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
parseFeatures() - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
parseFeatureURI(String, Feature) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
parseFeatureURI(String, Attribute) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
parseFeatureURI(String, Property) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
parseFeatureValues(Resource, Item) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
parseFeatureValues(Resource, Instance) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
parseFeatureValues(Resource, IStructureRecord) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
parseFromCommandLineString(String) - Static method in class ambit2.core.filter.MoleculeFilter
 
parseHAtomEnvironment(String[], String, List<String>) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
parseInput(InputStream) - Method in class ambit2.pubchem.DepictRequest
 
parseInput(String, InputStream) - Method in class ambit2.pubchem.EntrezSearchProcessor
 
parseInput(Target, InputStream) - Method in class ambit2.pubchem.HTTPRequest
 
parseInput(String, InputStream) - Method in class ambit2.pubchem.NCISearchProcessor
 
parseInterpretation(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseInterpretationCriteria(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseInterpretedResult(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseISALocations() - Method in class ambit2.export.isa.ISAExportConfig
 
parseISALocationString(String, String) - Method in class ambit2.export.isa.ISAExportConfig
 
parseJSONConfig(JsonNode) - Method in class ambit2.export.isa.ISAExportConfig
 
parseJSONConfig(JsonNode) - Method in class ambit2.export.isa.json.ISAJsonExportConfig
 
parseKeyWord(String, HAtomEnvironment, String, List<String>) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
parseLayerPos(ISALocation, String) - Static method in class ambit2.export.isa.base.ISALocation
 
parseLayerPos2(ISALocation, String) - Static method in class ambit2.export.isa.base.ISALocation
 
parseLine(String, HAtomEnvironment, String, List<String>) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
parseLineDense(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
parseLineDense(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixBitset
 
parseLineDense(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
parseLineSparse(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
parseLineSparse(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixBitset
 
parseLineSparse(String, long) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
parseList(String, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
parseList(String, int, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
parseObjectURI(RDFNode, Algorithm) - Method in class ambit2.rest.rdf.RDFAlgorithmIterator
 
parseObjectURI(RDFNode, Bookmark) - Method in class ambit2.rest.rdf.RDFBookmarkIterator
 
parseObjectURI(RDFNode, Item) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
parseObjectURI(RDFNode, M) - Method in class ambit2.rest.rdf.RDFMetaDatasetIterator
 
parseObjectURI(RDFNode, ModelWrapper<T, TrainingInstances, TestInstances, Content, String>) - Method in class ambit2.rest.rdf.RDFModelIterator
 
parseObjectURI(RDFNode, Item) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
parseObjectURI(RDFNode, Property) - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
parseObjectURI(RDFNode, ILiteratureEntry) - Method in class ambit2.rest.rdf.RDFReferenceIterator
 
parseObjectURI(RDFNode, RDFNode) - Method in class ambit2.rest.rdf.RDFResourceIterator
 
parseOutput(String, IAtomContainer) - Method in class ambit2.balloon.ShellBalloon
 
parseOutput(String, INPUT) - Method in class ambit2.base.external.CommandShell
Does nothing, override with smth meaningfull
parseOutput(String, INPUT, int) - Method in class ambit2.base.external.CommandShell
 
parseOutput(String, INPUT) - Method in class ambit2.core.external.ShellSDFoutput
 
parseOutput(String, String) - Method in class ambit2.core.smiles.OpenBabelDepiction
 
parseOutput(String, IAtomContainer) - Method in class ambit2.core.smiles.OpenBabelGen3D
 
parseOutput(String, IAtomContainer) - Method in class ambit2.dragon.DragonShell
 
parseOutput(String, IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
parseOutput(Document) - Static method in class ambit2.pubchem.PUGProcessor
parseOutput(String, IAtomContainer) - Method in class ambit2.some.SOMEShell
 
parseOutput(String, IAtomContainer) - Method in class ambit2.vega.VegaShell
 
parseOwner(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parsePairs(String, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
parseParameters(RDFNode, Algorithm) - Method in class ambit2.rest.rdf.RDFAlgorithmIterator
 
parseParams(ObjectNode) - Static method in class ambit2.core.io.json.SubstanceStudyParser
 
parseParams(ObjectNode) - Method in class ambit2.db.search.SQLFileQueryParams
 
parseProcess(ISALocation, String, boolean) - Static method in class ambit2.export.isa.base.ISALocation
 
parseProtocol(ObjectNode) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseProtocolApplication(Reader, SubstanceRecord) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseProtocolApplication(ObjectNode) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseProtocolApplications(JsonNode, SubstanceRecord) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parser - Variable in class ambit2.core.io.RawIteratingCSVReader
 
parser - Variable in class ambit2.core.smiles.SmilesParserWrapper
 
parser - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
parser - Variable in class ambit2.mopac.MopacUtilities
 
parser - Variable in class ambit2.pubchem.EntrezSearchProcessor
 
parser - Variable in class ambit2.rendering.CompoundImageTools
 
parser - Variable in class ambit2.smarts.SMIRKSManager
 
parseRankingRule(String) - Method in class ambit2.tautomers.RuleParser
 
parseReactionConditionsFromString(GenericReaction, String) - Static method in class ambit2.reactions.rules.ReactionParser
 
parseRecord(RDFNode, Algorithm) - Method in class ambit2.rest.rdf.RDFAlgorithmIterator
 
parseRecord(RDFNode, Bookmark) - Method in class ambit2.rest.rdf.RDFBookmarkIterator
 
parseRecord(RDFNode, Item) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
parseRecord(RDFNode, Instance) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
parseRecord(RDFNode, M) - Method in class ambit2.rest.rdf.RDFMetaDatasetIterator
 
parseRecord(RDFNode, ModelWrapper<T, TrainingInstances, TestInstances, Content, String>) - Method in class ambit2.rest.rdf.RDFModelIterator
 
parseRecord(RDFNode, Item) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
parseRecord(RDFNode, Property) - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
parseRecord(RDFNode, Property, int) - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
parseRecord(RDFNode, ILiteratureEntry) - Method in class ambit2.rest.rdf.RDFReferenceIterator
 
parseRecord(RDFNode, RDFNode) - Method in class ambit2.rest.rdf.RDFResourceIterator
 
parseRecord(String) - Method in class ambit2.some.SOMEResultsParser
 
parseRecord(String) - Method in class ambit2.some.SOMEVisualizer
 
parseReliability(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parserErrors - Variable in class ambit2.smarts.SMIRKSManager
 
parseResult(ObjectNode, EffectRecord) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseRetroSynthRule(String) - Method in class ambit2.reactions.rules.ReactionParser
 
parserType - Variable in class ambit2.smarts.query.SmartsPatternFactory
 
parseRule(String, Object) - Method in class ambit2.reactions.rules.GenericParserUtils
 
parseRule2JLine(String, String, HNMRKnowledgeBase) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
parseRule3JLine(String, String, HNMRKnowledgeBase) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
parseSLNSubstance(String) - Method in class ambit2.sln.SLNParser
 
parseSmiles(String) - Method in class ambit2.core.smiles.SmilesParserWrapper
 
parseSmiles(String, boolean) - Method in class ambit2.core.smiles.SmilesParserWrapper
 
parseString(String) - Static method in class ambit2.export.isa.base.ISALocation
 
parseStudyReference(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseSubElement(ISALocation, String) - Static method in class ambit2.export.isa.base.ISALocation
 
parseSubstance(Reader) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseSubstance(JsonNode) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseSubstance(ObjectNode, ProtocolApplication) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseTextValueProteomics(ObjectMapper, String) - Static method in class ambit2.core.io.json.SubstanceStudyParser
 
parseToken() - Method in class ambit2.core.io.QuotedTokenizer
Handle parsing of a quoted token here.
parseTransformation(String) - Method in class ambit2.groupcontribution.transformations.TransformationUtils
 
parseTransformation(ObjectNode, boolean) - Static method in class ambit2.smarts.processors.SMIRKSProcessor
 
parseValue(String) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
parseValueAnnotated(ObjectNode, ValueAnnotated) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
parseValuesAnnotated(ArrayNode, Protocol) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
ParticleTypes - Enum in ambit2.base.data.substance
 
PASSWORD - Static variable in class ambit2.base.config.Preferences
 
password - Variable in class ambit2.base.data.AmbitUser
 
password - Variable in class ambit2.db.LoginInfo
 
password - Variable in class ambit2.ui.editors.AmbitUserEditor
 
paste(MatrixDouble) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
path - Variable in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
path - Variable in class ambit2.reactions.retrosynth.RetroSynthNode
 
pathLenght - Variable in class ambit2.reactions.rules.scores.AtomComplexity
 
paths - Variable in class ambit2.reactions.retrosynth.RetroSynthesisResult
 
pca - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
pca - Variable in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
pca - Variable in class ambit2.rest.task.weka.FilteredWekaPredictor
 
pca - Variable in class ambit2.rest.task.weka.WekaModelBuilder
 
pca - Variable in class ambit2.rest.task.weka.WekaPredictor
 
pcaTransform - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
pCOATING - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pCOATING_DESCRIPTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
PCT_attribute_value - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_compression - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_compression_bzip2 - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_compression_gzip - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_compression_none - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_format - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_format_binary_asn - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_format_sdf - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_format_text_asn - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_download_format_xml - Static variable in class ambit2.pubchem.PUGProcessor
 
PCT_status - Static variable in class ambit2.pubchem.PUGProcessor
 
pDATA_GATHERING_INSTRUMENTS - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pDESCRIPTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pdfDoc - Variable in class ambit2.core.io.PDFWriter
 
PDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
Generates PDF
PDFReporter() - Constructor for class ambit2.db.reporters.PDFReporter
 
PDFReporter(Template) - Constructor for class ambit2.db.reporters.PDFReporter
 
PDFReporter(Template, Profile) - Constructor for class ambit2.db.reporters.PDFReporter
 
PDFWriter - Class in ambit2.core.io
Exporting set of structures as PDF file.
PDFWriter(OutputStream) - Constructor for class ambit2.core.io.PDFWriter
 
PDFWriter(OutputStream, ICompoundImageTools) - Constructor for class ambit2.core.io.PDFWriter
 
pdfWriter - Variable in class ambit2.core.io.PDFWriter
 
pDISTRIBUTION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pDISTRIBUTION_TYPE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pELEMENT_OR_GROUP - Static variable in class ambit2.base.ro.I5CONSTANTS
 
people - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
people - Variable in class ambit2.export.isa.v1_0.objects.Study
 
percentCompleted - Variable in class ambit2.rest.task.Task
 
percentCompleted - Variable in class ambit2.rest.task.TaskResult
 
performCrossValidation(CrossValidation) - Method in class ambit2.groupcontribution.Learner
 
performer - Variable in class ambit2.export.isa.v1_0.objects.Process
 
performExternalValidation() - Method in class ambit2.groupcontribution.Learner
 
performFragmentationOnly() - Method in class ambit2.groupcontribution.Learner
 
performLOOValidation() - Method in class ambit2.groupcontribution.Learner
 
performSelfTest(ValidationConfig) - Method in class ambit2.groupcontribution.Learner
 
performStructureStatistics(String, String, int, int, String) - Method in class ambit2.smarts.ChemObjectFactory
 
performYScrambling(int) - Method in class ambit2.groupcontribution.Learner
 
permutationToString(int[]) - Static method in class ambit2.smarts.ChiralPermutations
 
Person - Class in ambit2.export.isa.v1_0.objects
ISA person schema JSON-schema representing a person in the ISA model
Person() - Constructor for class ambit2.export.isa.v1_0.objects.Person
 
pFUNCTIONALIZATION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pGSD - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pH - Static variable in class ambit2.base.ro.I5CONSTANTS
 
phone - Variable in class ambit2.export.isa.v1_0.objects.Person
 
PhosphoricGroup - Class in ambit2.tautomers.zwitterion
 
PhosphoricGroup() - Constructor for class ambit2.tautomers.zwitterion.PhosphoricGroup
 
Physstate - Static variable in class ambit2.base.ro.I5CONSTANTS
 
PieChartGenerator<T extends ISourceDataset> - Class in ambit2.db.chart
Generates pie chart with number of chemicals per group
PieChartGenerator() - Constructor for class ambit2.db.chart.PieChartGenerator
 
pixel2WidthUnits(int) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
pixel units to excel width units(units of 1/256th of a character width)
PIXELS_PER_INCH - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
PIXELS_PER_MILLIMETRES - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
pKa - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pka - Variable in class ambit2.descriptors.PKANode
 
pka_range - Variable in class ambit2.descriptors.PKANode
 
PKANode - Class in ambit2.descriptors
 
PKANode() - Constructor for class ambit2.descriptors.PKANode
 
PKASmartsDescriptor - Class in ambit2.descriptors
pKa calculation
PKASmartsDescriptor() - Constructor for class ambit2.descriptors.PKASmartsDescriptor
 
PlanarityDescriptor - Class in ambit2.descriptors
/** Planarity descriptor (0,1); zero if planar .
PlanarityDescriptor() - Constructor for class ambit2.descriptors.PlanarityDescriptor
 
pMATERIAL_ISOTROPIC - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pMETHODDETAILS - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pMMAD - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pMMD - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pnum_batchExecutor - Variable in class ambit2.db.processors.ValueWriterNew
 
POINTS_PER_MILLIMETRE - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
pointsToMillimeters(double) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
pointsToPixels(double) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
policyError - Variable in class ambit2.rest.task.Task
 
poll() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
returns true if ready
poll() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
pollInterval - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
pollRDF() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
pollTimeout - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
pool - Variable in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
pool_external - Variable in class ambit2.rest.task.TaskStorage
 
pool_internal - Variable in class ambit2.rest.task.TaskStorage
 
populate(ResultSet) - Method in class ambit2.db.results.AmbitRows
 
populate(ResultSet, int) - Method in class ambit2.db.results.AmbitRows
 
PORT - Static variable in class ambit2.base.config.Preferences
 
port - Variable in class ambit2.db.LoginInfo
 
position - Variable in class ambit2.sln.SLNParserError
 
position - Variable in class ambit2.smarts.SmartsParserError
 
positionDistances - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
post(Representation, Variant) - Method in class ambit2.rest.AbstractResource
 
post(Model) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
post(Representation, MediaType) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
post(Representation, Variant) - Method in class ambit2.rest.task.LauncherResource
 
postProcess(HAtomEnvironment, String, List<String>) - Static method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase
 
postProcessRule() - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
postProcessRule() - Method in class ambit2.reactions.rules.RetroSynthRule
 
pPARTICLESIZE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pReactant - Static variable in class ambit2.base.ro.I5CONSTANTS
 
precondition_atom - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
precondition_atomtype - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
PredefinedKnowledgeBase - Class in ambit2.tautomers
 
PredefinedKnowledgeBase() - Constructor for class ambit2.tautomers.PredefinedKnowledgeBase
 
PredefinedReactionKnowledgeBase - Class in ambit2.reactions.retrosynth
 
PredefinedReactionKnowledgeBase() - Constructor for class ambit2.reactions.retrosynth.PredefinedReactionKnowledgeBase
 
PredefinedSLNDictionary - Class in ambit2.sln.dictionary
 
PredefinedSLNDictionary() - Constructor for class ambit2.sln.dictionary.PredefinedSLNDictionary
 
predicate - Variable in class ambit2.base.data.PropertyAnnotation
 
predict() - Method in interface ambit2.base.data.IModel
Makes predictions using a previously built model.
predict(IDataset<ID, Features, ResultType>, IModelStatistics<ResultType>) - Method in class ambit2.model.AbstractModel
 
predict(IDataset<ID, Features, ResultType>, IModelStatistics<ResultType>) - Method in interface ambit2.model.IModelDefinition
 
predict(ID, Features, ResultType, ResultType, IModelStatistics<ResultType>) - Method in interface ambit2.model.IModelDefinition
 
predict(Matrix) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
predict(Matrix) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
predict(Matrix) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
predict(DATA) - Method in interface ambit2.model.numeric.IDataCoverage
 
predict(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
predict(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
predict(OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
predict(Input) - Method in class ambit2.rest.model.predictor.CoveragePredictor
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExternalModel
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
predict(NativeTypeItem) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.Structure2DProcessor
 
predict(IStructureRecord) - Method in class ambit2.rest.model.predictor.StructureProcessor
 
predict(Instance) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
predict(Instance) - Method in class ambit2.rest.task.weka.WekaPredictor
 
predict(ID, Features, Double, Double, IModelStatistics<Double>) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
predict(IStructureRecord) - Method in class ambit2.vega.ExternalModelVega
 
PREDICTED - Static variable in class ambit2.core.config.AmbitCONSTANTS
Predicted data record
predicted - Variable in class ambit2.core.data.model.ModelWrapper
 
predicted - Variable in class ambit2.model.dataset.DoubleArrayDataset
 
predicted - Variable in class ambit2.similarity.stats.ConfusionMatrix
 
predicted - Variable in class ambit2.similarity.stats.ValuePair
 
predictedFeatureURI - Variable in class ambit2.rest.model.builder.CoverageModelBuilder
 
predictedFeatureURI - Variable in class ambit2.rest.model.builder.FingerprintsModelBuilder
 
predictedProperties - Variable in class ambit2.rest.model.predictor.ExternalModelPredictor
 
predictedVariables - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
PredictedVarsTemplate - Class in ambit2.base.data
 
PredictedVarsTemplate(String) - Constructor for class ambit2.base.data.PredictedVarsTemplate
 
predictionInstance(Instance) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
predictionInstance(Instance) - Method in class ambit2.rest.task.weka.WekaPredictor
 
predictionInstanceAsArray(IStructureRecord) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
PredictionModelStatistics<U extends Bin> - Class in ambit2.similarity.stats
 
PredictionModelStatistics(String) - Constructor for class ambit2.similarity.stats.PredictionModelStatistics
 
predictor - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
predictors - Variable in class ambit2.core.data.model.ModelWrapper
 
preferedStructure - Variable in class ambit2.base.data.StructureRecord
 
preferedStructure - Variable in class ambit2.db.readers.RetrieveStructure
 
Preferences - Class in ambit2.base.config
 
Preferences() - Constructor for class ambit2.base.config.Preferences
 
Preferences.VINDEX - Enum in ambit2.base.config
 
Preferences.VTAGS - Enum in ambit2.base.config
 
PreferencesPanel - Class in ambit2.ui.editors
 
PreferencesPanel() - Constructor for class ambit2.ui.editors.PreferencesPanel
 
PreferencesPanel(Preferences.VTAGS[]) - Constructor for class ambit2.ui.editors.PreferencesPanel
 
prefix - Variable in class ambit2.base.data.study.StructureRecordValidator
 
prefix - Variable in class ambit2.base.external.CommandShell
 
prefix - Variable in class ambit2.core.io.fp.MultiFingerprintsWriter
 
prefix - Variable in class ambit2.core.io.StringArrayHeader
 
prefix - Static variable in class ambit2.core.io.ToxcastAssayReader
 
prefix - Variable in class ambit2.rest.structure.CompoundURIReporter
 
prefix - Variable in class ambit2.structure2name.rules.CarbonData
 
prefix - Variable in class ambit2.structure2name.rules.FunctionalGroupData
 
PrefixFacetQuery<PARAM,FACET extends net.idea.modbcum.i.facet.IFacet<String>> - Class in ambit2.db.facets.datasets
 
PrefixFacetQuery(String) - Constructor for class ambit2.db.facets.datasets.PrefixFacetQuery
 
prepareBatchProperties(IStructureRecord, Connection) - Method in class ambit2.db.processors.ValueWriterNew
 
prepareBatchValues(IStructureRecord, Connection) - Method in class ambit2.db.processors.ValueWriterNew
 
PreparedStatementBatchExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> - Class in ambit2.db
 
PreparedStatementBatchExecutor() - Constructor for class ambit2.db.PreparedStatementBatchExecutor
 
prepareEditor(TableCellEditor, int) - Method in class ambit2.ui.EditableHeader
 
prepareForeignProcessing(Reference) - Method in class ambit2.rest.model.task.CallableModelPredictor
 
prepareInput(String, IAtomContainer) - Method in class ambit2.balloon.ShellBalloon
 
prepareInput(String, INPUT) - Method in class ambit2.base.external.CommandShell
Returns empty string, override with smth meaningfull
prepareInput(String, X) - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
prepareInput(String, IAtomContainer) - Method in class ambit2.core.smiles.OpenBabelGen3D
 
prepareInput(String, IAtomContainer) - Method in class ambit2.dragon.DragonShell
 
prepareInput(String, IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
prepareInput(String, IAtomContainer) - Method in class ambit2.smi23d.ShellMengine
 
prepareInput(String, IAtomContainer) - Method in class ambit2.smi23d.ShellSmi2SDF
 
prepareInput(String, IAtomContainer) - Method in class ambit2.some.SOMEShell
 
prepareInput(String, IAtomContainer) - Method in class ambit2.vega.VegaShell
 
prepareKeySequences(List<String>, int) - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
prepareList() - Method in class ambit2.db.results.MemoryRowsModel
 
prepareOutput(String, OutputStream) - Method in class ambit2.pubchem.EntrezSearchProcessor
 
prepareOutput(Target, OutputStream) - Method in class ambit2.pubchem.HTTPRequest
 
prepareOutput(String, OutputStream) - Method in class ambit2.pubchem.NCISearchProcessor
 
prepareScreening() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
prepareScreening() - Method in class ambit2.db.search.structure.QuerySMARTS
 
prepareStatement(Connection) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
prepareStatement(Connection) - Method in class ambit2.db.processors.FP1024Writer
 
prepareStatement(Connection) - Method in class ambit2.db.processors.RepositoryWriter
 
prepareStatement(Connection) - Method in class ambit2.db.RepositoryReader
 
prepareStatementValues(IStructureRecord, Property) - Method in class ambit2.db.processors.ValueWriterNew
 
prepareTargetForSMARTSSearch(boolean, boolean, boolean, boolean, boolean, boolean, IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
prepareTargetForSMARTSSearch(SmartsFlags, IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
prepareTargetForSMARTSSearchFull(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
preprocess(IStructureRecord) - Method in class ambit2.db.processors.AbstractDescriptorCalculator
 
preprocess(IStructureRecord) - Method in class ambit2.db.processors.DescriptorsCalculator
 
preprocessing() - Method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
 
preProcessStructure(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
preProcessStructure(IAtomContainer, boolean, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
preProcessStructure(IAtomContainer, boolean, boolean, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
prescreen(IQueryRetrieval<ResultType>, ResultType) - Method in class ambit2.db.DbReader
 
prescreen(IQueryRetrieval<IStructureRecord>, IStructureRecord) - Method in class ambit2.db.DbReaderStructure
 
present - Variable in class ambit2.descriptors.PKANode
 
presentationModel - Variable in class ambit2.dbui.QueryEditor
 
Pressure - Static variable in class ambit2.base.ro.I5CONSTANTS
 
prev() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
prev() - Method in interface ambit2.model.IDataset
 
prev(boolean) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
prev(boolean) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
prev() - Method in class ambit2.ui.table.BrowsableTableModel
 
prev() - Method in interface ambit2.ui.table.IRecordNavigator
 
previous() - Method in class ambit2.db.results.AmbitRows
 
previousLevel - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
previousPage() - Method in class ambit2.db.results.AmbitRows
 
previousPage() - Method in class ambit2.dbui.CachedRowSetTableModel
 
previousPage() - Method in class ambit2.ui.table.BrowsableTableModel
 
previousPage() - Method in interface ambit2.ui.table.IPageNavigator
 
previousProcess - Variable in class ambit2.export.isa.v1_0.objects.Process
 
prevLayerAtoms - Variable in class ambit2.smarts.AtomEquivalenceInfo
 
prevLevelMolecules - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
prevPage - Variable in class ambit2.ui.table.FindNavigator
 
prevPage - Variable in class ambit2.ui.table.PageNavigator
 
prevPage - Variable in class ambit2.ui.table.RecordNavigator
 
print(int, int, int, String, boolean, ReliabilityParams._r_flags) - Method in interface ambit2.core.io.study.IStudyPrinter
 
print(ResultSet, StringBuffer) - Method in class ambit2.db.processors.ConnectionStatusProcessor
 
print(int, int, int, String, boolean, ReliabilityParams._r_flags) - Method in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
print(CSVRecord, int) - Method in interface ambit2.ml.io.IMLOutput
 
print(CSVRecord, int) - Method in class ambit2.ml.io.OutputARFF
 
print(CSVRecord, int) - Method in class ambit2.ml.io.OutputVW
 
print(CSVRecord, int) - Method in class ambit2.ml.io.OutputVW_LDA
| word_id:word_ct word_id:word_ct word_id:word_ct word_id:word_ct
printConditions(int, IParams, ObjectNode, IStudyPrinter, ReliabilityParams._r_flags) - Method in class ambit2.core.io.study.StudyFormatter
 
printDebugInfo() - Method in class ambit2.smarts.IsomorphismTester
 
printDebugInfo() - Method in class ambit2.tautomers.TautomerManager
TODO: Rewrite with logger and proper logger levels
printHeader(int, int, int, String) - Method in interface ambit2.core.io.study.IStudyPrinter
 
printHeader(int, int, int, String) - Method in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
printHeaders(OutputStream, List<String>, String) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
printHelp(Options, String) - Static method in class ambit2.groupcontribution.cli.GCMPredictCli
 
printHelp(Options, String) - Static method in class ambit2.groupcontribution.cli.GroupContributionCli
 
printHelp(Options, String) - Static method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
printHelp(Options, String) - Static method in class ambit2.ml.io.app.AmbitML
 
printHelp(Options, String) - Static method in class ambit2.reactions.cli.AmbitSmirksCli
 
printHelp(Options, String) - Static method in class ambit2.reactions.cli.ReactorCli
 
printHelp(Options, String) - Static method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
printIntArray(int[]) - Static method in class ambit2.smarts.SmartsHelper
 
printMappingClusters(List<List<Integer>>, IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
printSmiles(IAtomContainer) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
printSSMap(IAtomContainer, List<IAtom>) - Method in class ambit2.smarts.SMIRKSManager
 
printValues(OutputStream, List<String>, JsonNode[]) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
printValues(OutputStream, List<String>, JsonNode[], boolean) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
priority - Static variable in class ambit2.sln.SLNConst
 
priority - Static variable in class ambit2.smarts.SmartsConst
 
priorityScore - Variable in class ambit2.reactions.GenericReaction
 
priorityScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
priorityScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
process(IStructureRecord) - Method in class ambit2.base.data.study.StructureRecordValidator
 
process(INPUT) - Method in class ambit2.base.external.CommandShell
 
process(String, SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler
 
process(INPUT) - Method in class ambit2.base.processors.batch.BatchProcessor
 
process(ItemList) - Method in class ambit2.base.processors.batch.BatchReporter
 
process(String) - Method in class ambit2.base.processors.CASProcessor
 
process(IStructureRecord) - Method in class ambit2.base.processors.search.AbstractFinder
 
process(IStructureRecord) - Method in class ambit2.base.processors.StructureRecordsAppender
 
process(U) - Method in class ambit2.base.ro.AbstractAnnotator
 
process(SubstanceRecord) - Method in class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
process(IAtomContainer) - Method in class ambit2.core.data.distances.AtomDistanceProcessor
 
process(D) - Method in interface ambit2.core.data.IObject2Properties
 
process(IStructureRecord) - Method in class ambit2.core.io.dx.DXParser
 
process(ProtocolEffectRecord<String, IParams, String>) - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
process(IAtomContainer) - Method in class ambit2.core.processors.FragmentProcessor
 
process(IAtomContainer) - Method in class ambit2.core.processors.IsotopesProcessor
 
process(Content) - Method in class ambit2.core.processors.ProcessorFileExport
 
process(IAtomContainer) - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.AtomConfigurator
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.CloneProcessor
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.FingerprintGenerator
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.InchiProcessor
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.CASKey
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.ChEMBLCompoundURI
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.DSSToxID
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.EINECSKey
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.EmptyKey
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.InchiKey
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PropertyKey
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PropertyNameKey
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PubchemCID
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PubchemSID
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.SmilesKey
 
process(IStructureRecord[]) - Method in class ambit2.core.processors.structure.MoleculePairProcessor
 
process(IStructureRecord[], IAtomContainer[]) - Method in class ambit2.core.processors.structure.MoleculePairProcessor
 
process(IStructureRecord) - Method in class ambit2.core.processors.structure.MoleculeReader
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.MoleculeWriter
 
process(IAtomContainer) - Method in class ambit2.core.processors.structure.StructureTypeProcessor
 
process(IAtomContainer) - Method in class ambit2.core.processors.Structure2DBuilder
 
process(IStructureRecord) - Method in class ambit2.core.processors.StructureNormalizer
 
process(ISourceDataset) - Method in class ambit2.db.chart.BarChartGeneratorDataset
 
process(ISourceDataset) - Method in class ambit2.db.chart.FingerprintHistogramDataset
 
process(IStoredQuery) - Method in class ambit2.db.chart.FuncGroupsChartGenerator
 
process(IStoredQuery) - Method in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
process(IStoredQuery) - Method in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
process(T) - Method in class ambit2.db.chart.PieChartGenerator
 
process(ISourceDataset) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
process(ISourceDataset) - Method in class ambit2.db.chart.XTabChartGenerator
 
process(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
process(T) - Method in class ambit2.db.processors.ConnectionStatisticsProcessor
 
process(T) - Method in class ambit2.db.processors.ConnectionStatusProcessor
 
process(IStructureRecord) - Method in class ambit2.db.processors.DescriptorsCalculator
 
process(IIteratingChemObjectReader) - Method in class ambit2.db.processors.ProcessorCloseReader
 
process(SessionID) - Method in class ambit2.db.processors.processorCloseSession
 
process(Profile<Property>) - Method in class ambit2.db.processors.ProcessorCreateProfileQuery
 
process(IQueryObject<IStructureRecord>) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
process(SessionID) - Method in class ambit2.db.processors.ProcessorCreateSession
 
process(File) - Method in class ambit2.db.processors.ProcessorFile2FileReader
 
process(Object) - Method in class ambit2.db.processors.ProcessorOntology
 
process(IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.processors.ProcessorSetQueryScope
 
process(IStructureRecord) - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
process(QueryInfo) - Method in class ambit2.db.processors.QueryInfo2Query
 
process(IStoredQuery) - Method in class ambit2.db.processors.QueryStatisticsProcessor
 
process(IStructureRecord) - Method in class ambit2.db.processors.StructureStatisticsProcessor
 
process(IStructureRecord) - Method in class ambit2.db.readers.ValuesByTemplateReader
 
process(Target) - Method in class ambit2.db.RepositoryReader
 
process(T) - Method in class ambit2.db.results.AmbitRows
 
process(IStructureRecord) - Method in class ambit2.db.search.property.ValuesReader
 
process(Q) - Method in class ambit2.db.search.QueryExecutor
 
process(IStructureRecord[]) - Method in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
process(IStructureRecord[]) - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
process(Profile<Property>) - Method in class ambit2.db.search.structure.ProcessorMissingDescriptorsQuery
 
process(Q) - Method in class ambit2.db.StatementExecutor
 
process(IStructureRecord) - Method in class ambit2.db.substance.processor.DBMatrixValueMarker
 
process(IStructureRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
process(IFacet) - Method in class ambit2.db.substance.study.facet.FacetAnnotator
 
process(IStructureRecord) - Method in class ambit2.db.update.chemical.InChIChemicalsWriter
 
process(Object) - Method in class ambit2.dbui.dictionary.OntologyEditor
 
process(Profile<Property>) - Method in class ambit2.dbui.ProfileEditor
 
process(IQueryRetrieval<Property>) - Method in class ambit2.dbui.QueryCombinedEditor
 
process(IQueryRetrieval<Property>) - Method in class ambit2.dbui.QueryEditor
 
process(IQueryRetrieval<Property>) - Method in class ambit2.dbui.QueryFieldEditor
 
process(IQueryRetrieval<Property>) - Method in class ambit2.dbui.QueryFieldNumericEditor
 
process(ScopeQuery) - Method in class ambit2.dbui.QueryScopeEditor
 
process(String) - Method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
process(IAtomContainer) - Method in class ambit2.descriptors.FunctionalGroup
 
process(ITEM) - Method in class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
process(String) - Method in class ambit2.descriptors.processors.AbstractDescriptorFactory
 
process(IAtomContainer) - Method in class ambit2.descriptors.processors.DescriptorEngineProcessor
 
process(DescriptorValue) - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
 
process(DescriptorValue) - Method in class ambit2.descriptors.processors.DescriptorValue2Property
 
process(SubstanceRecord) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
Process - Class in ambit2.export.isa.v1_0.objects
ISA process or protocol application schema, corresponds to 'Protocol REF' columns in the study and assay files JSON-schema representing a protocol application in the ISA model
Process() - Constructor for class ambit2.export.isa.v1_0.objects.Process
 
process(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
process(String) - Method in class ambit2.namestructure.Name2StructureProcessor
 
process(String) - Method in class ambit2.pubchem.BatchRetrievePubChem
 
process(String) - Method in class ambit2.pubchem.DepictRequest
 
process(InputStream) - Method in class ambit2.pubchem.EntrezESearchParser
 
process(String) - Method in class ambit2.pubchem.EntrezSearchProcessor
 
process(Target) - Method in class ambit2.pubchem.HTTPRequest
 
process(String) - Method in class ambit2.pubchem.NCISearchProcessor
 
process(List<IStructureRecord>) - Method in class ambit2.pubchem.PUGProcessor
Example: You want to download CID 1 and CID 99 being uids 1 and 99 in the 'pccompound' Entrez database in SDF format with gzip compression.
process(String) - Method in class ambit2.pubchem.rest.PUGRestRequest
 
process(IStructureRecord) - Method in class ambit2.rendering.StructureEditorProcessor
 
process(IStructureRecord) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
process(IStructureRecord) - Method in class ambit2.rest.dataset.RDFFileWriter
 
process(OTDataset) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Synchronous processing
process(OTDataset) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
process(OTDataset, OTFeature) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
process(OTDataset) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
process(OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
process(OTDataset) - Method in class ambit2.rest.legacy.OTProcessingContainers
Deprecated.
 
process(OTDataset, boolean) - Method in class ambit2.rest.legacy.OTProcessingContainers
Deprecated.
 
process(OTDataset) - Method in class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
process(OTDataset) - Method in class ambit2.rest.legacy.OTSuperModel
Deprecated.
 
process(Algorithm) - Method in class ambit2.rest.model.builder.CoverageModelBuilder
 
process(Algorithm) - Method in class ambit2.rest.model.builder.FingerprintsModelBuilder
 
process(Algorithm) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
process(Algorithm) - Method in class ambit2.rest.model.builder.SMSDModelBuilder
 
process(IStructureRecord) - Method in class ambit2.rest.model.predictor.ExternalModelPredictor
 
process(IStructureRecord) - Method in class ambit2.rest.model.predictor.FingerprintsPredictor
 
process(NativeTypeItem) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
process(ByteArrayOutputStream) - Method in class ambit2.rest.RemoteStreamConvertor
 
process(Q) - Method in class ambit2.rest.StreamConvertor
 
process(InputStream) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
process(SubstanceRecord) - Method in class ambit2.rest.substance.SubstanceRecordStaxWriter
 
process(Algorithm) - Method in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
process(Algorithm) - Method in class ambit2.rest.task.weka.WekaModelBuilder
 
process(String) - Method in class ambit2.search.chemidplus.ChemIdPlusRequest
 
process(String) - Method in class ambit2.search.csls.CSLSRequest
 
process(String) - Method in class ambit2.search.opentox.OpenToxRequest
 
process(IAtomContainer) - Method in class ambit2.smarts.processors.SMARTSPropertiesReader
 
process(IAtomContainer) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
process(IAtomContainer) - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
process(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsToChemObject
 
process(IAtomContainer) - Static method in class ambit2.smarts.smirks.Transformations
 
process(int, String, SOMERawReader.someindex, double, boolean) - Method in class ambit2.some.SOMEResultsParser
 
process(IAtomContainer) - Method in class ambit2.some.SOMEShell
 
process(int, String, SOMERawReader.someindex, double, boolean) - Method in class ambit2.some.SOMEVisualizer
 
process(IAtomContainer) - Method in class ambit2.some.SOMEVisualizer
 
process(IAtomContainer) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
process(IAtomContainer) - Method in class ambit2.tautomers.processor.TautomerProcessor
 
process() - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
process(IAtomContainer) - Method in class ambit2.ui.jmol.ImageTools3D
 
process(ExternalModel<VegaShell, IAtomContainer>) - Method in class ambit2.vega.ExternalModelVega
 
process(IAtomContainer) - Method in class ambit2.vega.VegaShell
 
processAcyclicComponent(AcyclicComponent) - Method in class ambit2.structure2name.IUPACNameGenerator
 
processAllLayers(IAtomContainer) - Method in class ambit2.smarts.AtomEquivalenceInfo
 
processAsync(OTDataset) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Initiate asyncronous processing of the dataset
processAsync(OTDataset, OTFeature) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
processAsync(OTDataset) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
processAsync(Form) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
processAsync(OTDataset) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
processAsync(OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
processAsync(OTDataset) - Method in class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
processCactus(String, String, NCISearchProcessor.METHODS, long, String) - Method in class ambit2.pubchem.SearchApplication
 
processChunks() - Method in class ambit2.db.reporters.QueryPacketReporter
 
processComment(String) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
processComment(String) - Method in class ambit2.core.io.ToxcastAssayReader
 
ProcessData(Matrix) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
processDetail(SubstanceRecord, IStructureRecord) - Method in class ambit2.db.substance.ids.ReadChemIdentifiersByComposition
 
processDetail(SubstanceRecord, IStructureRecord) - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
Hack for merging dataset properties with substances; This is not necessarily correct, as the substance may have many components!
processDetail(SubstanceRecord, List<ProtocolApplication>) - Method in class ambit2.db.substance.study.SubstanceStudyDetailsProcessor
 
processDownloadURL(Document, Element) - Static method in class ambit2.pubchem.PUGProcessor
 
processForm(Reference, Form) - Method in class ambit2.rest.task.CallableQueryProcessor
 
processHeader() - Method in class ambit2.core.io.bcf.EurasBCFReader
 
processHeader(BufferedReader) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
processHeader() - Method in class ambit2.core.io.IteratingXLSReader
 
processHeader(Row) - Method in class ambit2.core.io.IteratingXLSReader
 
processHeader(BufferedReader) - Method in class ambit2.core.io.ToxcastAssayReader
 
processID - Variable in class ambit2.export.isa.base.ISALocation
 
processIndex - Variable in class ambit2.export.isa.base.ISALocation
 
processIOSettingQuestion(IOSetting) - Method in class ambit2.core.io.SimpleIOListener
 
processIOSettingQuestion(IOSetting) - Method in class ambit2.ui.AmbitSettingsListener
 
processItem(Item, Output) - Method in class ambit2.base.processors.batch.BatchReporter
 
processItem(String, String, boolean) - Method in class ambit2.core.io.ToXMLReaderSimple
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.AbstractImageReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.ARFF3ColReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.ARFFReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.CMLReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.CSVReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.ImageAreaReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.PDFReporter
 
processItem(Property) - Method in class ambit2.db.reporters.QueryTemplateReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.RTFReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.SDFReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.SmilesReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.StructureListReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.StructureRecordReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
processItem(IStructureRecord) - Method in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
processItem(IStructureRecord) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
processItem(T, Writer) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
processItem(UUID, Writer) - Method in class ambit2.rest.reporters.TaskRDFReporter
 
processItem(SubstanceRecord) - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
processItem(SubstanceRecord) - Method in class ambit2.rest.substance.SubstanceRDFReporter
 
processItem(UUID, Writer) - Method in class ambit2.rest.task.TaskJSONReporter
 
processMolecule(IAtomContainer) - Static method in class ambit2.groupcontribution.dataset.DataSet
 
processNotFound(NotFoundException, Variant) - Method in class ambit2.rest.AbstractResource
 
processor - Variable in class ambit2.base.processors.batch.BatchProcessor
 
processor - Variable in exception ambit2.base.processors.ProcessorException
 
processor - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
processor - Variable in class ambit2.descriptors.InChI
 
processor - Variable in class ambit2.descriptors.processors.BitSetGenerator
 
ProcessorCloseReader - Class in ambit2.db.processors
 
ProcessorCloseReader() - Constructor for class ambit2.db.processors.ProcessorCloseReader
 
processorCloseSession - Class in ambit2.db.processors
Closes session designated by SessionID by updating the field "completed" in "sessions" table
processorCloseSession() - Constructor for class ambit2.db.processors.processorCloseSession
 
ProcessorCreateProfileQuery - Class in ambit2.db.processors
 
ProcessorCreateProfileQuery() - Constructor for class ambit2.db.processors.ProcessorCreateProfileQuery
 
ProcessorCreateQuery - Class in ambit2.db.processors
Inserts into query table idstructure numbers from a query identified by StoredQuery.
ProcessorCreateQuery() - Constructor for class ambit2.db.processors.ProcessorCreateQuery
 
ProcessorCreateSession - Class in ambit2.db.processors
 
ProcessorCreateSession() - Constructor for class ambit2.db.processors.ProcessorCreateSession
 
ProcessorException - Exception in ambit2.base.processors
 
ProcessorException(IProcessor, String) - Constructor for exception ambit2.base.processors.ProcessorException
 
ProcessorException(IProcessor, Exception) - Constructor for exception ambit2.base.processors.ProcessorException
 
ProcessorFile2FileReader - Class in ambit2.db.processors
Returns IIteratingChemObjectReader based on File.
ProcessorFile2FileReader() - Constructor for class ambit2.db.processors.ProcessorFile2FileReader
 
ProcessorFileExport<Content> - Class in ambit2.core.processors
TODO merge with representation convertor make use of http://jmimemagic.sourceforge.net/maven-reports.html for mime recognition
ProcessorFileExport() - Constructor for class ambit2.core.processors.ProcessorFileExport
 
ProcessorFileExport(FileOutputState) - Constructor for class ambit2.core.processors.ProcessorFileExport
 
ProcessorMissingDescriptorsQuery - Class in ambit2.db.search.structure
Creates a query to retrieve structures without given list of descriptors
ProcessorMissingDescriptorsQuery() - Constructor for class ambit2.db.search.structure.ProcessorMissingDescriptorsQuery
 
ProcessorMissingDescriptorsQuery(long) - Constructor for class ambit2.db.search.structure.ProcessorMissingDescriptorsQuery
 
ProcessorOntology - Class in ambit2.db.processors
 
ProcessorOntology() - Constructor for class ambit2.db.processors.ProcessorOntology
 
ProcessorOntology.OP - Enum in ambit2.db.processors
 
ProcessorOntology.SIDE - Enum in ambit2.db.processors
 
processors - Variable in class ambit2.base.processors.batch.BatchReporter
 
ProcessorSetQueryScope - Class in ambit2.db.processors
Sets a scope to the ProcessorSetQueryScope.query
ProcessorSetQueryScope() - Constructor for class ambit2.db.processors.ProcessorSetQueryScope
 
ProcessorStructurePairsRetrieval - Class in ambit2.db.search.structure.pairwise
 
ProcessorStructurePairsRetrieval() - Constructor for class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
ProcessorStructurePairsRetrieval(IQueryRetrieval<IStructureRecord[]>) - Constructor for class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
ProcessorStructureRetrieval - Class in ambit2.db.processors
 
ProcessorStructureRetrieval() - Constructor for class ambit2.db.processors.ProcessorStructureRetrieval
 
ProcessorStructureRetrieval(IQueryRetrieval<IStructureRecord>) - Constructor for class ambit2.db.processors.ProcessorStructureRetrieval
 
ProcessParameterValue - Class in ambit2.export.isa.v1_0.objects
ISA process parameter value schema JSON-schema representing a Parameter Value (associated with a Protocol REF) in the ISA model
ProcessParameterValue() - Constructor for class ambit2.export.isa.v1_0.objects.ProcessParameterValue
 
processPath(CachedImage<OUTPUT>, String) - Method in class ambit2.db.reporters.AbstractImageReporter
 
processProduct(IAtomContainer) - Method in class ambit2.smarts.SMIRKSManager
 
processRow(IAtomContainer) - Method in class ambit2.core.io.bcf.EurasBCFReader
 
processRow(IAtomContainer) - Method in class ambit2.core.io.IteratingXLSReader
 
processSequence - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
processSequence - Variable in class ambit2.export.isa.v1_0.objects.Study
 
processSolution(QuerySolution) - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
processSolution(QuerySolution) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
processSource(Resource, String, String) - Method in class ambit2.rest.rdf.RDFPropertyIterator
 
processStdOut(InputStream) - Method in class ambit2.base.external.CommandShell
 
processStream(InputStream, OutputStream) - Method in class ambit2.rest.RemoteStreamConvertor
 
processTautomer(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class ambit2.tautomers.TautomerManager
 
processTemplate(Dictionary, Template) - Method in class ambit2.db.update.model.CreateModel
 
processValue(ProtocolEffectRecord<String, String, String>, boolean) - Static method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
processValue(ProtocolEffectRecordMatrix<String, String, String>, boolean) - Static method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
processWaiting(Document, Element) - Static method in class ambit2.pubchem.PUGProcessor
 
prodChiralAtom - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
prodChirality - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
prodDBAt1 - Variable in class ambit2.smarts.StereoDBTransformation
 
prodDBAt2 - Variable in class ambit2.smarts.StereoDBTransformation
 
prodDBStereo - Variable in class ambit2.smarts.StereoDBTransformation
 
prodLigand1 - Variable in class ambit2.smarts.StereoDBTransformation
 
prodLigand1ReactMap - Variable in class ambit2.smarts.StereoDBTransformation
 
prodLigand2 - Variable in class ambit2.smarts.StereoDBTransformation
 
prodLigand2ReactMap - Variable in class ambit2.smarts.StereoDBTransformation
 
prodLigands - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
prodLigandsReactMap - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
prodTerminal1 - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
prodTerminal2 - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
produceRandomStructsFromMDL(String, int, int, int, List<StructInfo>, String) - Method in class ambit2.smarts.ChemObjectFactory
 
produceStructsFromMDL(String, int, int, int, List<StructInfo>, String) - Method in class ambit2.smarts.ChemObjectFactory
 
produceStructuresExhaustively(IAtomContainer, List<StructInfo>, int, int) - Method in class ambit2.smarts.ChemObjectFactory
 
produceStructuresRandomly(IAtomContainer, List<StructInfo>, int, int, int) - Method in class ambit2.smarts.ChemObjectFactory
 
product - Variable in class ambit2.smarts.SMIRKSReaction
 
productComplexityDescirptors - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
productComplexityScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
productComplexityWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
productFlags - Variable in class ambit2.smarts.SMIRKSReaction
 
productRecursiveAtoms - Variable in class ambit2.smarts.SMIRKSReaction
 
products - Variable in class ambit2.reactions.GenericReactionInstance
 
products - Variable in class ambit2.reactions.Reaction
 
products - Variable in class ambit2.smarts.SMIRKSReaction
 
productsCLG - Variable in class ambit2.smarts.SMIRKSReaction
 
productSimilarityScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
productSimilarityWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
productsSmarts - Variable in class ambit2.smarts.SMIRKSReaction
 
productStabilityScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
productStabilityWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
Profile<P extends Property> - Class in ambit2.base.data
A set of properties, defining a (e.g.
Profile() - Constructor for class ambit2.base.data.Profile
 
profile - Variable in class ambit2.base.processors.search.AbstractFinder
 
profile - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
profile - Variable in class ambit2.db.search.property.ValuesReader
 
profile - Variable in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
profile - Variable in class ambit2.dbui.ProfileEditor
 
profile - Variable in class ambit2.rest.freemarker.FreeMarkerApplication
 
profile - Variable in class ambit2.ui.editors.TemplateEditor
 
profile_property_added - Static variable in class ambit2.base.data.Profile
 
profile_property_change - Static variable in class ambit2.base.data.Profile
 
profile_property_removed - Static variable in class ambit2.base.data.Profile
 
ProfileEditor - Class in ambit2.dbui
 
ProfileEditor() - Constructor for class ambit2.dbui.ProfileEditor
 
ProfileListModel - Class in ambit2.base.data
 
ProfileListModel(Profile<Property>) - Constructor for class ambit2.base.data.ProfileListModel
 
ProfileListModel(Profile<Property>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel
 
ProfileListModel(Hashtable<String, Profile<Property>>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel
 
ProfileListModel(TypedListModel<Property>) - Constructor for class ambit2.base.data.ProfileListModel
 
ProfileListModel(TypedListModel<Property>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel
 
profileToHistogram(int) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
profileToString() - Method in class ambit2.model.structure.DataCoverageFingerprints
 
properties - Variable in class ambit2.base.data.AbstractDataset
 
properties - Variable in class ambit2.base.data.StructureRecord
 
properties - Variable in class ambit2.core.io.MolPropertiesIOSetting
 
properties - Variable in class ambit2.core.io.SimpleIOListener
 
properties - Variable in class ambit2.core.io.ToXMLReaderSimple
 
properties - Variable in class ambit2.db.results.StoredQueryTableModel
 
properties - Variable in class ambit2.dbui.QueryFieldEditor
 
properties - Variable in class ambit2.dbui.QueryFieldNumericEditor
 
properties - Variable in class ambit2.descriptors.FunctionalGroup
 
properties - Variable in class ambit2.groupcontribution.dataset.LocalProperties
 
properties - Variable in class ambit2.rest.aa.opensso.OpenSSOServicesConfig
 
properties - Static variable in class ambit2.rest.DBConnection
 
properties - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
properties - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
properties - Variable in class ambit2.ui.AmbitSettingsListener
 
properties - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
PROPERTIES_DX_uri - Static variable in class ambit2.base.data.LiteratureEntry
 
properties_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
PropertiesByDataset - Class in ambit2.db.search.property
Retrieves Property-es used by particular dataset
PropertiesByDataset() - Constructor for class ambit2.db.search.property.PropertiesByDataset
 
PropertiesByDataset.QField - Enum in ambit2.db.search.property
 
PropertiesByQuery - Class in ambit2.db.search.property
 
PropertiesByQuery() - Constructor for class ambit2.db.search.property.PropertiesByQuery
 
PropertiesByQuery.QField - Enum in ambit2.db.search.property
 
PropertiesChartGenerator - Class in ambit2.db.chart
 
PropertiesChartGenerator() - Constructor for class ambit2.db.chart.PropertiesChartGenerator
 
PropertiesTableModel - Class in ambit2.base.data
Table model for Profile
PropertiesTableModel(TypedListModel<Property>, boolean, int) - Constructor for class ambit2.base.data.PropertiesTableModel
 
Property - Class in ambit2.base.data
 
Property(String) - Constructor for class ambit2.base.data.Property
 
Property(String, ILiteratureEntry) - Constructor for class ambit2.base.data.Property
 
Property(String, String, ILiteratureEntry) - Constructor for class ambit2.base.data.Property
 
Property(String, String, String) - Constructor for class ambit2.base.data.Property
 
property - Variable in class ambit2.base.data.PropertyTemplateStats
 
property - Variable in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
property - Variable in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
property - Variable in class ambit2.db.chart.PieChartGenerator
 
property - Variable in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
property - Variable in class ambit2.db.search.property.FilteredCount
 
property - Variable in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
property - Variable in class ambit2.db.update.fpae.CreateAtomEnvironment
 
property - Variable in class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
property - Variable in class ambit2.db.update.qlabel.ValuesQualityCheck
 
property - Variable in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
property - Static variable in class ambit2.rest.AbstractResource
 
property - Variable in class ambit2.similarity.measure.DistanceComparable
 
Property.IO_QUESTION - Enum in ambit2.base.data
 
property_batchExecutor - Variable in class ambit2.db.processors.ValueWriterNew
Prepared statement for writing Property objects
PROPERTY_BATCHSTATS - Static variable in class ambit2.base.processors.batch.BatchProcessor
 
PROPERTY_COMBINE - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_COND1 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_COND2 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_COND3 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_DATASET - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_FIELDNAME1 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_FIELDNAME2 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_FIELDNAME3 - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_MAXPAGES - Static variable in interface ambit2.ui.table.IPageNavigator
 
PROPERTY_MAXRECORDS - Static variable in interface ambit2.ui.table.IRecordNavigator
 
PROPERTY_METHOD - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_MODE - Static variable in interface ambit2.ui.table.IBrowserMode
 
PROPERTY_PAGE - Static variable in interface ambit2.ui.table.IPageNavigator
 
PROPERTY_PAGERECORD - Static variable in interface ambit2.ui.table.IPageNavigator
 
PROPERTY_PAGESIZE - Static variable in interface ambit2.ui.table.IPageNavigator
 
PROPERTY_RECORD - Static variable in interface ambit2.ui.table.IRecordNavigator
 
PROPERTY_SCOPE - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_THRESHOLD - Static variable in class ambit2.db.search.QueryInfo
 
PROPERTY_VALUE - Static variable in interface ambit2.ui.table.IFindNavigator
 
PROPERTY_ZOOM - Static variable in interface ambit2.ui.table.IBrowserMode
 
PropertyAnnotation<OBJECT> - Class in ambit2.base.data
Additional triples for Property, or opentox:Feature
PropertyAnnotation() - Constructor for class ambit2.base.data.PropertyAnnotation
 
PropertyAnnotations - Class in ambit2.base.data
 
PropertyAnnotations() - Constructor for class ambit2.base.data.PropertyAnnotations
 
PropertyCalculationProcessor - Class in ambit2.descriptors.processors
 
PropertyCalculationProcessor() - Constructor for class ambit2.descriptors.processors.PropertyCalculationProcessor
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.core.smiles.SmilesParserWrapper
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.db.results.AmbitRows
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.db.results.MemoryRowsModel
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.db.results.RowsModel
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.ui.DelimitersPanel
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.ui.ImageCellRenderer
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.ui.jmol.Panel3D
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.ui.Panel2D
 
propertyChange(PropertyChangeEvent) - Method in class ambit2.ui.QueryBrowser
 
propertyChangeSupport - Static variable in class ambit2.base.config.Preferences
 
propertyChangeSupport - Static variable in class ambit2.ui.EditorPreferences
 
propertyColIndices - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
PropertyCount - Class in ambit2.db.search.property
 
PropertyCount() - Constructor for class ambit2.db.search.property.PropertyCount
 
PropertyCount.PropertyCriteria - Enum in ambit2.db.search.property
 
PropertyDatasetFacet<PROPERTY,DATASET> - Class in ambit2.db.facets.propertyvalue
 
PropertyDatasetFacet(String) - Constructor for class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
PropertyDatasetFacetQuery - Class in ambit2.db.facets.propertyvalue
Number of compounds grouped by value , given property and dataset
PropertyDatasetFacetQuery(String) - Constructor for class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
PropertyEditor - Class in ambit2.ui.editors
 
PropertyEditor() - Constructor for class ambit2.ui.editors.PropertyEditor
 
propertyEntry(Property) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
PropertyImporter - Class in ambit2.db.processors
Imports only properties, doesn't write structures - TODO merge with repository writer
PropertyImporter() - Constructor for class ambit2.db.processors.PropertyImporter
 
PropertyInchiKey - Static variable in class ambit2.reactions.reactor.Reactor
 
propertyIterator - Variable in class ambit2.rest.rdf.RDFStructuresIterator
 
PropertyKey<Result> - Class in ambit2.core.processors.structure.key
 
PropertyKey() - Constructor for class ambit2.core.processors.structure.key.PropertyKey
 
PropertyKey(Property) - Constructor for class ambit2.core.processors.structure.key.PropertyKey
 
propertyListener - Variable in class ambit2.db.results.StoredQueryTableModel
 
propertyListener - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
propertyname - Variable in class ambit2.db.results.AmbitRows
 
PROPERTYNAME_DATASET_ENABLED - Static variable in class ambit2.db.search.QueryInfo
 
PropertyNameKey - Class in ambit2.core.processors.structure.key
User defined name to join structure records
PropertyNameKey() - Constructor for class ambit2.core.processors.structure.key.PropertyNameKey
 
PropertyNameKey(String) - Constructor for class ambit2.core.processors.structure.key.PropertyNameKey
 
propertyNames - Variable in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
PropertyNotInTemplateException - Exception in ambit2.base.exceptions
 
PropertyNotInTemplateException() - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException
 
PropertyNotInTemplateException(Object, Template) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException
 
PropertyNotInTemplateException(String) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException
 
PropertyNotInTemplateException(Throwable) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException
 
PropertyNotInTemplateException(String, Throwable, Object, Template) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException
 
propertyQuery - Variable in class ambit2.db.readers.ValuesByTemplateReader
 
PropertyRange - Class in ambit2.db.search.property
Returns binned range of property (defined by Fieldname), number of bins is given by setValue()
PropertyRange() - Constructor for class ambit2.db.search.property.PropertyRange
 
PropertyReactionIds - Static variable in class ambit2.reactions.reactor.Reactor
 
propertyReporter - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
propertyReporter - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
propertyReporter - Variable in class ambit2.rest.model.predictor.NumericADPredictor
 
propertyReporter - Variable in class ambit2.rest.substance.SubstanceRDFReporter
 
PropertyRows - Class in ambit2.db.results
 
PropertyRows() - Constructor for class ambit2.db.results.PropertyRows
 
PropertyStats<T extends Comparable<T>> - Class in ambit2.base.data
 
PropertyStats() - Constructor for class ambit2.base.data.PropertyStats
 
propertyStats - Variable in class ambit2.dbui.QueryFieldNumericEditor
 
PropertyStatsNumeric - Class in ambit2.db.search.property
 
PropertyStatsNumeric() - Constructor for class ambit2.db.search.property.PropertyStatsNumeric
 
PropertyStatsString - Class in ambit2.db.search.property
 
PropertyStatsString() - Constructor for class ambit2.db.search.property.PropertyStatsString
 
PropertyTemplateStats - Class in ambit2.base.data
 
PropertyTemplateStats() - Constructor for class ambit2.base.data.PropertyTemplateStats
 
PropertyTemplateStats(Property, String, long) - Constructor for class ambit2.base.data.PropertyTemplateStats
 
PropertyURIReporter - Class in ambit2.rest.property
Generates uri of PropertyResource
PropertyURIReporter(Reference) - Constructor for class ambit2.rest.property.PropertyURIReporter
 
PropertyURIReporter(Request) - Constructor for class ambit2.rest.property.PropertyURIReporter
 
PropertyValue<T> - Class in ambit2.db.readers
 
PropertyValue() - Constructor for class ambit2.db.readers.PropertyValue
 
PropertyValue(Property) - Constructor for class ambit2.db.readers.PropertyValue
 
PropertyValue(Property, T) - Constructor for class ambit2.db.readers.PropertyValue
 
PropertyValue(Property, T, AbstractPropertyWriter.mode) - Constructor for class ambit2.db.readers.PropertyValue
 
PropertyValuesWriter - Class in ambit2.db.processors
writes properties
PropertyValuesWriter() - Constructor for class ambit2.db.processors.PropertyValuesWriter
 
propertyWithType - Static variable in class ambit2.db.update.property.ReadProperty
 
propertyWriter - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
propertyWriter - Variable in class ambit2.db.processors.DbStructureWriter
 
propertyWriter - Variable in class ambit2.db.processors.PropertyImporter
 
propertyX - Variable in class ambit2.db.chart.BarChartGenerator
 
propertyX - Variable in class ambit2.db.chart.PropertiesChartGenerator
 
propertyX - Variable in class ambit2.db.chart.XTabChartGenerator
 
propertyY - Variable in class ambit2.db.chart.BarChartGenerator
 
propertyY - Variable in class ambit2.db.chart.PropertiesChartGenerator
 
propertyY - Variable in class ambit2.db.chart.XTabChartGenerator
 
Proportion - Class in ambit2.base.relation.composition
 
Proportion() - Constructor for class ambit2.base.relation.composition.Proportion
 
proportion - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
proportion - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
proportion_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
proportionFromString(String) - Static method in class ambit2.sln.io.SLNIOHelpers
 
proportionToString(Proportion) - Static method in class ambit2.sln.io.SLNIOHelpers
 
props - Static variable in class ambit2.base.config.Preferences
 
props - Static variable in class ambit2.ui.EditorPreferences
 
protectAdminResource() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
protectCompoundResource() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
ProtectedResource - Class in ambit2.rest
 
ProtectedResource() - Constructor for class ambit2.rest.ProtectedResource
 
protectFeatureResource() - Method in class ambit2.rest.config.AMBITAppConfigInternal
 
Protocol - Class in ambit2.base.data.study
"protocol": { "topcategory": "TOX", "category": { "code": "TO_ACUTE_INHAL_SECTION", "title": "7.2.2Acutetoxicity-inhalation" }, "endpoint": "Acute toxicity: inhalation,IUC4#10/Ch.5.1.2", "guideline": [ "Method: other: sensoryirritationaccordingtoAlarie,Y.;(nofurtherdata)" ] }
Protocol(String) - Constructor for class ambit2.base.data.study.Protocol
 
Protocol(String, String) - Constructor for class ambit2.base.data.study.Protocol
 
protocol - Variable in class ambit2.base.data.study.ProtocolApplication
 
protocol - Variable in class ambit2.base.data.study.ProtocolEffectRecord
 
Protocol - Class in ambit2.export.isa.v1_0.objects
ISA protocol schema JSON-schema representing a protocol in the ISA model
Protocol() - Constructor for class ambit2.export.isa.v1_0.objects.Protocol
 
protocol - Static variable in class ambit2.model.numeric.DataCoverageLeverage
 
protocol - Static variable in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
Protocol._categories - Enum in ambit2.base.data.study
TODO refactor this to make ontology use easier
Protocol._fields - Enum in ambit2.base.data.study
 
ProtocolApplication<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT> - Class in ambit2.base.data.study
 
ProtocolApplication(PROTOCOL) - Constructor for class ambit2.base.data.study.ProtocolApplication
 
ProtocolApplication._fields - Enum in ambit2.base.data.study
 
ProtocolApplicationAnnotated<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT> - Class in ambit2.base.data.study
 
ProtocolApplicationAnnotated(PROTOCOL) - Constructor for class ambit2.base.data.study.ProtocolApplicationAnnotated
 
ProtocolApplicationSummaryFacet - Class in ambit2.db.substance.study.facet
 
ProtocolApplicationSummaryFacet(String) - Constructor for class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
ProtocolEffectRecord<ENDPOINT,CONDITIONS,UNIT> - Class in ambit2.base.data.study
Extension of EffectRecord to be able to attach the protocol
ProtocolEffectRecord() - Constructor for class ambit2.base.data.study.ProtocolEffectRecord
 
ProtocolEffectRecord2SubstanceProperty - Class in ambit2.core.io.study
 
ProtocolEffectRecord2SubstanceProperty() - Constructor for class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
ProtocolEffectRecordMatrix<ENDPOINT,CONDITIONS,UNIT> - Class in ambit2.base.data.study
 
ProtocolEffectRecordMatrix() - Constructor for class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
ProtocolParameter - Class in ambit2.export.isa.v1_0.objects
ISA protocol parameter schema JSON-schema representing a parameter for a protocol (category declared in the investigation file) in the ISA model
ProtocolParameter() - Constructor for class ambit2.export.isa.v1_0.objects.ProtocolParameter
 
protocolParamLoc - Variable in class ambit2.export.isa.ISAExportConfig
 
protocolParamLocString - Variable in class ambit2.export.isa.ISAExportConfig
 
protocols - Variable in class ambit2.export.isa.v1_0.objects.Study
 
protocolType - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
ps - Variable in class ambit2.model.AbstractModel
 
ps - Variable in class ambit2.ui.table.BrowsableTableModel
 
ps_bitset - Variable in class ambit2.db.processors.FP1024Writer
 
ps_descriptorvalue_number - Variable in class ambit2.db.processors.ValueWriter
 
ps_descriptorvalue_string - Variable in class ambit2.db.processors.ValueWriter
 
ps_insertstring - Variable in class ambit2.db.processors.ValueWriter
 
ps_seekdataset - Variable in class ambit2.db.processors.RepositoryWriter
 
ps_structurebyid - Variable in class ambit2.db.RepositoryReader
 
ps_structures - Variable in class ambit2.db.RepositoryReader
 
pSAMPLING - Static variable in class ambit2.base.ro.I5CONSTANTS
 
psql - Variable in class ambit2.db.search.SQLFileQueryParams
 
pstring_batchExecutor - Variable in class ambit2.db.processors.ValueWriterNew
Prepared statements for writing string and numeric values into property_values table
pTESTMAT_FORM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
pThreshold - Variable in class ambit2.model.numeric.DataCoverage
 
pTYPE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
PUBCHEM_CID - Static variable in class ambit2.pubchem.PUGProcessor
 
PubchemCID - Class in ambit2.core.processors.structure.key
returns pubchem CID given the structure properties
PubchemCID() - Constructor for class ambit2.core.processors.structure.key.PubchemCID
 
PubchemFinder - Class in ambit2.pubchem
 
PubchemFinder(Template, AbstractFinder.MODE) - Constructor for class ambit2.pubchem.PubchemFinder
 
PubChemFingerprinter - Class in ambit2.descriptors.fingerprints
Generates a Pubchem fingerprint for a molecule.
PubChemFingerprinter() - Constructor for class ambit2.descriptors.fingerprints.PubChemFingerprinter
 
PubChemFingerprinterAmbitSmarts - Class in ambit2.descriptors.fingerprints
Reimplemented org.openscience.cdk.fingerprint.PubchemFingerprinter for performance reasons
PubChemFingerprinterAmbitSmarts() - Constructor for class ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts
 
PubChemFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
Wrapper for PubchemFingerprinter , implementing IMolecularDescriptor
PubChemFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.PubChemFingerprinterWrapper
 
PubChemRestFinder - Class in ambit2.pubchem.rest
 
PubChemRestFinder(Template, AbstractFinder.MODE, PUGRestRequest.COMPOUND_DOMAIN_INPUT) - Constructor for class ambit2.pubchem.rest.PubChemRestFinder
 
PubchemSID - Class in ambit2.core.processors.structure.key
returns pubchem SID given the structure properties
PubchemSID() - Constructor for class ambit2.core.processors.structure.key.PubchemSID
 
Public_name - Static variable in class ambit2.base.data.LiteratureEntry
 
Publication - Class in ambit2.export.isa.v1_0.objects
ISA investigation schema JSON-schema representing an investigation in the ISA model
Publication() - Constructor for class ambit2.export.isa.v1_0.objects.Publication
 
publications - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
publications - Variable in class ambit2.export.isa.v1_0.objects.Study
 
publicName - Variable in class ambit2.base.data.SubstanceRecord
 
publicReleaseDate - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
publicReleaseDate - Variable in class ambit2.export.isa.v1_0.objects.Study
 
pubMedID - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
pug - Variable in class ambit2.pubchem.EntrezSearchProcessor
 
PUGProcessor - Class in ambit2.pubchem
Queries Pubchem Power User Gateway.
PUGProcessor() - Constructor for class ambit2.pubchem.PUGProcessor
 
PUGREST_COMPOUND_URL - Static variable in class ambit2.pubchem.rest.PUGRestRequest
 
PUGREST_URL - Static variable in class ambit2.pubchem.rest.PUGRestRequest
 
PUGRestCompoundRequest - Class in ambit2.pubchem.rest
 
PUGRestCompoundRequest(PUGRestRequest.COMPOUND_DOMAIN_INPUT) - Constructor for class ambit2.pubchem.rest.PUGRestCompoundRequest
 
PUGRestCompoundRequest(PUGRestRequest.COMPOUND_DOMAIN_INPUT, PUGRestRequest.COMPOUND_DOMAIN_OUTPUT) - Constructor for class ambit2.pubchem.rest.PUGRestCompoundRequest
 
PUGRestImageRequest - Class in ambit2.pubchem.rest
 
PUGRestImageRequest() - Constructor for class ambit2.pubchem.rest.PUGRestImageRequest
 
PUGRestImageRequest.IMAGE_SIZE - Enum in ambit2.pubchem.rest
 
PUGRestImageRequest.RECORD_TYPE - Enum in ambit2.pubchem.rest
 
PUGRestRequest<R> - Class in ambit2.pubchem.rest
 
PUGRestRequest() - Constructor for class ambit2.pubchem.rest.PUGRestRequest
 
PUGRestRequest.COMPOUND_DOMAIN_INPUT - Enum in ambit2.pubchem.rest
 
PUGRestRequest.COMPOUND_DOMAIN_OPERATION - Enum in ambit2.pubchem.rest
 
PUGRestRequest.COMPOUND_DOMAIN_OUTPUT - Enum in ambit2.pubchem.rest
 
pugURL - Static variable in class ambit2.pubchem.PUGProcessor
 
put(String, VALUE) - Method in class ambit2.base.data.study.Params
 
put(OTDatasets) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
Adds datasets to the current one
put(OTDatasets) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
sends PUT request , adding datasets to the current one
put(Model) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
putAll(Map<? extends String, ? extends VALUE>) - Method in class ambit2.base.data.study.Params
 
putDataInObject(String, ISALocation, Object, boolean) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
Data is put into the Object using element and subElement information
putDouble(Double, ISALocation) - Method in interface ambit2.export.isa.base.IISADataMapper
 
putDouble(Double, ISALocation) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
putInteger(Integer, ISALocation) - Method in interface ambit2.export.isa.base.IISADataMapper
 
putInteger(Integer, ISALocation) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
putObject(Object, ISALocation) - Method in interface ambit2.export.isa.base.IISADataMapper
 
putObject(Object, ISALocation) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
putString(String, ISALocation) - Method in interface ambit2.export.isa.base.IISADataMapper
 
putString(String, ISALocation, boolean) - Method in interface ambit2.export.isa.base.IISADataMapper
 
putString(String, ISALocation) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
putString(String, ISALocation, boolean) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 

Q

q_addtobundle - Variable in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
q_composition - Variable in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
q_create - Variable in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
QA_ATTR_c - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_f - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_hac - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_hc - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_htc - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_is - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_mapNum - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_mw - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_n - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_not - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_ntc - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_r - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_rbc - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_src - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_tac - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_tbo - Static variable in class ambit2.sln.SLNConst
 
QA_ATTR_v - Static variable in class ambit2.sln.SLNConst
 
QA_COVERED_n - Static variable in class ambit2.sln.SLNConst
 
QA_COVERED_o - Static variable in class ambit2.sln.SLNConst
 
QA_COVERED_y - Static variable in class ambit2.sln.SLNConst
 
QB_ATTR_r - Static variable in class ambit2.sln.SLNConst
 
QB_ATTR_rbc - Static variable in class ambit2.sln.SLNConst
 
QB_ATTR_src - Static variable in class ambit2.sln.SLNConst
 
QB_ATTR_type - Static variable in class ambit2.sln.SLNConst
 
qe - Variable in class ambit2.db.search.structure.QueryAtomEnvironment
 
qe - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
qexec - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
QLabel - Class in ambit2.base.data
Quality label Q(experts) = (100*a+100*b +1) / (100*d + 10*c+1) 10 experts max labels OK,ProbablyOK,Unknown,ProbablyERROR,ERROR 1)automatic verification -> assigns OK, ? , Not OK 2)Expert verification (up to 10 experts) - assigns (a)OK(expert), (b) Almost OK (expert), (c) Almost Not OK (expert), (d) Not OK (expert)
QLabel() - Constructor for class ambit2.base.data.QLabel
 
QLabel(QLabel.QUALITY) - Constructor for class ambit2.base.data.QLabel
 
QLabel.QUALITY - Enum in ambit2.base.data
 
QMap<P extends Property> - Class in ambit2.db.simiparity.space
Quantitative SAS map header
QMap() - Constructor for class ambit2.db.simiparity.space.QMap
 
QMap(int) - Constructor for class ambit2.db.simiparity.space.QMap
 
QMap(ISourceDataset, P, double, double) - Constructor for class ambit2.db.simiparity.space.QMap
 
qmap - Variable in class ambit2.db.simiparity.space.QMapSpace
 
QMapSpace - Class in ambit2.db.simiparity.space
 
QMapSpace() - Constructor for class ambit2.db.simiparity.space.QMapSpace
 
QMapSpace(QMap) - Constructor for class ambit2.db.simiparity.space.QMapSpace
 
qNumber - Variable in class ambit2.db.processors.ValueWriterNew
Prepared statements for writing string and numeric values into property_values table
qProperty - Variable in class ambit2.db.processors.ValueWriterNew
 
QR_PREFIX - Variable in class ambit2.db.update.dataset.QueryCount
 
QSARModelException - Exception in ambit2.base.exceptions
Moved here for compatibility, since qsar package is removed from CDK > 1.3.4 Exception that is thrown by model routines when a problem has occured.
QSARModelException(String) - Constructor for exception ambit2.base.exceptions.QSARModelException
Constructs a new QSARModelException with the given message.
QSARModelException(String, Throwable) - Constructor for exception ambit2.base.exceptions.QSARModelException
 
QSARPOINT - Static variable in class ambit2.core.config.AmbitCONSTANTS
QSAR point
qString - Variable in class ambit2.db.processors.ValueWriterNew
 
QualityLabelWriter - Class in ambit2.db.processors.quality
 
QualityLabelWriter() - Constructor for class ambit2.db.processors.quality.QualityLabelWriter
 
QualityStatisticsProcessor - Class in ambit2.db.processors
 
QualityStatisticsProcessor() - Constructor for class ambit2.db.processors.QualityStatisticsProcessor
 
QualityValueWriter - Class in ambit2.db.processors.quality
 
QualityValueWriter() - Constructor for class ambit2.db.processors.quality.QualityValueWriter
 
qualityVerifier - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
queries - Variable in class ambit2.db.search.QueryCombined
 
queries - Variable in class ambit2.dbui.QueryStoredResultsEditor
 
query(String) - Method in class ambit2.base.processors.search.AbstractFinder
 
query(String) - Method in class ambit2.chebi.ChebiFinder
 
query - Variable in class ambit2.db.processors.ProcessorSetQueryScope
 
query - Variable in class ambit2.db.processors.ProcessorStructureRetrieval
 
query - Variable in class ambit2.db.processors.quality.QualityLabelWriter
 
query - Variable in class ambit2.db.processors.quality.QualityValueWriter
 
query - Variable in class ambit2.db.processors.RepositoryWriter
 
query - Variable in class ambit2.db.results.AmbitRows
 
query - Variable in class ambit2.db.search.property.FilteredCount
 
query - Variable in class ambit2.db.search.StoredQuery
 
query - Variable in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
query - Variable in class ambit2.db.search.structure.QueryFunctionalGroups
 
query - Variable in class ambit2.db.search.structure.QueryLookupStructure
 
query - Variable in class ambit2.db.search.structure.QuerySimilarityStructure
 
query - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
query - Variable in class ambit2.descriptors.FunctionalGroup
 
query(String) - Method in class ambit2.namestructure.Name2StructureFinder
 
query(String) - Method in class ambit2.pubchem.PubchemFinder
 
query(String) - Method in class ambit2.pubchem.rest.PubChemRestFinder
 
query - Variable in class ambit2.reactions.fragmentation.FragmentationRule
 
query(String) - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
query - Variable in class ambit2.rest.wrapper.WrappedService
 
query(String) - Method in class ambit2.search.AllSourcesFinder
 
query - Variable in class ambit2.smarts.IsomorphismTester
 
query - Variable in class ambit2.smarts.query.FastSmartsMatcher
 
query - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
query - Variable in class ambit2.tautomers.rules.CustomTautomerRegion
 
query_effectrecord - Variable in class ambit2.db.substance.processor.DBMatrixValueMarker
 
query_interpretation_result - Variable in class ambit2.db.substance.processor.DBMatrixValueMarker
 
query_property - Variable in class ambit2.db.processors.PropertyImporter
 
QueryAddTemplate - Class in ambit2.db.update.storedquery
 
QueryAddTemplate() - Constructor for class ambit2.db.update.storedquery.QueryAddTemplate
 
QueryAtomContainerToSLNContainer(IQueryAtomContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
QueryAtomEnvironment - Class in ambit2.db.search.structure
Similarity via atom environment matrix /query/similarity?search=c1ccccc1O&threshold=0.5&mode=ae
QueryAtomEnvironment() - Constructor for class ambit2.db.search.structure.QueryAtomEnvironment
 
QueryAtomEnvironment(QueryAtomEnvironment.q_modifier) - Constructor for class ambit2.db.search.structure.QueryAtomEnvironment
 
QueryAtomEnvironment.q_modifier - Enum in ambit2.db.search.structure
 
queryAtomToSLNAtom(IQueryAtom) - Method in class ambit2.sln.io.SLN2ChemObject
 
queryBondToSLNBond(IQueryBond) - Method in class ambit2.sln.io.SLN2ChemObject
 
QueryBrowser<T extends TableModel> - Class in ambit2.ui
 
QueryBrowser() - Constructor for class ambit2.ui.QueryBrowser
 
QueryBrowser(T) - Constructor for class ambit2.ui.QueryBrowser
 
QueryBrowser(T, Dimension) - Constructor for class ambit2.ui.QueryBrowser
 
QueryByIdentifierWithStructureFallback - Class in ambit2.db.search.structure
Calls findByProperty stored procedure
QueryByIdentifierWithStructureFallback() - Constructor for class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
QueryCachedResults<T> - Class in ambit2.db.cache
 
QueryCachedResults() - Constructor for class ambit2.db.cache.QueryCachedResults
 
QueryCachedResults(String, String, IStructureRecord) - Constructor for class ambit2.db.cache.QueryCachedResults
 
QueryCachedResultsBoolean - Class in ambit2.db.cache
Returns results of a previously executed query (e.g.
QueryCachedResultsBoolean() - Constructor for class ambit2.db.cache.QueryCachedResultsBoolean
 
QueryCachedResultsBoolean(String, String, IStructureRecord) - Constructor for class ambit2.db.cache.QueryCachedResultsBoolean
 
QueryChangeEvent<T> - Class in ambit2.db.results
 
QueryChangeEvent(Object, String, IQueryRetrieval<T>, IQueryRetrieval<T>) - Constructor for class ambit2.db.results.QueryChangeEvent
 
QueryChemicalEditor - Class in ambit2.dbui
 
QueryChemicalEditor() - Constructor for class ambit2.dbui.QueryChemicalEditor
 
QueryCombined<T> - Class in ambit2.db.search
Set of IQueryObject, combined with logical "and or logical "or".
QueryCombined() - Constructor for class ambit2.db.search.QueryCombined
 
QueryCombined.COMBINE - Enum in ambit2.db.search
 
QueryCombinedEditor - Class in ambit2.dbui
 
QueryCombinedEditor() - Constructor for class ambit2.dbui.QueryCombinedEditor
 
QueryCombinedStructure - Class in ambit2.db.search.structure
 
QueryCombinedStructure() - Constructor for class ambit2.db.search.structure.QueryCombinedStructure
 
QueryComplement - Class in ambit2.db.search.structure
Complement of the scope query
QueryComplement() - Constructor for class ambit2.db.search.structure.QueryComplement
 
queryCompounds - Static variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
QueryConsensus - Class in ambit2.db.search.qlabel
 
QueryConsensus() - Constructor for class ambit2.db.search.qlabel.QueryConsensus
 
QueryConsensus(IStructureRecord, String) - Constructor for class ambit2.db.search.qlabel.QueryConsensus
 
QueryCount<FACET extends net.idea.modbcum.i.facet.IFacet<String>> - Class in ambit2.db.update.dataset
Number of chemicals
QueryCount(String) - Constructor for class ambit2.db.update.dataset.QueryCount
 
QueryCountBundles - Class in ambit2.db.substance
 
QueryCountBundles(String) - Constructor for class ambit2.db.substance.QueryCountBundles
 
QueryCountChemicalInDataset - Class in ambit2.db.update.dataset
 
QueryCountChemicalInDataset(String) - Constructor for class ambit2.db.update.dataset.QueryCountChemicalInDataset
 
QueryCountDataset - Class in ambit2.db.update.dataset
 
QueryCountDataset(String) - Constructor for class ambit2.db.update.dataset.QueryCountDataset
 
QueryCountDatasetIntersection<FACET extends net.idea.modbcum.i.facet.IFacet<String>> - Class in ambit2.db.update.dataset
 
QueryCountDatasetIntersection(String) - Constructor for class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
QueryCountEndpoints<E extends EffectRecord<String,Object,String>> - Class in ambit2.db.substance
 
QueryCountEndpoints(String) - Constructor for class ambit2.db.substance.QueryCountEndpoints
 
QueryCountInterpretationResults - Class in ambit2.db.substance
 
QueryCountInterpretationResults(String) - Constructor for class ambit2.db.substance.QueryCountInterpretationResults
 
QueryCountModels - Class in ambit2.db.model
Number of models
QueryCountModels(String) - Constructor for class ambit2.db.model.QueryCountModels
 
QueryCountProperties - Class in ambit2.db.update.dataset
 
QueryCountProperties(String) - Constructor for class ambit2.db.update.dataset.QueryCountProperties
 
QueryCountProtocolApplications<F extends SubstanceByCategoryFacet> - Class in ambit2.db.substance
 
QueryCountProtocolApplications(String) - Constructor for class ambit2.db.substance.QueryCountProtocolApplications
 
QueryCountProtocolApplications(String, QueryCountProtocolApplications._mode_related) - Constructor for class ambit2.db.substance.QueryCountProtocolApplications
 
QueryCountProtocolApplications._mode_related - Enum in ambit2.db.substance
 
QueryCountSubstances - Class in ambit2.db.substance
 
QueryCountSubstances(String) - Constructor for class ambit2.db.substance.QueryCountSubstances
 
QueryCountSubstanceTypes - Class in ambit2.db.substance
 
QueryCountSubstanceTypes(String) - Constructor for class ambit2.db.substance.QueryCountSubstanceTypes
 
QueryCountValues - Class in ambit2.db.update.dataset
 
QueryCountValues(String) - Constructor for class ambit2.db.update.dataset.QueryCountValues
 
queryCreate - Variable in class ambit2.db.processors.AbstractUpdateProcessor
 
queryData - Static variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
QueryDataset - Class in ambit2.db.search.structure
src_dataset.name = ?
QueryDataset(SourceDataset) - Constructor for class ambit2.db.search.structure.QueryDataset
 
QueryDataset() - Constructor for class ambit2.db.search.structure.QueryDataset
 
QueryDataset(String) - Constructor for class ambit2.db.search.structure.QueryDataset
 
QueryDatasetByFeatures - Class in ambit2.db.update.dataset
 
QueryDatasetByFeatures() - Constructor for class ambit2.db.update.dataset.QueryDatasetByFeatures
 
QueryDatasetByFeatures(Property, StringCondition) - Constructor for class ambit2.db.update.dataset.QueryDatasetByFeatures
 
QueryDatasetByFeatures.c_feature - Enum in ambit2.db.update.dataset
 
QueryDatasetByID - Class in ambit2.db.search.structure
 
QueryDatasetByID(SourceDataset) - Constructor for class ambit2.db.search.structure.QueryDatasetByID
 
QueryDatasetByID() - Constructor for class ambit2.db.search.structure.QueryDatasetByID
 
QueryDatasetByID(Integer) - Constructor for class ambit2.db.search.structure.QueryDatasetByID
 
QueryDatasetEditor - Class in ambit2.dbui
 
QueryDatasetEditor() - Constructor for class ambit2.dbui.QueryDatasetEditor
 
queryDatasets - Static variable in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
queryDelete - Variable in class ambit2.db.processors.AbstractUpdateProcessor
 
QueryDeleteStructure - Class in ambit2.db.update.storedquery
 
QueryDeleteStructure(IStoredQuery, IStructureRecord) - Constructor for class ambit2.db.update.storedquery.QueryDeleteStructure
 
QueryDeleteStructure() - Constructor for class ambit2.db.update.storedquery.QueryDeleteStructure
 
QueryDeleteTemplate - Class in ambit2.db.update.storedquery
 
QueryDeleteTemplate() - Constructor for class ambit2.db.update.storedquery.QueryDeleteTemplate
 
QueryDistance - Class in ambit2.db.search.structure
Distance between two atoms, provided as symbols.
QueryDistance() - Constructor for class ambit2.db.search.structure.QueryDistance
 
QueryEditor<F,T,C extends net.idea.modbcum.i.IQueryCondition,ResultType,Q extends AbstractQuery<F,T,C,ResultType>> - Class in ambit2.dbui
 
QueryEditor() - Constructor for class ambit2.dbui.QueryEditor
 
QueryExactStructure - Class in ambit2.db.search.structure
Deprecated.
Convert to InChI and use QueryStructure
QueryExactStructure() - Constructor for class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
queryexec - Variable in class ambit2.db.processors.AbstractRepositoryWriter
 
queryExecutor - Variable in class ambit2.db.results.StoredQueryTableModel
 
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> - Class in ambit2.db.search
Executes arbitrary IQueryObject
QueryExecutor() - Constructor for class ambit2.db.search.QueryExecutor
 
QueryExperiment<T,C extends net.idea.modbcum.i.IQueryCondition,ResultType> - Class in ambit2.db.search
 
QueryExperiment() - Constructor for class ambit2.db.search.QueryExperiment
 
QueryField - Class in ambit2.db.search.structure
Search for a structure with property with given name and value
QueryField() - Constructor for class ambit2.db.search.structure.QueryField
//FASTER!!!!!! select idchemical,idstructure from structure join ( select distinct(s1.idchemical) from structure s1 join property_values using(idstructure) join property_string using (idvalue_string) join properties using(idproperty) where lower(value)='hexane' ) a using(idchemical) where preferred=1 limit 1 --even faster SELECT s1.idchemical, s1.idstructure, s1.preference,s1.type_structure,value,name,comments FROM structure s1 LEFT JOIN structure s2 ON s1.idchemical = s2.idchemical AND s1.preference > s2.preference join ( select distinct(idchemical),group_concat(distinct value SEPARATOR ';') as value,group_concat(distinct name) as name,group_concat(distinct comments) as comments from structure join property_values using(idstructure) join property_string using (idvalue_string) join properties using(idproperty) where lower(value) regexp '^benzene' ) a on a.idchemical=s1.idchemical where s2.idchemical is null;
queryField - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
 
QueryFieldAbstract<T,C extends net.idea.modbcum.i.IQueryCondition,NC extends net.idea.modbcum.i.IQueryCondition> - Class in ambit2.db.search.structure
 
QueryFieldAbstract() - Constructor for class ambit2.db.search.structure.QueryFieldAbstract
 
QueryFieldEditor - Class in ambit2.dbui
 
QueryFieldEditor() - Constructor for class ambit2.dbui.QueryFieldEditor
 
queryFieldExecutor - Variable in class ambit2.db.results.StoredQueryTableModel
 
QueryFieldMultiple - Class in ambit2.db.search.structure
 
QueryFieldMultiple() - Constructor for class ambit2.db.search.structure.QueryFieldMultiple
 
QueryFieldNumeric - Class in ambit2.db.search.structure
 
QueryFieldNumeric() - Constructor for class ambit2.db.search.structure.QueryFieldNumeric
 
QueryFieldNumeric(String, String, boolean, boolean, Property) - Constructor for class ambit2.db.search.structure.QueryFieldNumeric
 
QueryFieldNumericEditor - Class in ambit2.dbui
 
QueryFieldNumericEditor() - Constructor for class ambit2.dbui.QueryFieldNumericEditor
 
queryFields - Variable in class ambit2.db.results.StoredQueryTableModel
 
QueryFingerprints - Class in ambit2.db.update.fp
Expects 1024 bit fingerprint in the form of "0-0-0-0-0-20000000-0-0-0-0-0-0-0-0-0-10000000" (16x 64 bits)
QueryFingerprints() - Constructor for class ambit2.db.update.fp.QueryFingerprints
 
QueryFingerprints._order - Enum in ambit2.db.update.fp
 
queryFolder - Variable in class ambit2.db.update.storedquery.CreateStoredQuery
 
QueryFunctionalGroups - Class in ambit2.db.search.structure
 
QueryFunctionalGroups() - Constructor for class ambit2.db.search.structure.QueryFunctionalGroups
 
QueryFunctionalGroupsEditor - Class in ambit2.dbui
 
QueryFunctionalGroupsEditor() - Constructor for class ambit2.dbui.QueryFunctionalGroupsEditor
 
QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> - Class in ambit2.db.reporters
Generates report from a query with header at a top (e.g.
QueryHeaderReporter() - Constructor for class ambit2.db.reporters.QueryHeaderReporter
 
QueryInfo - Class in ambit2.db.search
TODO add a working test
QueryInfo() - Constructor for class ambit2.db.search.QueryInfo
 
QueryInfo2Query - Class in ambit2.db.processors
 
QueryInfo2Query() - Constructor for class ambit2.db.processors.QueryInfo2Query
 
QueryInfoEditor - Class in ambit2.dbui
 
QueryInfoEditor() - Constructor for class ambit2.dbui.QueryInfoEditor
 
queryKey - Variable in class ambit2.db.processors.PropertyImporter
 
queryKeysToString() - Method in class ambit2.smarts.Screening
 
QueryLookupStructure - Class in ambit2.db.search.structure
This is a wrapper around QueryStructure , allowing to use IStructureRecord as a parameter
QueryLookupStructure() - Constructor for class ambit2.db.search.structure.QueryLookupStructure
 
QueryLookupStructure(ExactStructureSearchMode) - Constructor for class ambit2.db.search.structure.QueryLookupStructure
 
QueryMetricRange - Class in ambit2.db.search.property
 
QueryMetricRange(IStoredQuery, Integer) - Constructor for class ambit2.db.search.property.QueryMetricRange
 
QueryMetricRange() - Constructor for class ambit2.db.search.property.QueryMetricRange
 
QueryMissingDescriptor - Class in ambit2.db.search.structure
reads structures, for each there are / or there are not (depending on getCondition) descriptors with given idname and reference title.
QueryMissingDescriptor() - Constructor for class ambit2.db.search.structure.QueryMissingDescriptor
 
QueryMissingDistances - Class in ambit2.db.search.structure
Reads structures without precalculated pairwise atom distances from the database.
QueryMissingDistances() - Constructor for class ambit2.db.search.structure.QueryMissingDistances
 
QueryMissingProperty - Class in ambit2.db.search.structure
 
QueryMissingProperty() - Constructor for class ambit2.db.search.structure.QueryMissingProperty
 
QueryModel - Class in ambit2.db.update.model
 
QueryModel(ModelQueryResults) - Constructor for class ambit2.db.update.model.QueryModel
 
queryMolecule - Variable in class ambit2.db.results.StoredQueryTableModel
 
queryName - Variable in class ambit2.db.cache.RetrieveStructureImagePath
 
queryName - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
queryNum - Variable in class ambit2.db.processors.RepositoryWriter
 
queryObject - Variable in class ambit2.rest.AbstractResource
 
QueryOntology - Class in ambit2.db.search.property
 
QueryOntology(Dictionary) - Constructor for class ambit2.db.search.property.QueryOntology
 
QueryOntology() - Constructor for class ambit2.db.search.property.QueryOntology
 
QueryPacketReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> - Class in ambit2.db.reporters
 
QueryPacketReporter(Profile<Property>, int) - Constructor for class ambit2.db.reporters.QueryPacketReporter
 
QueryPairwiseTanimoto - Class in ambit2.db.search.property
Generatise pairwise similarities between structures in given datasets
QueryPairwiseTanimoto() - Constructor for class ambit2.db.search.property.QueryPairwiseTanimoto
 
QueryPairwiseTanimotoAndProperty - Class in ambit2.db.search.property
Similar to QueryPairwiseTanimoto , but returns also property values
QueryPairwiseTanimotoAndProperty() - Constructor for class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
queryParams - Variable in class ambit2.db.search.SQLFileQueryParams
 
queryParams(String...) - Method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
 
queryPredictedFeatures - Static variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
QueryPrescreenBitSet - Class in ambit2.db.search.structure
First bitset is from structural keys, second from fingerprints
QueryPrescreenBitSet() - Constructor for class ambit2.db.search.structure.QueryPrescreenBitSet
 
QueryProperyReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<Property>,Output> - Class in ambit2.db.reporters
 
QueryProperyReporter() - Constructor for class ambit2.db.reporters.QueryProperyReporter
 
QueryQLabel - Class in ambit2.db.search.qlabel
 
QueryQLabel(AmbitUser, IStructureRecord) - Constructor for class ambit2.db.search.qlabel.QueryQLabel
 
QueryQLabel() - Constructor for class ambit2.db.search.qlabel.QueryQLabel
 
QueryQMap - Class in ambit2.db.simiparity.space
Reads QMap
QueryQMap() - Constructor for class ambit2.db.simiparity.space.QueryQMap
 
QueryQMapSpace - Class in ambit2.db.simiparity.space
Reads QMapSpace
QueryQMapSpace() - Constructor for class ambit2.db.simiparity.space.QueryQMapSpace
 
QueryQMapStructures - Class in ambit2.db.simiparity.space
 
QueryQMapStructures(SourceDataset) - Constructor for class ambit2.db.simiparity.space.QueryQMapStructures
 
QueryQMapStructures() - Constructor for class ambit2.db.simiparity.space.QueryQMapStructures
 
QueryQMapStructures(Integer) - Constructor for class ambit2.db.simiparity.space.QueryQMapStructures
 
QueryScopeEditor - Class in ambit2.dbui
 
QueryScopeEditor() - Constructor for class ambit2.dbui.QueryScopeEditor
 
QuerySequenceElement - Class in ambit2.smarts
 
QuerySequenceElement() - Constructor for class ambit2.smarts.QuerySequenceElement
 
QuerySimilarity<F,T,C extends net.idea.modbcum.i.IQueryCondition> - Class in ambit2.db.search.structure
 
QuerySimilarity() - Constructor for class ambit2.db.search.structure.QuerySimilarity
 
QuerySimilarityBitset - Class in ambit2.db.search.structure
Tanimoto similarity of BitSet.
QuerySimilarityBitset() - Constructor for class ambit2.db.search.structure.QuerySimilarityBitset
 
QuerySimilarityEditor - Class in ambit2.dbui
 
QuerySimilarityEditor() - Constructor for class ambit2.dbui.QuerySimilarityEditor
 
QuerySimilarityStructure - Class in ambit2.db.search.structure
 
QuerySimilarityStructure() - Constructor for class ambit2.db.search.structure.QuerySimilarityStructure
 
QuerySMARTS - Class in ambit2.db.search.structure
Select structures by querying fungroups table by smarts
QuerySMARTS() - Constructor for class ambit2.db.search.structure.QuerySMARTS
 
QuerySMARTS(IChemObjectBuilder) - Constructor for class ambit2.db.search.structure.QuerySMARTS
 
QuerySmartsEditor - Class in ambit2.dbui
An editor for QuerySMARTS
QuerySmartsEditor() - Constructor for class ambit2.dbui.QuerySmartsEditor
 
QuerySmartsEditor(IChemObjectBuilder) - Constructor for class ambit2.dbui.QuerySmartsEditor
 
querySmiles - Variable in class ambit2.db.processors.quality.QualityLabelWriter
 
QuerySmilesByID - Class in ambit2.db.search
 
QuerySmilesByID() - Constructor for class ambit2.db.search.QuerySmilesByID
 
QuerySmilesByID(IStructureRecord) - Constructor for class ambit2.db.search.QuerySmilesByID
 
QuerySmilesByID(int) - Constructor for class ambit2.db.search.QuerySmilesByID
 
QuerySmilesByID(int, int) - Constructor for class ambit2.db.search.QuerySmilesByID
 
QueryStatisticsProcessor - Class in ambit2.db.processors
 
QueryStatisticsProcessor() - Constructor for class ambit2.db.processors.QueryStatisticsProcessor
 
QueryStaXReporter<T,Q extends net.idea.modbcum.i.IQueryRetrieval<T>,R extends AbstractStaxRDFWriter<T,T>> - Class in ambit2.rest
TODO replace with modbcum class same name
QueryStaXReporter(String, Request) - Constructor for class ambit2.rest.QueryStaXReporter
 
QueryStoredResults - Class in ambit2.db.search.structure
 
QueryStoredResults() - Constructor for class ambit2.db.search.structure.QueryStoredResults
 
QueryStoredResults(IStoredQuery) - Constructor for class ambit2.db.search.structure.QueryStoredResults
 
QueryStoredResultsByName - Class in ambit2.db.search.structure
Retrieve structure collections from query table by name and folder (sessions table)
QueryStoredResultsByName() - Constructor for class ambit2.db.search.structure.QueryStoredResultsByName
 
QueryStoredResultsByName(IStoredQuery) - Constructor for class ambit2.db.search.structure.QueryStoredResultsByName
 
QueryStoredResultsEditor - Class in ambit2.dbui
 
QueryStoredResultsEditor() - Constructor for class ambit2.dbui.QueryStoredResultsEditor
 
queryStringStartsWith - Variable in class ambit2.dbui.QueryFieldEditor
 
QueryStructure - Class in ambit2.db.search.structure
Search for smiles, inchi, formula
QueryStructure() - Constructor for class ambit2.db.search.structure.QueryStructure
 
QueryStructureByID - Class in ambit2.db.search.structure
Selects a structure by idstructure
QueryStructureByID() - Constructor for class ambit2.db.search.structure.QueryStructureByID
 
QueryStructureByID(IStructureRecord) - Constructor for class ambit2.db.search.structure.QueryStructureByID
 
QueryStructureByID(int) - Constructor for class ambit2.db.search.structure.QueryStructureByID
 
QueryStructureByID(int, int) - Constructor for class ambit2.db.search.structure.QueryStructureByID
 
QueryStructureByProperty<Q extends AbstractStructureQuery> - Class in ambit2.db.search.structure.byproperty
 
QueryStructureByProperty() - Constructor for class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
QueryStructureByPropertyInCompounds - Class in ambit2.db.search.structure.byproperty
 
QueryStructureByPropertyInCompounds() - Constructor for class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds
 
QueryStructureByPropertyInDataset - Class in ambit2.db.search.structure.byproperty
 
QueryStructureByPropertyInDataset() - Constructor for class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset
 
QueryStructureByQuality - Class in ambit2.db.search.structure
 
QueryStructureByQuality() - Constructor for class ambit2.db.search.structure.QueryStructureByQuality
 
QueryStructureByQuality(QLabel) - Constructor for class ambit2.db.search.structure.QueryStructureByQuality
 
QueryStructureByQuality(QLabel.QUALITY) - Constructor for class ambit2.db.search.structure.QueryStructureByQuality
 
QueryStructureByQualityEditor - Class in ambit2.dbui
 
QueryStructureByQualityEditor() - Constructor for class ambit2.dbui.QueryStructureByQualityEditor
 
QueryStructureByQualityPairLabel - Class in ambit2.db.search.structure
 
QueryStructureByQualityPairLabel() - Constructor for class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
QueryStructureByQualityPairLabel(ConsensusLabel.CONSENSUS_LABELS) - Constructor for class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
QueryStructureByQualityPairLabel(String) - Constructor for class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
QueryStructureByValueQuality - Class in ambit2.db.search.structure
 
QueryStructureByValueQuality() - Constructor for class ambit2.db.search.structure.QueryStructureByValueQuality
 
QueryStructureByValueQuality(QLabel) - Constructor for class ambit2.db.search.structure.QueryStructureByValueQuality
 
QueryStructureByValueQuality(QLabel.QUALITY) - Constructor for class ambit2.db.search.structure.QueryStructureByValueQuality
 
QueryStructureByValueQualityEditor - Class in ambit2.dbui
 
QueryStructureByValueQualityEditor() - Constructor for class ambit2.dbui.QueryStructureByValueQualityEditor
 
QueryStructurePairs<Dataset1,Dataset2> - Class in ambit2.db.search.structure.pairwise
returns idstructure of two molecules
QueryStructurePairs() - Constructor for class ambit2.db.search.structure.pairwise.QueryStructurePairs
 
QueryStructurePairsDataset - Class in ambit2.db.search.structure.pairwise
Selects a structure by idstructure
QueryStructurePairsDataset() - Constructor for class ambit2.db.search.structure.pairwise.QueryStructurePairsDataset
 
QueryStructurePairsMixed - Class in ambit2.db.search.structure.pairwise
 
QueryStructurePairsMixed() - Constructor for class ambit2.db.search.structure.pairwise.QueryStructurePairsMixed
 
QueryStructurePairsRDataset - Class in ambit2.db.search.structure.pairwise
 
QueryStructurePairsRDataset() - Constructor for class ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset
 
QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> - Class in ambit2.db.reporters
Parent class for all reporters working with structure queries.
QueryStructureReporter() - Constructor for class ambit2.db.reporters.QueryStructureReporter
 
QueryStructuresByPropertyInResults - Class in ambit2.db.search.structure.byproperty
 
QueryStructuresByPropertyInResults() - Constructor for class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults
 
QueryStructureType - Class in ambit2.db.search.structure
 
QueryStructureType() - Constructor for class ambit2.db.search.structure.QueryStructureType
 
QueryStructureType(IStructureRecord.STRUC_TYPE) - Constructor for class ambit2.db.search.structure.QueryStructureType
 
QueryStrucType - Class in ambit2.db.search.structure
 
QueryStrucType() - Constructor for class ambit2.db.search.structure.QueryStrucType
 
QueryStrucType(IStructureRecord.STRUC_TYPE) - Constructor for class ambit2.db.search.structure.QueryStrucType
 
QueryStrucType(IStructureRecord.STRUC_TYPE[]) - Constructor for class ambit2.db.search.structure.QueryStrucType
 
QuerySupport<Target,Result> - Class in ambit2.pubchem
Executes a query.
QuerySupport() - Constructor for class ambit2.pubchem.QuerySupport
 
QueryTemplateReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<Property>> - Class in ambit2.db.reporters
Adds Properties into a Template
QueryTemplateReporter(Template) - Constructor for class ambit2.db.reporters.QueryTemplateReporter
 
queryUpdate - Variable in class ambit2.db.processors.AbstractUpdateProcessor
 
QueryUser - Class in ambit2.db.search
Searches in users table
QueryUser(String) - Constructor for class ambit2.db.search.QueryUser
 
QueryUser() - Constructor for class ambit2.db.search.QueryUser
 
queryValueCaseInsensitive - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
 
queryValueCaseInsensitive - Static variable in class ambit2.db.search.structure.QueryFieldMultiple
 
queryValueCaseSensitive - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
 
queryValueCaseSensitive - Static variable in class ambit2.db.search.structure.QueryFieldMultiple
 
quickFindEquivalentTerminalHAtoms() - Method in class ambit2.smarts.EquivalenceTester
 
QuickImportBatchProcessor - Class in ambit2.db.processors
 
QuickImportBatchProcessor(File) - Constructor for class ambit2.db.processors.QuickImportBatchProcessor
 
QuickImportBatchProcessor(File, boolean) - Constructor for class ambit2.db.processors.QuickImportBatchProcessor
 
QuotedTokenizer - Class in ambit2.core.io
The QuotedTokenizer class is used to break a string into simple tokens or quoted tokens.
QuotedTokenizer(String, char) - Constructor for class ambit2.core.io.QuotedTokenizer
Constructs a tokenizer for the specified string.
qx - Variable in class ambit2.db.substance.processor.DBBundleStudyWriter
 

R

r - Variable in class ambit2.core.io.pdb.RawIteratingPDBReader
 
r - Variable in class ambit2.core.io.RawIteratingMOLReader
 
r - Variable in class ambit2.core.io.RawIteratingSDFReader
 
r - Variable in class ambit2.core.io.RawIteratingWrapper
 
R - Variable in class ambit2.domain.stats.transforms.densityestimation.Kernel
 
range - Variable in class ambit2.base.data.PropertyStats
 
Range<T extends Comparable<T>> - Class in ambit2.base.data
 
Range() - Constructor for class ambit2.base.data.Range
 
Range(T) - Constructor for class ambit2.base.data.Range
 
Range(T, T) - Constructor for class ambit2.base.data.Range
 
RangeProfile - Class in ambit2.reactions.generator.score.components
 
RangeProfile() - Constructor for class ambit2.reactions.generator.score.components.RangeProfile
 
rank - Variable in class ambit2.structure2name.components.AbstractComponent
 
RankingRule - Class in ambit2.tautomers
 
RankingRule() - Constructor for class ambit2.tautomers.RankingRule
 
rankingRule - Variable in class ambit2.tautomers.Rule
 
rankingRules - Variable in class ambit2.tautomers.KnowledgeBase
 
rankingRules - Static variable in class ambit2.tautomers.PredefinedKnowledgeBase
 
RawIteratingCSVReader - Class in ambit2.core.io
CSV parser implemented using CSVParser
RawIteratingCSVReader(Reader) - Constructor for class ambit2.core.io.RawIteratingCSVReader
 
RawIteratingCSVReader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.RawIteratingCSVReader
 
RawIteratingCSVReader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.RawIteratingCSVReader
 
RawIteratingCSVReader(InputStream, CSVFormat) - Constructor for class ambit2.core.io.RawIteratingCSVReader
 
RawIteratingCSVReader(Reader, CSVFormat) - Constructor for class ambit2.core.io.RawIteratingCSVReader
 
RawIteratingFolderReader - Class in ambit2.core.io
 
RawIteratingFolderReader(File[]) - Constructor for class ambit2.core.io.RawIteratingFolderReader
 
RawIteratingFolderReader.FileNameMode - Enum in ambit2.core.io
 
RawIteratingMOLReader - Class in ambit2.core.io
 
RawIteratingMOLReader(Reader) - Constructor for class ambit2.core.io.RawIteratingMOLReader
 
RawIteratingPDBReader - Class in ambit2.core.io.pdb
 
RawIteratingPDBReader(Reader) - Constructor for class ambit2.core.io.pdb.RawIteratingPDBReader
 
RawIteratingReader<T> - Class in ambit2.core.io
 
RawIteratingReader(Reader) - Constructor for class ambit2.core.io.RawIteratingReader
 
RawIteratingSDFReader - Class in ambit2.core.io
 
RawIteratingSDFReader(Reader) - Constructor for class ambit2.core.io.RawIteratingSDFReader
 
RawIteratingWrapper<R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader> - Class in ambit2.core.io
 
RawIteratingWrapper(R) - Constructor for class ambit2.core.io.RawIteratingWrapper
 
rCRYSTALLINE_PHASE_BRAVAIS_LATTICE - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rCRYSTALLINE_PHASE_COMMON_NAME - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rCRYSTALLINE_PHASE_CRYSTAL_SYSTEM - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rCRYSTALLINE_PHASE_CRYSTGRPH_PLANES - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rCRYSTALLINE_PHASE_POINT_GROUP - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rCRYSTALLINE_PHASE_SPACE_GROUP - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rDECOMPOSITION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rDegradation - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rDegradationRateConstant - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rdf - Static variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
rdf_writer - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
RDFAbstractCompoundIterator<COMPOUND,PROPERTY> - Class in ambit2.rest.rdf.sparql
 
RDFAbstractCompoundIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
RDFAbstractCompoundIterator(Reference, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
RDFAbstractCompoundIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
RDFAbstractCompoundIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
RDFAbstractCompoundIterator(Model, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
RDFAbstractFeatureIterator<PROPERTY> - Class in ambit2.rest.legacy
Deprecated.
RDFAbstractFeatureIterator(Representation, MediaType) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator(Reference, String) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator(InputStream, MediaType) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator(Model, String) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator(Model) - Constructor for class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
RDFAbstractFeatureIterator<PROPERTY> - Class in ambit2.rest.rdf.sparql
Parses an OpenTox RDF via SPAQRL query and iterates over property instances.
RDFAbstractFeatureIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAbstractFeatureIterator(Reference, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAbstractFeatureIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAbstractFeatureIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAbstractFeatureIterator(Model, String) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAbstractFeatureIterator(Model) - Constructor for class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
RDFAlgorithmIterator - Class in ambit2.rest.rdf
Parses RDF representation of Algorithm
RDFAlgorithmIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFAlgorithmIterator
 
RDFAlgorithmIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFAlgorithmIterator
 
RDFAlgorithmIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFAlgorithmIterator
 
RDFAlgorithmIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFAlgorithmIterator
 
RDFAlgorithmIterator(OntModel) - Constructor for class ambit2.rest.rdf.RDFAlgorithmIterator
 
RDFBatchParser<Item> - Class in ambit2.rest
Parent class for all RDF parsers
RDFBatchParser(String, String) - Constructor for class ambit2.rest.RDFBatchParser
 
RDFBookmarkIterator - Class in ambit2.rest.rdf
 
RDFBookmarkIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFBookmarkIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFBookmarkIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFBookmarkIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFBookmarkIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFBookmarkIterator(Model) - Constructor for class ambit2.rest.rdf.RDFBookmarkIterator
 
RDFCompoundIterator - Class in ambit2.rest.rdf.sparql
 
RDFCompoundIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
RDFCompoundIterator(Reference, String) - Constructor for class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
RDFCompoundIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
RDFCompoundIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
RDFCompoundIterator(OntModel, String) - Constructor for class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
RDFDataEntryIterator<Item,Feature> - Class in ambit2.rest.rdf
 
RDFDataEntryIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFDataEntryIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFDataEntryIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFDataEntryIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFDataEntryIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFDataEntryIterator(Model) - Constructor for class ambit2.rest.rdf.RDFDataEntryIterator
 
RDFFeatureIterator - Class in ambit2.rest.rdf.sparql
 
RDFFeatureIterator(Reference, String) - Constructor for class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
RDFFeatureIterator(Model) - Constructor for class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
RDFFeaturesIterator - Class in ambit2.rest.legacy
Deprecated.
RDFFeaturesIterator(String, String) - Constructor for class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
RDFFeaturesIterator(Reference, String) - Constructor for class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
RDFFileWriter - Class in ambit2.rest.dataset
 
RDFFileWriter(File, Reference, Template) - Constructor for class ambit2.rest.dataset.RDFFileWriter
 
rdfFileWriter - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
RDFInstancesIterator - Class in ambit2.rest.rdf
 
RDFInstancesIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesIterator(Model) - Constructor for class ambit2.rest.rdf.RDFInstancesIterator
 
RDFInstancesParser - Class in ambit2.rest.dataset
Reads dataset into weka instances
RDFInstancesParser(String, String) - Constructor for class ambit2.rest.dataset.RDFInstancesParser
 
RDFMetaDatasetIterator<M extends ISourceDataset> - Class in ambit2.rest.rdf
Iterates over SourceDataset
RDFMetaDatasetIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFMetaDatasetIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFMetaDatasetIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFMetaDatasetIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFMetaDatasetIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFMetaDatasetIterator(Model) - Constructor for class ambit2.rest.rdf.RDFMetaDatasetIterator
 
RDFModelIterator<T,TrainingInstances extends T,TestInstances extends T,Content> - Class in ambit2.rest.rdf
Parses RDF representation of a OpenTox Model ModelQueryResults
RDFModelIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFModelIterator
 
RDFModelIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFModelIterator
 
RDFModelIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFModelIterator
 
RDFModelIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFModelIterator
 
RDFModelIterator(OntModel) - Constructor for class ambit2.rest.rdf.RDFModelIterator
 
RDFObjectIterator<Item> - Class in ambit2.rest.rdf
Iterates over objects of a specified OT.class TODO make use of http://jena.sourceforge.net/ARP/standalone.html
RDFObjectIterator(Representation, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
RDFObjectIterator(Reference, String, String) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
RDFObjectIterator(Reference, MediaType, String, String) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
RDFObjectIterator(InputStream, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
RDFObjectIterator(Model, String, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
RDFObjectIterator(Model, String) - Constructor for class ambit2.rest.rdf.RDFObjectIterator
 
rdfObjectIterator - Variable in class ambit2.rest.RDFBatchParser
 
RDFPropertyIterator - Class in ambit2.rest.rdf
Parses RDF representation of a Feature Property
RDFPropertyIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFPropertyIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFPropertyIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFPropertyIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFPropertyIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFPropertyIterator(Model) - Constructor for class ambit2.rest.rdf.RDFPropertyIterator
 
RDFReferenceIterator - Class in ambit2.rest.rdf
Parses RDF representatiion of LiteratureEntry
RDFReferenceIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFReferenceIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFReferenceIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFReferenceIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFReferenceIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFReferenceIterator(Model) - Constructor for class ambit2.rest.rdf.RDFReferenceIterator
 
RDFResourceIterator - Class in ambit2.rest.rdf
 
RDFResourceIterator(OntModel, String) - Constructor for class ambit2.rest.rdf.RDFResourceIterator
 
rdfs - Static variable in class ambit2.rest.substance.SubstanceRecordStaxWriter
 
RDFSparqlIterator<Item> - Class in ambit2.rest.rdf.sparql
Abstract class to iterate over OpenTox objects in RDF model.
RDFSparqlIterator(Representation, MediaType, String, String) - Constructor for class ambit2.rest.rdf.sparql.RDFSparqlIterator
OpenTox object iterator - reads restlet representation
RDFSparqlIterator(Reference, String, String) - Constructor for class ambit2.rest.rdf.sparql.RDFSparqlIterator
OpenTox object iterator - reads RDF, assumes application/rdf+xml
RDFSparqlIterator(Reference, MediaType, String, String) - Constructor for class ambit2.rest.rdf.sparql.RDFSparqlIterator
OpenTox object iterator - reads RDF representation , given a reference ad mime type
RDFSparqlIterator(InputStream, MediaType, String) - Constructor for class ambit2.rest.rdf.sparql.RDFSparqlIterator
OpenTox object iterator over input stream
RDFSparqlIterator(Model, String) - Constructor for class ambit2.rest.rdf.sparql.RDFSparqlIterator
Allows to initialize the iterator over existing model
RDFStructuresIterator - Class in ambit2.rest.rdf
Parses RDF representation of OpenTox dataset into IStructureRecord
RDFStructuresIterator(Representation, MediaType) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresIterator(Reference, String) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresIterator(Reference, MediaType, String) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresIterator(InputStream, MediaType) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresIterator(Model, StmtIterator) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresIterator(Model) - Constructor for class ambit2.rest.rdf.RDFStructuresIterator
 
RDFStructuresReader - Class in ambit2.rest.dataset
Reads RDF representation of a dataset and converts it into iterator of IStructureRecord
RDFStructuresReader(String, String) - Constructor for class ambit2.rest.dataset.RDFStructuresReader
 
RDFTermsSubstance - Enum in ambit2.rest.substance
 
rdfWriter() - Method in class ambit2.rest.DBConnection
 
react(IAtomContainer) - Method in class ambit2.reactions.reactor.Reactor
 
reactant - Variable in class ambit2.smarts.SMIRKSReaction
 
reactantCLG - Variable in class ambit2.smarts.SMIRKSReaction
 
reactantFlags - Variable in class ambit2.smarts.SMIRKSReaction
 
reactantRecursiveAtoms - Variable in class ambit2.smarts.SMIRKSReaction
 
reactants - Variable in class ambit2.reactions.Reaction
 
reactants - Variable in class ambit2.reactions.retrosynth.RetroSynthStep
 
reactants - Variable in class ambit2.smarts.SMIRKSReaction
 
reactantsSmarts - Variable in class ambit2.smarts.SMIRKSReaction
 
reactChiralAtom - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
reactChirality - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
reactDBAt1 - Variable in class ambit2.smarts.StereoDBTransformation
 
reactDBAt2 - Variable in class ambit2.smarts.StereoDBTransformation
 
reactDBStereo - Variable in class ambit2.smarts.StereoDBTransformation
 
reaction - Variable in class ambit2.reactions.GenericReactionInstance
 
Reaction - Class in ambit2.reactions
 
Reaction() - Constructor for class ambit2.reactions.Reaction
 
reaction - Variable in class ambit2.reactions.reactor.ReactorInfoPack
 
reaction - Variable in class ambit2.reactions.rules.RetroSynthRule
 
ReactionAtomMapping - Class in ambit2.reactions.mapping
 
ReactionAtomMapping() - Constructor for class ambit2.reactions.mapping.ReactionAtomMapping
 
reactionCenterComplexityMethod - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
reactionCenterComplexityScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
reactionCenterComplexityWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
reactionCenterIndices - Variable in class ambit2.reactions.GenericReaction
 
reactionCenterPositionScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
reactionCenterPositionWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
reactionCenterScoreFunction - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
reactionClass - Variable in class ambit2.reactions.GenericReaction
 
reactionClass - Variable in class ambit2.reactions.Reaction
 
reactionClass - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
reactionClassScores - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
ReactionConst - Class in ambit2.reactions
 
ReactionConst() - Constructor for class ambit2.reactions.ReactionConst
 
ReactionData - Class in ambit2.reactions.sets
 
ReactionData() - Constructor for class ambit2.reactions.sets.ReactionData
 
ReactionDataBase - Class in ambit2.reactions
 
ReactionDataBase() - Constructor for class ambit2.reactions.ReactionDataBase
 
ReactionDataBase(String) - Constructor for class ambit2.reactions.ReactionDataBase
 
ReactionDataBase(String, Map<String, Integer>) - Constructor for class ambit2.reactions.ReactionDataBase
 
ReactionDataBase(String, Map<String, Integer>, int) - Constructor for class ambit2.reactions.ReactionDataBase
 
ReactionDataBase(List<String>) - Constructor for class ambit2.reactions.ReactionDataBase
 
reactionDataBase - Variable in class ambit2.reactions.reactor.Reactor
 
ReactionDataObject() - Constructor for class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
ReactionGroup - Class in ambit2.reactions.sets
 
ReactionGroup() - Constructor for class ambit2.reactions.sets.ReactionGroup
 
ReactionGroupCondition - Class in ambit2.reactions.rules.conditions
 
ReactionGroupCondition(ReactionGroupCondition.RGConditionType, String, SmartsParser, IsomorphismTester) - Constructor for class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
ReactionGroupCondition.RGConditionType - Enum in ambit2.reactions.rules.conditions
 
ReactionKnowledgeBase - Class in ambit2.reactions.retrosynth
 
ReactionKnowledgeBase() - Constructor for class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
ReactionKnowledgeBase(String) - Constructor for class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
ReactionParser - Class in ambit2.reactions.rules
 
ReactionParser() - Constructor for class ambit2.reactions.rules.ReactionParser
 
reactionPathToString(IAtomContainer, boolean) - Method in class ambit2.reactions.reactor.Reactor
 
ReactionReadUtils - Class in ambit2.reactions.io
 
ReactionReadUtils() - Constructor for class ambit2.reactions.io.ReactionReadUtils
 
ReactionReadUtils.ReactionDataObject - Class in ambit2.reactions.io
 
reactionScore - Variable in class ambit2.reactions.GenericReactionInstance
 
ReactionScore - Class in ambit2.reactions.rules.scores
 
ReactionScore() - Constructor for class ambit2.reactions.rules.scores.ReactionScore
 
reactionScore - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScore
 
reactionScoreSchema - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
ReactionScoreSchema - Class in ambit2.reactions.rules.scores
 
ReactionScoreSchema() - Constructor for class ambit2.reactions.rules.scores.ReactionScoreSchema
 
reactionScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
ReactionSearch - Class in ambit2.smarts.smirks
 
ReactionSearch() - Constructor for class ambit2.smarts.smirks.ReactionSearch
 
ReactionSequence - Class in ambit2.reactions.retrosynth
 
ReactionSequence() - Constructor for class ambit2.reactions.retrosynth.ReactionSequence
 
ReactionSequence.InchiEntry - Class in ambit2.reactions.retrosynth
 
ReactionSequence.MoleculeStatus - Enum in ambit2.reactions.retrosynth
 
ReactionSequence.SortingMethod - Enum in ambit2.reactions.retrosynth
 
ReactionSequenceLevel - Class in ambit2.reactions.retrosynth
 
ReactionSequenceLevel() - Constructor for class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
ReactionSequenceScore - Class in ambit2.reactions.rules.scores
 
ReactionSequenceScore() - Constructor for class ambit2.reactions.rules.scores.ReactionSequenceScore
 
ReactionSequenceScoreSchema - Class in ambit2.reactions.rules.scores
 
ReactionSequenceScoreSchema() - Constructor for class ambit2.reactions.rules.scores.ReactionSequenceScoreSchema
 
reactionSequenceScoreSchema - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
ReactionSequenceStep - Class in ambit2.reactions.retrosynth
 
ReactionSequenceStep() - Constructor for class ambit2.reactions.retrosynth.ReactionSequenceStep
 
ReactionSet - Class in ambit2.reactions.sets
 
ReactionSet() - Constructor for class ambit2.reactions.sets.ReactionSet
 
reactionType - Variable in class ambit2.reactions.GenericReaction
 
ReactionWriteUtils - Class in ambit2.reactions.io
 
ReactionWriteUtils() - Constructor for class ambit2.reactions.io.ReactionWriteUtils
 
reactLigand1 - Variable in class ambit2.smarts.StereoDBTransformation
 
reactLigand2 - Variable in class ambit2.smarts.StereoDBTransformation
 
reactLigands - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
reactNext(int) - Method in class ambit2.reactions.reactor.Reactor
 
Reactor - Class in ambit2.reactions.reactor
 
Reactor() - Constructor for class ambit2.reactions.reactor.Reactor
 
reactor - Variable in class ambit2.reactions.reactor.ReactorInfoPack
 
ReactorCli - Class in ambit2.reactions.cli
 
ReactorCli() - Constructor for class ambit2.reactions.cli.ReactorCli
 
reactorConfigFile - Variable in class ambit2.reactions.cli.ReactorCli
 
ReactorConsole - Class in ambit2.reactions.reactor
 
ReactorConsole() - Constructor for class ambit2.reactions.reactor.ReactorConsole
 
ReactorDescriptorSolver - Class in ambit2.reactions.reactor
 
ReactorDescriptorSolver() - Constructor for class ambit2.reactions.reactor.ReactorDescriptorSolver
 
ReactorInfoPack - Class in ambit2.reactions.reactor
 
ReactorInfoPack() - Constructor for class ambit2.reactions.reactor.ReactorInfoPack
 
ReactorNode - Class in ambit2.reactions.reactor
 
ReactorNode() - Constructor for class ambit2.reactions.reactor.ReactorNode
 
ReactorNode.State - Enum in ambit2.reactions.reactor
 
reactorNodes - Variable in class ambit2.reactions.reactor.Reactor
 
reactorResult - Variable in class ambit2.reactions.reactor.Reactor
 
ReactorResult - Class in ambit2.reactions.reactor
 
ReactorResult() - Constructor for class ambit2.reactions.reactor.ReactorResult
 
ReactorStrategy - Class in ambit2.reactions.reactor
 
ReactorStrategy() - Constructor for class ambit2.reactions.reactor.ReactorStrategy
 
ReactorStrategy(File) - Constructor for class ambit2.reactions.reactor.ReactorStrategy
 
reactTerminal1 - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
reactTerminal2 - Variable in class ambit2.smarts.StereoChiralAtTransformation
 
read(IChemObject) - Method in class ambit2.core.io.DelimitedFileReader
 
read(IChemObject) - Method in class ambit2.core.io.MDLReader
Takes an object which subclasses IChemObject, e.g.
read(char[], int, int) - Method in class ambit2.core.io.MultiNewlineFilterReader
 
read(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
read(IChemObject) - Method in class ambit2.mopac.Mopac7Reader
 
read(InputStream) - Method in class ambit2.pubchem.rest.PUGRestCompoundRequest
 
read(InputStream) - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
read(String) - Method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
read(String, Hashtable<String, String>) - Method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
read() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
read(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
read(InputStream) - Method in class ambit2.search.chemidplus.AbstractSearchRequest
 
read(InputStream) - Method in class ambit2.search.chemidplus.ChemIdPlusRequest
 
read(InputStream) - Method in class ambit2.search.csls.CSLSImageRequest
 
read(InputStream) - Method in class ambit2.search.csls.CSLSStringRequest
 
read(InputStream) - Method in class ambit2.search.opentox.OpenToxRequest
 
read_structurebyid - Static variable in class ambit2.db.RepositoryReader
 
read_structures - Static variable in class ambit2.db.RepositoryReader
 
ReadAnnotation - Class in ambit2.db.update.bookmark
 
ReadAnnotation(String) - Constructor for class ambit2.db.update.bookmark.ReadAnnotation
 
readAttributes() - Method in class ambit2.core.io.ToXMLReaderSimple
 
ReadBookmark - Class in ambit2.db.update.bookmark
Bookmark
ReadBookmark(Integer) - Constructor for class ambit2.db.update.bookmark.ReadBookmark
 
ReadBookmark(Integer, Bookmark) - Constructor for class ambit2.db.update.bookmark.ReadBookmark
 
ReadBookmark() - Constructor for class ambit2.db.update.bookmark.ReadBookmark
 
ReadBundle - Class in ambit2.db.update.bundle
Retrieve SourceDataset by id
ReadBundle(Set<UpdateBundle._published_status>) - Constructor for class ambit2.db.update.bundle.ReadBundle
 
ReadBundle(String, Set<UpdateBundle._published_status>) - Constructor for class ambit2.db.update.bundle.ReadBundle
 
ReadBundleVersion - Class in ambit2.db.update.bundle
 
ReadBundleVersion(Set<UpdateBundle._published_status>) - Constructor for class ambit2.db.update.bundle.ReadBundleVersion
 
ReadByReliabilityFlags - Class in ambit2.db.substance
 
ReadByReliabilityFlags(String, String) - Constructor for class ambit2.db.substance.ReadByReliabilityFlags
 
ReadChemicalIds - Class in ambit2.db.readers
 
ReadChemicalIds() - Constructor for class ambit2.db.readers.ReadChemicalIds
 
ReadChemicalsByBundle - Class in ambit2.db.update.bundle.chemicals
 
ReadChemicalsByBundle() - Constructor for class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
ReadChemicalsByBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
ReadChemIdentifiersByComposition - Class in ambit2.db.substance.ids
compound identifiers for each of the substance composition components Retrieves
ReadChemIdentifiersByComposition() - Constructor for class ambit2.db.substance.ids.ReadChemIdentifiersByComposition
 
ReadChemPropertiesByComposition - Class in ambit2.db.substance.properties
compound identifiers for each of the substance composition components Retrieves
ReadChemPropertiesByComposition() - Constructor for class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
readCMLMolecule(String) - Static method in class ambit2.core.data.MoleculeTools
 
readCMLMolecule(InputStream) - Static method in class ambit2.core.data.MoleculeTools
 
readCompositionRelation(CompositionRelation, ResultSet, SubstanceEndpointsBundle) - Static method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
readContent(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
readDataset - Variable in class ambit2.db.readers.RetrieveDatasets
 
ReadDataset - Class in ambit2.db.update.dataset
Retrieve SourceDataset by id
ReadDataset() - Constructor for class ambit2.db.update.dataset.ReadDataset
 
ReadDatasetLicense - Class in ambit2.db.update.dataset
Retrieve SourceDataset by id
ReadDatasetLicense() - Constructor for class ambit2.db.update.dataset.ReadDatasetLicense
 
readDatasetQuery - Variable in class ambit2.db.processors.DbStructureWriter
 
ReadDatasetRelation - Class in ambit2.db.chemrelation
Similar to ReadStructureRelation , but retrieves the related compounds for the entire dataset
ReadDatasetRelation() - Constructor for class ambit2.db.chemrelation.ReadDatasetRelation
 
ReadDatasetRelation(String, ISourceDataset) - Constructor for class ambit2.db.chemrelation.ReadDatasetRelation
 
ReadEffectRecord - Class in ambit2.db.substance.study
Reads effects records given document uuid
ReadEffectRecord() - Constructor for class ambit2.db.substance.study.ReadEffectRecord
 
ReadEffectRecordAbstract<F,ER extends EffectRecord<String,String,String>> - Class in ambit2.db.substance.study
 
ReadEffectRecordAbstract() - Constructor for class ambit2.db.substance.study.ReadEffectRecordAbstract
 
ReadEffectRecordByBundle - Class in ambit2.db.update.bundle.effects
 
ReadEffectRecordByBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.effects.ReadEffectRecordByBundle
 
ReadEffectRecordByBundleMatrix - Class in ambit2.db.update.bundle.matrix
 
ReadEffectRecordByBundleMatrix(SubstanceEndpointsBundle, ReadEffectRecordByBundleMatrix._matrix) - Constructor for class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix
 
ReadEffectRecordByBundleMatrix._matrix - Enum in ambit2.db.update.bundle.matrix
 
ReadEffectRecordBySubstance - Class in ambit2.db.substance.study
 
ReadEffectRecordBySubstance() - Constructor for class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
ReadEndpointsByBundle - Class in ambit2.db.update.bundle.endpoints
 
ReadEndpointsByBundle() - Constructor for class ambit2.db.update.bundle.endpoints.ReadEndpointsByBundle
 
readEnergyRuleSet(JsonNode) - Method in class ambit2.tautomers.rules.JsonRuleParser
 
reader - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
reader - Variable in class ambit2.core.io.I5ReaderSimple
 
reader - Variable in class ambit2.core.io.IteratingFileReader
 
reader - Variable in class ambit2.core.io.IteratingFolderReader
 
reader - Variable in class ambit2.core.io.RawIteratingWrapper
 
reader - Variable in class ambit2.core.io.ToXMLReaderSimple
 
reader - Variable in class ambit2.core.processors.batch.DefaultInputState
 
reader - Variable in class ambit2.core.processors.structure.AbstractPropertyGenerator
 
reader - Variable in class ambit2.core.processors.structure.MoleculePairProcessor
 
reader - Variable in class ambit2.db.processors.DescriptorsCalculator
 
reader - Variable in class ambit2.db.readers.RetrieveAtomContainer
 
reader - Variable in class ambit2.db.reporters.AbstractImageReporter
 
reader - Variable in class ambit2.db.reporters.CMLReporter
 
reader - Variable in class ambit2.db.reporters.PDFReporter
 
reader - Variable in class ambit2.db.reporters.SDFReporter
 
reader - Variable in class ambit2.db.search.property.ValuesReader
 
reader - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
reader - Variable in class ambit2.db.search.structure.QueryLookupStructure
 
reader - Variable in class ambit2.db.search.structure.QuerySMARTS
 
reader - Variable in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
reader - Variable in class ambit2.rest.model.predictor.FingerprintsPredictor
 
reader - Variable in class ambit2.rest.model.predictor.Structure2DProcessor
 
reader - Variable in class ambit2.rest.model.predictor.StructureProcessor
 
reader - Variable in class ambit2.smarts.query.FastSmartsMatcher
 
reader - Variable in class ambit2.smarts.query.SmartsPatternAmbit
 
reader - Variable in class ambit2.vega.ExternalModelVega
 
readFeaturesRDF(String, Template, Reference, String) - Static method in class ambit2.rest.rdf.RDFPropertyIterator
 
readFromCfg(String) - Static method in class ambit2.groupcontribution.io.DataSetReader
 
readFromCfg(String) - Static method in class ambit2.groupcontribution.io.ModelReader
 
readFromSDF(String) - Static method in class ambit2.groupcontribution.io.DataSetReader
 
readFromXML(String) - Static method in class ambit2.groupcontribution.io.ModelReader
 
readGACode() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
readIdentifiers(String) - Method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
readImageMapFile(File) - Method in class ambit2.db.reporters.ImageAreaReporter
 
readMatrix(ObjectInputStream) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
readMatrix(ObjectInputStream) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
readMM(Path, int, IProcessor<T, T>) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
ReadModel - Class in ambit2.db.update.model
ModelQueryResults
ReadModel(Integer) - Constructor for class ambit2.db.update.model.ReadModel
 
ReadModel() - Constructor for class ambit2.db.update.model.ReadModel
 
readMolfile(Reader) - Static method in class ambit2.core.data.MoleculeTools
 
readMolfile(String) - Static method in class ambit2.core.data.MoleculeTools
 
readOutput - Variable in class ambit2.core.external.ShellSDFoutput
 
readPDBfile(String) - Static method in class ambit2.core.data.MoleculeTools
 
readPropertiesFile(String) - Method in class ambit2.groupcontribution.io.GCM2Properties
 
readProperty - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
ReadProperty - Class in ambit2.db.update.property
Reads Property by id
ReadProperty(Integer) - Constructor for class ambit2.db.update.property.ReadProperty
 
ReadProperty() - Constructor for class ambit2.db.update.property.ReadProperty
 
ReadPropertyAnnotations - Class in ambit2.db.update.propertyannotations
 
ReadPropertyAnnotations() - Constructor for class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
ReadPropertyAnnotations._fields - Enum in ambit2.db.update.propertyannotations
 
ReadQueryFolder - Class in ambit2.db.update.queryfolder
Retrieve query folder header by id or name
ReadQueryFolder(AmbitUser, SessionID) - Constructor for class ambit2.db.update.queryfolder.ReadQueryFolder
 
ReadQueryFolder() - Constructor for class ambit2.db.update.queryfolder.ReadQueryFolder
 
readRDF(String, String) - Method in class ambit2.rest.legacy.OTFeatures
Deprecated.
 
readReactorStrategyFromJSON(File) - Static method in class ambit2.reactions.reactor.ReactorStrategy
 
readReactorStrategyFromJSONFile(File, ReactorStrategy) - Static method in class ambit2.reactions.reactor.ReactorStrategy
 
readReactorStrategyFromJsonNode(JsonNode) - Static method in class ambit2.reactions.reactor.ReactorStrategy
 
readReactorStrategyFromJsonNode(JsonNode, ReactorStrategy) - Static method in class ambit2.reactions.reactor.ReactorStrategy
 
readRecord(int) - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader
 
ReadReference - Class in ambit2.db.update.reference
Retrieve references (by id or all)
ReadReference(Integer) - Constructor for class ambit2.db.update.reference.ReadReference
 
ReadReference() - Constructor for class ambit2.db.update.reference.ReadReference
 
readReferences() - Method in class ambit2.core.io.bcf.EurasBCFReader
 
readRuleSetFromJSON(String) - Static method in class ambit2.tautomers.rules.JsonRuleParser
 
ReadStoredQuery - Class in ambit2.db.update.storedquery
 
ReadStoredQuery() - Constructor for class ambit2.db.update.storedquery.ReadStoredQuery
 
ReadStoredQuery(int) - Constructor for class ambit2.db.update.storedquery.ReadStoredQuery
 
ReadStoredQuery._query - Enum in ambit2.db.update.storedquery
 
readStructure(RDFNode, Item) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
readStructure(RDFNode, Instance) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
readStructure(RDFNode, IStructureRecord) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
readStructure - Variable in class ambit2.rest.structure.CompoundURIReporter
 
ReadStructureRelation - Class in ambit2.db.chemrelation
 
ReadStructureRelation(IStructureRecord) - Constructor for class ambit2.db.chemrelation.ReadStructureRelation
 
ReadStructureRelation() - Constructor for class ambit2.db.chemrelation.ReadStructureRelation
 
ReadStructureRelation(String, Integer) - Constructor for class ambit2.db.chemrelation.ReadStructureRelation
 
ReadStructuresByFingerprint - Class in ambit2.db.update.fp
 
ReadStructuresByFingerprint() - Constructor for class ambit2.db.update.fp.ReadStructuresByFingerprint
 
ReadSubstance - Class in ambit2.db.substance
 
ReadSubstance() - Constructor for class ambit2.db.substance.ReadSubstance
 
ReadSubstance(SubstanceRecord) - Constructor for class ambit2.db.substance.ReadSubstance
 
ReadSubstance(CompositionRelation) - Constructor for class ambit2.db.substance.ReadSubstance
 
ReadSubstanceByExternalIDentifier - Class in ambit2.db.substance
 
ReadSubstanceByExternalIDentifier() - Constructor for class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
ReadSubstanceByExternalIDentifier(String, String) - Constructor for class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
ReadSubstanceByName - Class in ambit2.db.substance
 
ReadSubstanceByName() - Constructor for class ambit2.db.substance.ReadSubstanceByName
 
ReadSubstanceByName(String, String) - Constructor for class ambit2.db.substance.ReadSubstanceByName
 
ReadSubstanceByName._namecondition - Enum in ambit2.db.substance
 
ReadSubstanceByOwner - Class in ambit2.db.substance
All substance given an owner name or UUID
ReadSubstanceByOwner() - Constructor for class ambit2.db.substance.ReadSubstanceByOwner
 
ReadSubstanceByOwner(ReadSubstanceByOwner._ownersearchmode, String) - Constructor for class ambit2.db.substance.ReadSubstanceByOwner
 
ReadSubstanceByOwner._ownersearchmode - Enum in ambit2.db.substance
 
ReadSubstanceByStudy - Class in ambit2.db.substance
 
ReadSubstanceByStudy() - Constructor for class ambit2.db.substance.ReadSubstanceByStudy
 
ReadSubstanceByStudy(ReadSubstanceByStudy._studysearchmode, String) - Constructor for class ambit2.db.substance.ReadSubstanceByStudy
 
ReadSubstanceByStudy._studysearchmode - Enum in ambit2.db.substance
 
ReadSubstanceByType - Class in ambit2.db.substance
 
ReadSubstanceByType(String) - Constructor for class ambit2.db.substance.ReadSubstanceByType
 
ReadSubstanceChemicalsUnionByBundle - Class in ambit2.db.update.bundle.substance
 
ReadSubstanceChemicalsUnionByBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.substance.ReadSubstanceChemicalsUnionByBundle
 
ReadSubstanceComposition - Class in ambit2.db.substance.relation
 
ReadSubstanceComposition() - Constructor for class ambit2.db.substance.relation.ReadSubstanceComposition
 
ReadSubstanceIdentifiers - Class in ambit2.db.substance.ids
 
ReadSubstanceIdentifiers() - Constructor for class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
ReadSubstanceProperty - Class in ambit2.db.substance.study
 
ReadSubstanceProperty() - Constructor for class ambit2.db.substance.study.ReadSubstanceProperty
 
ReadSubstanceRelation - Class in ambit2.db.substance.relation
Reads all structures, related to the query substance via substance_relation table
ReadSubstanceRelation(SubstanceRecord) - Constructor for class ambit2.db.substance.relation.ReadSubstanceRelation
 
ReadSubstanceRelation() - Constructor for class ambit2.db.substance.relation.ReadSubstanceRelation
 
ReadSubstanceRelation(STRUCTURE_RELATION, SubstanceRecord) - Constructor for class ambit2.db.substance.relation.ReadSubstanceRelation
 
ReadSubstances - Class in ambit2.db.substance
Retrieve set of substances given array of substance UUIDs
ReadSubstances() - Constructor for class ambit2.db.substance.ReadSubstances
 
ReadSubstances(String[]) - Constructor for class ambit2.db.substance.ReadSubstances
 
ReadSubstancesByBundle - Class in ambit2.db.update.bundle.substance
 
ReadSubstancesByBundle() - Constructor for class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
ReadSubstancesByBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
ReadSubstancesByBundleCompounds - Class in ambit2.db.update.bundle.substance
Retrieve substances, containing compounds defined by the /bundle/id/compound
ReadSubstancesByBundleCompounds() - Constructor for class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds
 
ReadSubstancesByBundleCompounds(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds
 
ReadSubstanceStudy<PA extends ProtocolApplication<Protocol,String,String,IParams,String>> - Class in ambit2.db.substance.study
 
ReadSubstanceStudy() - Constructor for class ambit2.db.substance.study.ReadSubstanceStudy
 
ReadSubstanceStudyFlat - Class in ambit2.db.substance.study
 
ReadSubstanceStudyFlat() - Constructor for class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
readTextLineAsName() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
readVersionLong() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
readVersionShort() - Method in class ambit2.rest.config.AMBITAppConfigProperties
 
ready - Variable in class ambit2.db.results.AmbitRows
 
reagent - Variable in class ambit2.reactions.reactor.ReactorInfoPack
 
reagents - Variable in class ambit2.reactions.reactor.ReactorNode
 
real_lower - Variable in class ambit2.base.relation.composition.Proportion
 
real_lowervalue - Variable in class ambit2.base.relation.composition.Proportion
 
real_unit - Variable in class ambit2.base.relation.composition.Proportion
 
real_upper - Variable in class ambit2.base.relation.composition.Proportion
 
real_uppervalue - Variable in class ambit2.base.relation.composition.Proportion
 
ReciprocalFunction - Class in ambit2.rules.functions
 
ReciprocalFunction() - Constructor for class ambit2.rules.functions.ReciprocalFunction
 
recognizeSlnObjectType() - Method in class ambit2.sln.SLNContainer
 
record - Variable in class ambit2.chebi.ChEBIClient
 
record - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
record - Variable in class ambit2.core.io.I5ReaderSimple
 
record - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
record - Variable in class ambit2.core.io.json.SubstanceStudyParser
 
record - Variable in class ambit2.core.io.ToXMLReaderSimple
 
record - Variable in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
record - Variable in class ambit2.db.facets.bundle.BundleSummaryQuery
 
record - Variable in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
record - Variable in class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
record - Variable in class ambit2.db.facets.compounds.ChemicalRoleByBundle
 
record - Variable in class ambit2.db.facets.compounds.CollectionsByChemical
 
record - Variable in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
record - Variable in class ambit2.db.facets.datasets.PrefixFacetQuery
 
record - Variable in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
record - Variable in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
record - Variable in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
record - Variable in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
record - Variable in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
record - Variable in class ambit2.db.readers.RetrieveProfileValues
 
record - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
record - Variable in class ambit2.db.readers.RetrieveTemplateStructure
 
record - Variable in class ambit2.db.simiparity.space.QMapSpace
 
record - Variable in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
record - Variable in class ambit2.db.substance.ReadSubstances
 
record - Variable in class ambit2.db.substance.relation.ReadSubstanceComposition
 
record - Variable in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
record - Variable in class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
record - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
record - Variable in class ambit2.db.substance.study.ReadEffectRecordBySubstance
 
record - Variable in class ambit2.db.substance.study.ReadSubstanceStudy
 
record - Variable in class ambit2.model.dataset.DoubleArrayDataset
 
record - Variable in class ambit2.namestructure.Name2StructureFinder
 
record - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
record - Variable in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
record - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
record - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
record - Variable in class ambit2.ui.table.BrowsableTableModel
 
recordBuffer - Variable in class ambit2.core.io.RawIteratingReader
 
recordCount - Variable in class ambit2.core.io.ToXMLReaderSimple
 
recordIDVar - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
recordIndex - Variable in class ambit2.export.isa.base.ExternalDataFileLocation
 
RecordIntervalCondition - Class in ambit2.core.filter
 
RecordIntervalCondition() - Constructor for class ambit2.core.filter.RecordIntervalCondition
 
recordIterator - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
RecordNavigator - Class in ambit2.ui.table
 
RecordNavigator(IRecordNavigator) - Constructor for class ambit2.ui.table.RecordNavigator
 
recordNode - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
recordReady(T) - Method in class ambit2.base.io.format.MatrixMarketReaderAbstract
 
records - Variable in class ambit2.base.processors.StructureRecordsAppender
 
records - Variable in class ambit2.db.results.ResultSetTableModel
 
records - Variable in class ambit2.db.search.structure.pairwise.QueryStructurePairs
 
records - Variable in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
records - Variable in class ambit2.dbui.CachedRowSetTableModel
 
records - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
records_error - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
records_processed - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
records_read - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
records_to_delete - Variable in class ambit2.base.data.study.ProtocolApplicationAnnotated
 
recordToCell(int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
recordType - Variable in class ambit2.pubchem.rest.PUGRestImageRequest
 
recordWriter - Variable in class ambit2.rest.dataset.RDFFileWriter
 
recordWriter - Variable in class ambit2.rest.QueryStaXReporter
 
recreateTableColumn(TableColumnModel) - Method in class ambit2.ui.EditableHeader
 
recSmartsContainers - Variable in class ambit2.smarts.SmartsAtomExpression
 
recSmartsMatches - Variable in class ambit2.smarts.SmartsAtomExpression
 
recSmartsStrings - Variable in class ambit2.smarts.SmartsAtomExpression
 
redFont - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
redFont - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
reference - Variable in class ambit2.base.data.Property
 
reference - Variable in class ambit2.base.data.SourceDataset
 
reference - Variable in class ambit2.base.data.StructureRecord
 
reference - Variable in class ambit2.base.data.study.ProtocolApplication
 
reference - Variable in class ambit2.core.io.I5ReaderSimple
 
reference - Variable in class ambit2.core.io.RawIteratingCSVReader
 
reference - Variable in class ambit2.core.io.RawIteratingReader
 
reference - Variable in class ambit2.core.io.RawIteratingWrapper
 
reference - Variable in class ambit2.db.processors.BatchDBProcessor
 
reference - Variable in class ambit2.db.processors.PropertyValuesWriter
 
reference - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
reference - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
reference_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
referenceID - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
references - Variable in class ambit2.core.io.bcf.EurasBCFReader
 
referenceSubstanceUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
ReferenceSubstanceUUID - Class in ambit2.core.processors.structure.key
 
ReferenceSubstanceUUID() - Constructor for class ambit2.core.processors.structure.key.ReferenceSubstanceUUID
 
referer - Variable in class ambit2.rest.dataset.RDFInstancesParser
 
referer - Variable in class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
referer - Variable in class ambit2.rest.model.builder.ModelBuilder
 
referer - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
referer - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
referer - Variable in class ambit2.rest.task.CallableDatasetCreator
 
referer - Variable in class ambit2.rest.task.CallablePOST
 
referer - Variable in class ambit2.rest.task.CallableQueryProcessor
 
refIterator - Variable in class ambit2.rest.rdf.RDFMetaDatasetIterator
 
refreshRow() - Method in class ambit2.db.results.AmbitRows
 
refsubstance_uuid - Variable in class ambit2.base.data.SubstanceRecord
 
regid - Variable in class ambit2.sln.SLNContainerAttributes
 
registerBestRankTautomer(IAtomContainer) - Method in class ambit2.tautomers.TautomerManager
 
registerDecriptor(String, String, Class, int, int, IValueTransformation) - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
registerEvent(IReactionSequenceHandler.RSEvent) - Method in interface ambit2.reactions.retrosynth.IReactionSequenceHandler
 
registerGroup(Map<String, Integer>, IGroup) - Static method in class ambit2.groupcontribution.Calculator
 
registerGroup(String, Map<String, Integer>) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
registerHAtomEnvironmentInstance(HAtomEnvironmentInstance) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
registerOutParameters(CallableStatement) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
registerOutParameters(CallableStatement) - Method in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
registerOutParameters(CallableStatement) - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
registerOutParameters(CallableStatement) - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
registerOutParameters(CallableStatement) - Method in class ambit2.db.update.dataset.DeleteDataset
 
registerTautomer(IAtomContainer) - Method in class ambit2.tautomers.TautomerManager
 
registrationProperty - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
registrationProperty - Variable in class ambit2.core.io.I5ReaderSimple
 
regStatus - Variable in class ambit2.base.data.AmbitUser
 
regStatus - Variable in class ambit2.ui.editors.AmbitUserEditor
 
relatedStructures - Variable in class ambit2.base.data.SubstanceRecord
 
relation - Variable in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
relation - Variable in class ambit2.db.search.property.QueryPairwiseTanimoto
 
relation - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
relation - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
relationMetric - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
relationMetric - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
relationMetric_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
relations - Variable in class ambit2.tautomers.TautomerRelationGraph
 
relationship - Variable in class ambit2.base.data.Dictionary
 
RelationToOtherToxicEffects - Static variable in class ambit2.base.ro.I5CONSTANTS
 
relationType - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
relationType - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
relationType_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
relative(int) - Method in class ambit2.db.results.AmbitRows
 
relativeEntropy(Histogram) - Method in class ambit2.domain.stats.datastructures.Histogram
Kullback-Leibler distance (or relative entropy) between two discrete probability distributions pi and qi * @param hist
relativeEntropy(Histogram) - Method in class ambit2.similarity.stats.Histogram
Kullback-Leibler distance (or relative entropy) between two discrete probability distributions pi and qi * @param hist
release() - Method in class ambit2.db.results.AmbitRows
 
relevance - Variable in class ambit2.base.data.Bookmark
 
reliability - Variable in class ambit2.base.data.study.ProtocolApplication
 
ReliabilityParams<VALUE> - Class in ambit2.base.data.study
Corresponds to Klimish codes
ReliabilityParams() - Constructor for class ambit2.base.data.study.ReliabilityParams
 
ReliabilityParams._r_flags - Enum in ambit2.base.data.study
 
reliabilityScore - Variable in class ambit2.reactions.GenericReaction
 
remark - Variable in class ambit2.base.data.study.ValueAnnotated
 
Remark - Static variable in class ambit2.base.ro.I5CONSTANTS
 
remarks - Variable in class ambit2.base.facet.BundleRoleFacet
 
REMOTELOOKUP - Static variable in class ambit2.base.config.Preferences
 
REMOTELOOKUP_URI - Static variable in class ambit2.base.config.Preferences
 
RemoteStreamConvertor - Class in ambit2.rest
 
RemoteStreamConvertor(WrappedService<UsernamePasswordCredentials>, ByteArrayOutputStream, MediaType, Method, MediaType) - Constructor for class ambit2.rest.RemoteStreamConvertor
 
remove(Object) - Method in class ambit2.base.data.study.Params
 
remove() - Method in class ambit2.chebi.ChEBIClient
 
remove() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator
 
remove(Object) - Method in class ambit2.core.groups.FilteredList
 
remove(int) - Method in class ambit2.core.groups.FilteredList
 
remove(IAtomContainer) - Method in class ambit2.core.groups.SuppleAtomContainer
 
remove() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
remove() - Method in class ambit2.core.io.IteratingFileReader
 
remove() - Method in class ambit2.core.io.RawIteratingWrapper
 
remove() - Method in class ambit2.db.results.MemoryRowsModel
 
remove() - Method in class ambit2.db.results.RowsModel
 
remove() - Method in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
remove(T) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
remove(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
remove() - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
remove() - Method in class ambit2.rest.rdf.RDFObjectIterator
Not available
remove() - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
Not supported
remove() - Method in class ambit2.rest.task.FilteredTasksIterator
 
remove() - Method in class ambit2.rest.task.SingleTaskIterator
 
removeAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList
 
removeAllBonds() - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAllElectronContainers() - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAllElements() - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAtom(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAtom(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAtomAndConnectedElectronContainers(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAtomOnly(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeAtomOnly(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeBond(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeBond(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeBond(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeCDKTitle - Variable in class ambit2.core.processors.structure.MoleculeReader
 
removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.IteratingFileReader
 
removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RawIteratingWrapper
 
removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
removeColumns() - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
removeDatasetFragment(String) - Static method in class ambit2.rest.OpenTox
 
removeDatasetFragment(String) - Static method in class ambit2.rest.rdf.RDFObjectIterator
 
removedTautomers - Variable in class ambit2.tautomers.FilterTautomers
 
removeEditor() - Method in class ambit2.ui.EditableHeader
 
removeElectronContainer(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeElectronContainer(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeExplcitHNeighbours(IAtom, IAtomContainer, int) - Static method in class ambit2.smarts.smirks.Transformations
 
removeFacet(IFacet) - Method in class ambit2.base.data.StructureRecord
 
removeFacet(IFacet) - Method in interface ambit2.base.interfaces.IStructureRecord
 
removeFacet(IFacet) - Method in class ambit2.base.relation.composition.CompositionRelation
 
removeFacet(BundleRoleFacet) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
removeFromFilter(int) - Method in class ambit2.core.groups.FilteredList
 
removeFromFilter(T) - Method in class ambit2.core.groups.FilteredList
 
removeFromFilter(T) - Method in interface ambit2.core.groups.IFiltered
 
removeFromFilter(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeFromFilter(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeLonePair(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeMolecule(IAtomContainer, boolean) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.data.Profile
 
removePropertyChangeListener(PropertyChangeListener) - Method in class ambit2.rest.task.CallableDatasetCreator
 
removePropertyChangeListener(PropertyChangeListener) - Method in class ambit2.ui.table.BrowsableTableModel
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IBrowserMode
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IFindNavigator
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IPageNavigator
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface ambit2.ui.table.IRecordNavigator
 
removeRecordProperty(Property) - Method in class ambit2.base.data.StructureRecord
 
removeRecordProperty(Property) - Method in interface ambit2.base.interfaces.IStructureRecord
 
removeRecordProperty(Property) - Method in class ambit2.base.relation.composition.CompositionRelation
 
removeRowSetListener(RowSetListener) - Method in class ambit2.db.results.AmbitRows
 
removeSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeSingleElectron(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer
 
removeStep(int) - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
removeStringDelimiters(String) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
removeStringDelimiters(String) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
removeTask(String) - Method in class ambit2.rest.task.TaskStorage
 
removeTasks() - Method in class ambit2.rest.task.TaskStorage
 
removeTasks() - Method in class ambit2.rest.TaskApplication
 
renameTags(IAtomContainer, Map<Object, Property>) - Static method in class ambit2.tautomers.processor.StructureStandardizer
 
renameTags(IAtomContainer, Map<Object, Property>, boolean) - Static method in class ambit2.tautomers.processor.StructureStandardizer
 
renderCompoundFeatures(String, Model, Writer, String, String, String, Reference) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
RendererModelWrapper - Class in ambit2.rendering
 
repairBondOrder4(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools
 
report(String) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
report(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
report(String) - Method in class ambit2.rest.legacy.OTOntologyService
Deprecated.
 
report(Reference, OTDataset) - Static method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
report(String) - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
report(Writer, OTDatasets, OTDatasets) - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
report(OTDataset, boolean, OTFeatures, boolean, OTFeatures, String, int, int) - Static method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
report(OTDataset, OTFeatures, String, int, int) - Static method in class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
report(OTDataset, OTFeatures, String, int, int) - Static method in class ambit2.rest.task.dsl.OTDatasetTableReport
 
report_level - Static variable in class ambit2.rest.freemarker.FreeMarkerStatusService
 
reportContributions - Variable in class ambit2.groupcontribution.GCMReportConfig
 
reportErrorsAsString() - Method in class ambit2.groupcontribution.dataset.DataSet
 
reportGeneralInputInfo - Variable in class ambit2.groupcontribution.GCMReportConfig
 
reportGroups - Variable in class ambit2.groupcontribution.GCMReportConfig
 
reportLevel - Variable in class ambit2.rest.freemarker.FreeMarkerStatusService
 
reportMatrices - Variable in class ambit2.groupcontribution.GCMReportConfig
 
RepositoryReader<Target> - Class in ambit2.db
TODO parameterize
RepositoryReader() - Constructor for class ambit2.db.RepositoryReader
 
RepositoryWriter - Class in ambit2.db.processors
tables chemicals, structure
RepositoryWriter() - Constructor for class ambit2.db.processors.RepositoryWriter
 
representation - Variable in class ambit2.search.csls.CSLSRequest
 
ReproductiveEffectsObserved - Static variable in class ambit2.base.ro.I5CONSTANTS
 
request - Variable in class ambit2.base.processors.search.AbstractFinder
 
request - Variable in class ambit2.rest.reporters.CatalogURIReporter
 
requestref - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
requestref - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
requirement - Variable in class ambit2.core.data.model.Algorithm
 
reset() - Method in class ambit2.groupcontribution.Learner
 
reset() - Method in class ambit2.groupcontribution.utils.math.ValidationConfig
 
reset() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
reset() - Method in class ambit2.smarts.smirks.ReactionSearch
 
resetCombination(int[]) - Method in class ambit2.smarts.ComponentMapping
 
resolved - Variable in class ambit2.reactions.retrosynth.RetroSynthNode
 
resource - Static variable in class ambit2.rest.property.PropertyURIReporter
 
resource - Static variable in class ambit2.rest.SimpleTaskResource
 
resourceBundle - Static variable in class ambit2.core.config.Resources
 
resourceID - Static variable in class ambit2.rest.SimpleTaskResource
 
resourceKey - Static variable in class ambit2.rest.SimpleTaskResource
 
Resources - Class in ambit2.core.config
Localisation resources (singleton)
response_status - Variable in class ambit2.rest.AbstractResource
 
responseType - Variable in class ambit2.core.io.FileState
 
responseType - Variable in class ambit2.core.processors.batch.DefaultIOState
 
RESTComponent - Class in ambit2.rest
 
RESTComponent(Context, Application[]) - Constructor for class ambit2.rest.RESTComponent
 
restoreDBStereo(IAtomContainer, DoubleBondStereochemistry, StereoChange) - Static method in class ambit2.smarts.StereoChemUtils
 
restoreOriginal() - Method in class ambit2.db.results.AmbitRows
 
result - Variable in class ambit2.db.chemrelation.ReadDatasetRelation
 
result - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
result - Variable in class ambit2.db.substance.study.facet.ResultsCountFacet
 
result - Variable in class ambit2.descriptors.VerboseDescriptorResult
 
result - Variable in class ambit2.jchempaint.editor.JChemPaintDialog
 
result(ResultType) - Method in interface ambit2.pubchem.ResultListener
 
result - Variable in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
result - Variable in class ambit2.rest.task.LauncherResource
 
result - Variable in class ambit2.rest.task.Task
 
result - Variable in class ambit2.similarity.AbstractSimilarityModel
 
resultBufferOutFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
resultDir - Variable in class ambit2.pubchem.BatchRetrievePubChem
 
resultList - Variable in class ambit2.chebi.ChEBIClient
 
ResultListener<ResultType> - Interface in ambit2.pubchem
 
resultPos - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
results - Variable in class ambit2.core.data.HashDescriptorResult
 
results - Variable in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
ResultsCountFacet<E> - Class in ambit2.db.substance.study.facet
 
ResultsCountFacet(String, E) - Constructor for class ambit2.db.substance.study.facet.ResultsCountFacet
 
resultSet - Variable in class ambit2.db.DbReader
 
resultSet - Variable in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
ResultSetTableModel - Class in ambit2.db.results
 
ResultSetTableModel() - Constructor for class ambit2.db.results.ResultSetTableModel
 
resultType - Variable in class ambit2.db.search.QueryExecutor
 
resultTypeConcurency - Variable in class ambit2.db.search.QueryExecutor
 
resultURI - Variable in class ambit2.rest.task.CallableMockup
 
retainAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList
 
RetieveFeatures - Class in ambit2.db.search.property
Given IStructureRecord , find if its properties are already in the properties table.
RetieveFeatures() - Constructor for class ambit2.db.search.property.RetieveFeatures
 
retrieve(IStructureRecord) - Method in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
retrieve_sdf - Variable in class ambit2.pubchem.EntrezSearchProcessor
 
RetrieveAtomContainer - Class in ambit2.db.readers
 
RetrieveAtomContainer() - Constructor for class ambit2.db.readers.RetrieveAtomContainer
 
retrieveComposition - Variable in class ambit2.db.substance.ReadSubstance
 
retrieveConformers - Variable in class ambit2.pubchem.PUGProcessor
 
RetrieveDatasets - Class in ambit2.db.readers
 
RetrieveDatasets(IStructureRecord, SourceDataset) - Constructor for class ambit2.db.readers.RetrieveDatasets
 
RetrieveDatasets() - Constructor for class ambit2.db.readers.RetrieveDatasets
 
retrieveDatasets() - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
RetrieveDescriptor - Class in ambit2.db.readers
 
RetrieveDescriptor() - Constructor for class ambit2.db.readers.RetrieveDescriptor
 
retrieveFeatures(OTFeatures, String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
RetrieveField<ResultType> - Class in ambit2.db.readers
 
RetrieveField() - Constructor for class ambit2.db.readers.RetrieveField
 
retrieveField - Variable in class ambit2.db.results.StoredQueryTableModel
 
RetrieveFieldNames - Class in ambit2.db.search.property
 
RetrieveFieldNames() - Constructor for class ambit2.db.search.property.RetrieveFieldNames
 
RetrieveFieldNamesByAlias - Class in ambit2.db.search.property
Finds properties by alias
RetrieveFieldNamesByAlias() - Constructor for class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
RetrieveFieldNamesByAlias(String) - Constructor for class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
RetrieveFieldNamesByType - Class in ambit2.db.search.property
Retrieve names of string properties if setValue(0) ; real valued properties if setValue(1) int properties if setValue(2)
RetrieveFieldNamesByType(boolean) - Constructor for class ambit2.db.search.property.RetrieveFieldNamesByType
 
RetrieveFieldNamesByType() - Constructor for class ambit2.db.search.property.RetrieveFieldNamesByType
 
RetrieveFieldPropertyValue - Class in ambit2.db.readers
Retrive property-value pairs
RetrieveFieldPropertyValue() - Constructor for class ambit2.db.readers.RetrieveFieldPropertyValue
 
RetrieveFieldStructure - Class in ambit2.db.readers
Retrieve property value pairs and assign to a structure record
RetrieveFieldStructure() - Constructor for class ambit2.db.readers.RetrieveFieldStructure
 
RetrieveGroupedValuesByAlias - Class in ambit2.db.readers
 
RetrieveGroupedValuesByAlias(Profile) - Constructor for class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
retrieveImage(URL) - Method in class ambit2.pubchem.DepictRequest
 
retrieveMetric(IStructureRecord, ResultSet) - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
retrieveMetric(IStructureRecord, ResultSet) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
retrieveMetric(IStructureRecord, ResultSet) - Method in class ambit2.db.search.structure.QuerySimilarity
 
retrieveMetric(IStructureRecord, ResultSet) - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
retrieveMetric(IStructureRecord, ResultSet) - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
RetrieveModelTemplates<ResultType> - Class in ambit2.db.readers
Retrieves property values given a model
RetrieveModelTemplates() - Constructor for class ambit2.db.readers.RetrieveModelTemplates
 
RetrieveModelTemplatesPropertyValue - Class in ambit2.db.readers
Retrieves property values given a model
RetrieveModelTemplatesPropertyValue() - Constructor for class ambit2.db.readers.RetrieveModelTemplatesPropertyValue
 
retrieveMolecule - Variable in class ambit2.db.results.StoredQueryTableModel
 
RetrieveProfile - Class in ambit2.db.search.property
 
RetrieveProfile(RetrieveProfile.QueryMode) - Constructor for class ambit2.db.search.property.RetrieveProfile
 
RetrieveProfile() - Constructor for class ambit2.db.search.property.RetrieveProfile
 
RetrieveProfile.QueryMode - Enum in ambit2.db.search.property
 
RetrieveProfileValues - Class in ambit2.db.readers
 
RetrieveProfileValues() - Constructor for class ambit2.db.readers.RetrieveProfileValues
 
RetrieveProfileValues(RetrieveProfileValues.SearchMode, Profile, boolean) - Constructor for class ambit2.db.readers.RetrieveProfileValues
 
RetrieveProfileValues.SearchMode - Enum in ambit2.db.readers
 
RetrieveProfileValuesAsRow - Class in ambit2.db.readers
 
RetrieveProfileValuesAsRow() - Constructor for class ambit2.db.readers.RetrieveProfileValuesAsRow
 
RetrieveProfileValuesAsRow(Profile, boolean) - Constructor for class ambit2.db.readers.RetrieveProfileValuesAsRow
 
retrieveProperties(IStructureRecord) - Method in class ambit2.db.processors.ValueWriterNew
 
retrieveProperties - Variable in class ambit2.db.search.structure.QueryFieldAbstract
 
retrieveProperty(ResultSet) - Method in class ambit2.db.readers.RetrieveProfileValues
 
retriever - Variable in class ambit2.db.DbReaderStructure
 
RetrieveStructure - Class in ambit2.db.readers
 
RetrieveStructure() - Constructor for class ambit2.db.readers.RetrieveStructure
 
RetrieveStructure(boolean) - Constructor for class ambit2.db.readers.RetrieveStructure
 
RetrieveStructureImagePath - Class in ambit2.db.cache
Cached images
RetrieveStructureImagePath(String) - Constructor for class ambit2.db.cache.RetrieveStructureImagePath
 
RetrieveStructureImagePath(String, IStructureRecord) - Constructor for class ambit2.db.cache.RetrieveStructureImagePath
 
RetrieveStructurePair - Class in ambit2.db.search.structure.pairwise
 
RetrieveStructurePair() - Constructor for class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
RetrieveStructurePair.rs_index - Enum in ambit2.db.search.structure.pairwise
 
retrieveStrucType(IStructureRecord, ResultSet) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
retrieveStrucType(IStructureRecord, ResultSet) - Method in class ambit2.db.search.structure.QueryStrucType
 
RetrieveTemplate<ResultType> - Class in ambit2.db.readers
 
RetrieveTemplate() - Constructor for class ambit2.db.readers.RetrieveTemplate
 
RetrieveTemplate(Template) - Constructor for class ambit2.db.readers.RetrieveTemplate
 
RetrieveTemplatePropertyValue - Class in ambit2.db.readers
Retrieves properties by given template
RetrieveTemplatePropertyValue() - Constructor for class ambit2.db.readers.RetrieveTemplatePropertyValue
 
RetrieveTemplateStructure - Class in ambit2.db.readers
 
RetrieveTemplateStructure() - Constructor for class ambit2.db.readers.RetrieveTemplateStructure
 
RetrieveTemplateStructure(Template) - Constructor for class ambit2.db.readers.RetrieveTemplateStructure
 
retrieveValue(IStructureRecord, Property) - Method in class ambit2.base.processors.search.AbstractFinder
 
retrieveValue(ResultSet, IStructureRecord, Property) - Method in class ambit2.db.readers.RetrieveProfileValues
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.QueryStructureType
 
retrieveValue(ResultSet) - Method in class ambit2.db.search.structure.QueryStrucType
 
retrieveValue(IStructureRecord, Property) - Method in class ambit2.pubchem.rest.PubChemRestFinder
 
RetroSynthesis - Class in ambit2.reactions.retrosynth
 
RetroSynthesis() - Constructor for class ambit2.reactions.retrosynth.RetroSynthesis
 
RetroSynthesis(String) - Constructor for class ambit2.reactions.retrosynth.RetroSynthesis
 
RetroSynthesisResult - Class in ambit2.reactions.retrosynth
 
RetroSynthesisResult() - Constructor for class ambit2.reactions.retrosynth.RetroSynthesisResult
 
retroSynthesisWeight - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
RetroSynthNode - Class in ambit2.reactions.retrosynth
 
RetroSynthNode() - Constructor for class ambit2.reactions.retrosynth.RetroSynthNode
 
RetroSynthPath - Class in ambit2.reactions.retrosynth
 
RetroSynthPath() - Constructor for class ambit2.reactions.retrosynth.RetroSynthPath
 
RetroSynthRule - Class in ambit2.reactions.rules
 
RetroSynthRule() - Constructor for class ambit2.reactions.rules.RetroSynthRule
 
RetroSynthRuleInstance - Class in ambit2.reactions.rules
 
RetroSynthRuleInstance() - Constructor for class ambit2.reactions.rules.RetroSynthRuleInstance
 
retroSynthRules - Static variable in class ambit2.reactions.retrosynth.PredefinedReactionKnowledgeBase
 
retroSynthRules - Variable in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
RetroSynthStep - Class in ambit2.reactions.retrosynth
 
RetroSynthStep() - Constructor for class ambit2.reactions.retrosynth.RetroSynthStep
 
returnInstance(SmilesParserWrapper) - Static method in class ambit2.core.smiles.SmilesParserWrapper
 
returnKeys(int) - Method in class ambit2.db.substance.CreateSubstance
 
returnKeys(int) - Method in class ambit2.db.update.bookmark.CreateBookmark
 
returnKeys(int) - Method in class ambit2.db.update.bundle.CreateBundle
 
returnKeys(int) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
returnKeys(int) - Method in class ambit2.db.update.chemical.CreateChemical
 
returnKeys(int) - Method in class ambit2.db.update.dataset.CreateDataset
 
returnKeys(int) - Method in class ambit2.db.update.dataset.DatasetAddStructure
 
returnKeys(int) - Method in class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
returnKeys(int) - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
returnKeys(int) - Method in class ambit2.db.update.model.CreateModel
 
returnKeys(int) - Method in class ambit2.db.update.property.CreateProperty
 
returnKeys(int) - Method in class ambit2.db.update.property.CreatePropertyReferenceID
 
returnKeys(int) - Method in class ambit2.db.update.queryfolder.CreateQueryFolder
 
returnKeys(int) - Method in class ambit2.db.update.reference.CreateReference
 
returnKeys(int) - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
returnKeys(int) - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
returnKeys(int) - Method in class ambit2.db.update.storedquery.QueryAddTemplate
 
returnKeys(int) - Method in class ambit2.db.update.storedquery.QueryDeleteTemplate
 
returnKeys(int) - Method in class ambit2.db.update.structure.CreateStructure
 
returnProperties - Static variable in class ambit2.rest.AbstractResource
 
reuseRecord - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
riAtomIndices - Variable in class ambit2.tautomers.TautomerUtils.TautomerPair
 
right - Variable in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
rightsHolder - Variable in class ambit2.base.data.SourceDataset
 
rightsHolder - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
rightsHolder - Variable in class ambit2.db.search.StoredQuery
 
rInfo - Variable in class ambit2.reactions.reactor.ReactorDescriptorSolver
 
RingClosure - Class in ambit2.smarts
 
RingClosure() - Constructor for class ambit2.smarts.RingClosure
 
ringClosureBondFA - Variable in class ambit2.tautomers.Rule
 
ringClosureBondNum - Variable in class ambit2.tautomers.Rule
 
ringClosureBondOrder - Variable in class ambit2.tautomers.Rule
 
ringClosureBondSA - Variable in class ambit2.tautomers.Rule
 
ringClosureState - Variable in class ambit2.tautomers.Rule
 
RingComplexity - Class in ambit2.reactions.rules.scores
 
RingComplexity() - Constructor for class ambit2.reactions.rules.scores.RingComplexity
 
ringComplexity(IAtomContainer) - Static method in class ambit2.reactions.rules.scores.RingComplexity
 
ringComplexity(IRingSet) - Static method in class ambit2.reactions.rules.scores.RingComplexity
 
RingData - Static variable in class ambit2.smarts.CMLUtilities
 
RingData2 - Static variable in class ambit2.smarts.CMLUtilities
 
RingInfo - Class in ambit2.descriptors.utils
 
RingInfo() - Constructor for class ambit2.descriptors.utils.RingInfo
 
ringNumbers - Variable in class ambit2.structure2name.components.CyclicComponent
 
RingQueryBond - Class in ambit2.smarts
 
RingQueryBond(IChemObjectBuilder) - Constructor for class ambit2.smarts.RingQueryBond
 
ringSet - Variable in class ambit2.structure2name.IUPACNameGenerator
 
RMSE - Static variable in class ambit2.similarity.stats.PredictionModelStatistics
 
rmsError(MatrixDouble, MatrixDouble) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
rmsError(List<Double>, List<Double>) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
rNo - Static variable in class ambit2.base.ro.I5CONSTANTS
 
role - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
roles - Variable in class ambit2.export.isa.v1_0.objects.Person
 
rollback() - Method in class ambit2.db.results.AmbitRows
 
rollback(Savepoint) - Method in class ambit2.db.results.AmbitRows
 
root - Variable in class ambit2.descriptors.PKASmartsDescriptor
 
root - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
root - Variable in class ambit2.pubchem.DepictRequest
 
rOrgCarbonPercent - Static variable in class ambit2.base.ro.I5CONSTANTS
 
RotatableBondFractionDescriptor - Class in ambit2.descriptors.constitutional
Rotatable bond fraction.
RotatableBondFractionDescriptor() - Constructor for class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
rowDeleted() - Method in class ambit2.db.results.AmbitRows
 
rowIndex - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
rowIndex - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
rowInserted() - Method in class ambit2.db.results.AmbitRows
 
rows - Variable in class ambit2.db.results.MemoryRowsModel
 
rows - Variable in class ambit2.db.results.RowsModel
 
rows - Variable in class ambit2.db.search.StoredQuery
 
rows - Variable in class ambit2.dbui.dictionary.OntologyEditor
 
rows2List() - Method in class ambit2.db.results.MemoryRowsModel
 
rowset - Variable in class ambit2.db.results.AmbitRows
 
rowSetPopulated(RowSetEvent, int) - Method in class ambit2.db.results.AmbitRows
 
RowsModel<T> - Class in ambit2.db.results
 
RowsModel(AmbitRows<T>) - Constructor for class ambit2.db.results.RowsModel
 
rowUpdated() - Method in class ambit2.db.results.AmbitRows
 
rowValue(int, int, String, String, String, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
rPERCENTILE_DT50 - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rq - Variable in class ambit2.db.substance.processor.DBBundleStudyWriter
 
RRelieFFAttributeSelection<T> - Class in ambit2.featureselection
 
RRelieFFAttributeSelection() - Constructor for class ambit2.featureselection.RRelieFFAttributeSelection
 
RResourceException - Exception in ambit2.rest.exception
Same as ResourceException , but with additional variant to go in the message body, as specified in OpenTox error reports.
RResourceException(int, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
 
RResourceException(int, String, String, String, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(int, String, String, String, Throwable, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(int, Throwable, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(Status, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(Status, String, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(Status, String, Throwable, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(Status, Throwable, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor.
RResourceException(Throwable, Variant) - Constructor for exception ambit2.rest.exception.RResourceException
Constructor that set the status to Status.SERVER_ERROR_INTERNAL including the related error or exception.
rs - Variable in class ambit2.db.RepositoryReader
 
RSEvent(IReactionSequenceHandler.EventType, int, Object[]) - Constructor for class ambit2.reactions.retrosynth.IReactionSequenceHandler.RSEvent
 
rSTD_DEV - Static variable in class ambit2.base.ro.I5CONSTANTS
 
rSUBLIMATION - Static variable in class ambit2.base.ro.I5CONSTANTS
 
RT_MobileGroup - Static variable in class ambit2.tautomers.TautomerConst
 
RT_RingChain - Static variable in class ambit2.tautomers.TautomerConst
 
RTFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
RTFReporter() - Constructor for class ambit2.db.reporters.RTFReporter
 
Rule - Class in ambit2.tautomers
 
Rule() - Constructor for class ambit2.tautomers.Rule
 
rule - Variable in class ambit2.tautomers.RuleInstance
 
Rule2J - Class in ambit2.groupcontribution.nmr.nmr_1h
 
Rule2J() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.Rule2J
 
Rule3J - Class in ambit2.groupcontribution.nmr.nmr_1h
 
Rule3J() - Constructor for class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
RULE_ORDER_BY_SIZE - Static variable in class ambit2.tautomers.TautomerConst
 
RULE_ORDER_NONE - Static variable in class ambit2.tautomers.TautomerConst
 
ruleDataBase - Variable in class ambit2.structure2name.IUPACNameGenerator
 
ruleid - Variable in class ambit2.some.SOMEVisualizer
 
RuleInfo - Variable in class ambit2.tautomers.Rule
 
RuleInstance - Class in ambit2.tautomers
 
RuleInstance() - Constructor for class ambit2.tautomers.RuleInstance
 
RuleInstance(RuleInstance) - Constructor for class ambit2.tautomers.RuleInstance
 
ruleKBIndex - Variable in class ambit2.tautomers.TautomerUtils.TautomerPair
 
RuleManager - Class in ambit2.tautomers
 
RuleManager(TautomerManager) - Constructor for class ambit2.tautomers.RuleManager
 
ruleName - Variable in class ambit2.tautomers.rules.EnergyRule
 
ruleNumberLimit - Variable in class ambit2.tautomers.RuleSelector
 
RuleParser - Class in ambit2.tautomers
 
RuleParser() - Constructor for class ambit2.tautomers.RuleParser
 
rules - Variable in class ambit2.tautomers.KnowledgeBase
 
rules - Static variable in class ambit2.tautomers.PredefinedKnowledgeBase
GROUP_POS describes the position of mobile group i.e.
rules - Variable in class ambit2.tautomers.ranking.EnergyRanking
 
rules - Variable in class ambit2.tautomers.TautomerRelation
 
rules2j - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
rules3j - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
RuleSelector - Class in ambit2.tautomers
 
RuleSelector() - Constructor for class ambit2.tautomers.RuleSelector
 
RuleStateBondDistribution - Class in ambit2.tautomers
 
RuleStateBondDistribution() - Constructor for class ambit2.tautomers.RuleStateBondDistribution
 
RuleStateFlags - Class in ambit2.tautomers
 
RuleStateFlags() - Constructor for class ambit2.tautomers.RuleStateFlags
 
ruleType - Variable in class ambit2.reactions.fragmentation.FragmentationRule
 
run(String[]) - Method in class ambit2.groupcontribution.cli.GCMPredictCli
 
run(String[]) - Method in class ambit2.groupcontribution.cli.GroupContributionCli
 
run(String[]) - Method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
run(String, String, int) - Method in class ambit2.ml.mlib.ClusteringApp
 
run(String[]) - Method in class ambit2.reactions.cli.AmbitSmirksCli
 
run(String[]) - Method in class ambit2.reactions.cli.ReactorCli
 
run(String[]) - Method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
run() - Method in class ambit2.reactions.retrosynth.RetroSynthesis
 
run() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
run(int) - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
run(Reference) - Method in class ambit2.rest.task.CallableDatasetCreator
 
run() - Method in class ambit2.rest.task.ExecutableTask
 
runAsync - Variable in class ambit2.base.external.CommandShell
 
runBatch(Object) - Method in class ambit2.rest.model.task.CallableModelPredictor
 
runBatch(Target) - Method in class ambit2.rest.task.CallableQueryProcessor
 
runCalculation() - Method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
runGCM() - Method in class ambit2.groupcontribution.cli.GroupContributionCli
 
runGCMPredict() - Method in class ambit2.groupcontribution.cli.GCMPredictCli
 
runHNMR() - Method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
running() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
runReactor() - Method in class ambit2.reactions.cli.ReactorCli
 
runShell(INPUT) - Method in class ambit2.base.external.CommandShell
 
runShell(INPUT, String) - Method in class ambit2.base.external.CommandShell
 
runShell(IAtomContainer) - Method in class ambit2.dragon.AbstractDescriptorShell
 
runShell(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
runShell(IAtomContainer) - Method in class ambit2.some.SOMEShell
 
runShell(IAtomContainer) - Method in class ambit2.vega.VegaShell
 
runSmirks() - Method in class ambit2.reactions.cli.AmbitSmirksCli
 

S

s_idquery - Static variable in class ambit2.db.cache.RetrieveStructureImagePath
 
s_text - Static variable in class ambit2.db.cache.RetrieveStructureImagePath
 
SADescriptors - Class in ambit2.reactions.syntheticaccessibility
 
SADescriptors() - Constructor for class ambit2.reactions.syntheticaccessibility.SADescriptors
 
sameas() - Method in enum ambit2.core.io.ToXMLReaderSimple.toxml_names
 
Sample - Class in ambit2.export.isa.v1_0.objects
ISA sample schema JSON-schema representing a sample in the ISA model.
Sample() - Constructor for class ambit2.export.isa.v1_0.objects.Sample
 
sampleID - Variable in class ambit2.base.data.study.EffectRecord
 
SampleKey - Class in ambit2.core.processors.structure.key
 
SampleKey() - Constructor for class ambit2.core.processors.structure.key.SampleKey
 
samples - Variable in class ambit2.export.isa.v1_0.objects.Materials
 
samples - Variable in class ambit2.export.isa.v1_0.objects.Materials_
 
SaturationCheckerVerifier - Class in ambit2.descriptors
 
SaturationCheckerVerifier() - Constructor for class ambit2.descriptors.SaturationCheckerVerifier
 
save(OutputStream) - Method in class ambit2.base.data.Property
 
save(Writer) - Method in class ambit2.base.data.Property
 
save(OutputStream) - Method in class ambit2.base.data.Template
 
save(Writer) - Method in class ambit2.base.data.Template
 
saveBufferAsFile(File) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
saveFragments(OutputStream, Collection<FunctionalGroup>) - Static method in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
saveProperties(String) - Static method in class ambit2.base.config.Preferences
 
saveProperties(String) - Static method in class ambit2.ui.EditorPreferences
 
saveSmilesToFile(ArrayList<String>, String) - Method in class ambit2.smarts.ChemObjectFactory
 
saveSmilesTuplesToFile(ArrayList<ArrayList<String>>, String) - Method in class ambit2.smarts.ChemObjectFactory
 
scale - Variable in class ambit2.model.numeric.DataCoverageDescriptors
 
scaleImage(JTable, boolean, Image) - Method in class ambit2.ui.ImageCellRenderer
 
SCHEME - Static variable in class ambit2.base.config.Preferences
 
scheme - Variable in class ambit2.db.LoginInfo
 
scope - Variable in class ambit2.core.data.model.Parameter
 
scope - Variable in class ambit2.db.search.QueryCombined
 
scope - Variable in class ambit2.db.search.QueryInfo
 
SCOPE - Enum in ambit2.db.search.structure
 
scope - Variable in class ambit2.dbui.QueryInfoEditor
 
SCOPE_DATABASE - Static variable in class ambit2.db.search.QueryInfo
 
SCOPE_DATASET - Static variable in class ambit2.db.search.QueryInfo
 
scope_options - Static variable in class ambit2.db.search.QueryInfo
 
SCOPE_QUERY - Static variable in class ambit2.db.search.QueryInfo
 
ScopeQuery - Class in ambit2.db.search.structure
A convenience class for a query used to restrict the scope of other queries
ScopeQuery(SCOPE) - Constructor for class ambit2.db.search.structure.ScopeQuery
 
ScopeQuery() - Constructor for class ambit2.db.search.structure.ScopeQuery
 
score2eV - Static variable in class ambit2.tautomers.CACTVSRanking
 
scoreFragmentsToString(int, int, int, int, int, int, int, int, int) - Static method in class ambit2.tautomers.CACTVSRanking
 
ScoreFunction - Class in ambit2.reactions.generator.score
 
ScoreFunction() - Constructor for class ambit2.reactions.generator.score.ScoreFunction
 
ScoreFunctionParser - Class in ambit2.reactions.generator.score
 
ScoreFunctionParser() - Constructor for class ambit2.reactions.generator.score.ScoreFunctionParser
 
screening - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
screening - Variable in class ambit2.db.search.structure.QuerySMARTS
 
Screening - Class in ambit2.smarts
 
Screening(IChemObjectBuilder) - Constructor for class ambit2.smarts.Screening
Screening by fingerprints and structural keys
Screening(boolean) - Constructor for class ambit2.smarts.Screening
Fingerprints screening is on always
Screening(List<String>) - Constructor for class ambit2.smarts.Screening
structural keys by external file
ScreeningData - Class in ambit2.smarts
 
ScreeningData() - Constructor for class ambit2.smarts.ScreeningData
 
sd - Variable in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
sd - Variable in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
SDFBrokenLineTerminationConverter - Class in ambit2.core.io
 
SDFBrokenLineTerminationConverter() - Constructor for class ambit2.core.io.SDFBrokenLineTerminationConverter
 
SDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
SDFReporter() - Constructor for class ambit2.db.reporters.SDFReporter
 
SDFReporter(Template, Profile, boolean) - Constructor for class ambit2.db.reporters.SDFReporter
 
SDFReporter(Template, Profile, boolean, boolean) - Constructor for class ambit2.db.reporters.SDFReporter
 
sdg - Variable in class ambit2.core.processors.Structure2DBuilder
 
sdg - Variable in class ambit2.jchempaint.editor.MoleculeEditAction
 
sdg - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
SEARCH_FORMULA - Static variable in class ambit2.db.search.QueryInfo
 
SEARCH_INCHI - Static variable in class ambit2.db.search.QueryInfo
 
search_param - Static variable in class ambit2.rest.AbstractResource
 
SEARCH_SMILES - Static variable in class ambit2.db.search.QueryInfo
 
SearchApplication - Class in ambit2.pubchem
 
SearchApplication() - Constructor for class ambit2.pubchem.SearchApplication
 
searchIn(IAtomContainer) - Method in class ambit2.smarts.SmartsManager
 
searchMode - Variable in class ambit2.db.readers.RetrieveField
 
searchMode - Variable in class ambit2.db.readers.RetrieveProfileValues
 
searchMode - Variable in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
searchMode - Variable in class ambit2.db.search.structure.QueryFieldAbstract
 
searchMode - Variable in class ambit2.db.search.structure.QueryFieldNumeric
 
searchStatus - Variable in class ambit2.rest.SimpleTaskResource
 
SearchStoredQueries - Class in ambit2.db.update.storedquery
 
SearchStoredQueries() - Constructor for class ambit2.db.update.storedquery.SearchStoredQueries
 
searchStoredQuery - Variable in class ambit2.dbui.QueryStoredResultsEditor
 
sectionStyle - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
seeAlso - Variable in class ambit2.rest.legacy.OTDataset
Deprecated.
 
seek_dataset - Static variable in class ambit2.db.processors.RepositoryWriter
 
select_AND - Static variable in class ambit2.db.readers.RetrieveDatasets
 
select_cas - Static variable in class ambit2.db.update.qlabel.CreateQLabelCAS
 
select_chemical - Static variable in class ambit2.db.readers.RetrieveDatasets
 
select_datasets - Static variable in class ambit2.db.update.bundle.ReadBundle
 
select_datasets - Static variable in class ambit2.db.update.bundle.ReadBundleVersion
 
select_datasets - Static variable in class ambit2.db.update.dataset.ReadDataset
 
select_datasets_bystruc - Static variable in class ambit2.db.readers.RetrieveDatasets
 
select_einecs - Static variable in class ambit2.db.update.qlabel.CreateQLabelEINECS
 
select_license_byid - Static variable in class ambit2.db.update.dataset.ReadDatasetLicense
 
select_license_byname - Static variable in class ambit2.db.update.dataset.ReadDatasetLicense
 
select_number - Static variable in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
select_number_compound - Static variable in class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
select_sql - Static variable in class ambit2.db.update.storedquery.SelectStoredQuery
 
select_string - Static variable in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
select_string_compound - Static variable in class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
select_structure - Static variable in class ambit2.db.readers.RetrieveDatasets
 
select_WHERE - Static variable in class ambit2.db.readers.RetrieveDatasets
 
selected - Variable in class ambit2.base.data.SelectionBean
 
selected - Variable in class ambit2.base.data.StructureRecord
 
selected - Variable in class ambit2.db.search.AbstractQuery
 
selected - Variable in class ambit2.db.update.storedquery.SelectStoredQuery
 
selected - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
selected - Variable in class ambit2.some.SOMEVisualizer
 
selected - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
SELECTED_ATOM_COLOR - Static variable in class ambit2.rendering.CompoundImageTools
 
SELECTED_ATOM_SIZE - Static variable in class ambit2.rendering.CompoundImageTools
 
selectedAndCurrentIcon - Variable in class ambit2.ui.table.BrowsableTableModel
 
SelectedColor - Static variable in class ambit2.ui.editors.ClassHolderEditor
 
selectedIcon - Variable in class ambit2.ui.table.BrowsableTableModel
 
selectedObject - Variable in class ambit2.ui.HeaderComboBoxModel
 
selectField - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
SelectFieldsPanel - Class in ambit2.ui.editors
 
SelectFieldsPanel() - Constructor for class ambit2.ui.editors.SelectFieldsPanel
 
SelectFieldsPanel(TypedListModel<Property>, String) - Constructor for class ambit2.ui.editors.SelectFieldsPanel
 
SelectFieldsPanel(TypedListModel<Property>, TypedListModel<Property>, TypedListModel<Property>, String) - Constructor for class ambit2.ui.editors.SelectFieldsPanel
 
SelectFieldsPanel.MOVE - Enum in ambit2.ui.editors
 
selectFile(Component, String, String, String[], String[], boolean) - Static method in class ambit2.base.io.MyIOUtilities
 
selectFile(Component, String, String, String[], String[], boolean, JComponent) - Static method in class ambit2.base.io.MyIOUtilities
Invokes OpenFile or SaveFile dialog
selectFiles(Component, String, String, String[], String[], boolean, JComponent) - Static method in class ambit2.base.io.MyIOUtilities
 
selection - Variable in class ambit2.groupcontribution.utils.math.CrossValidation
 
SelectionBean<T> - Class in ambit2.base.data
 
SelectionBean(List<T>) - Constructor for class ambit2.base.data.SelectionBean
 
SelectionBean() - Constructor for class ambit2.base.data.SelectionBean
 
SelectionBean(T[]) - Constructor for class ambit2.base.data.SelectionBean
 
SelectionBean(T[], String) - Constructor for class ambit2.base.data.SelectionBean
 
selectionInList - Variable in class ambit2.ui.editors.ListEditor
 
selectionMode - Variable in class ambit2.db.results.StoredQueryTableModel
 
selectionMode - Variable in class ambit2.tautomers.RuleSelector
 
selectionOrder - Variable in class ambit2.tautomers.RuleSelector
 
selector - Variable in class ambit2.ui.Panel2D
 
selectProperties(IOSetting) - Method in class ambit2.core.io.SimpleIOListener
 
selectRecords(IStructureRecord, boolean) - Method in class ambit2.db.results.StoredQueryTableModel
 
selectRecords(ISelectableRecords.SELECTION_MODE) - Method in class ambit2.db.results.StoredQueryTableModel
 
selectResult(IStructureRecord, ResultSet) - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
selectRules(TautomerManager, List<IRuleInstance>) - Method in class ambit2.tautomers.RuleSelector
 
SelectStoredQuery - Class in ambit2.db.update.storedquery
Sets selected field in query table for a given query
SelectStoredQuery() - Constructor for class ambit2.db.update.storedquery.SelectStoredQuery
 
SelectStoredQuery(boolean) - Constructor for class ambit2.db.update.storedquery.SelectStoredQuery
 
SelfBin<T extends Comparable> - Class in ambit2.similarity.stats
 
SelfBin(T) - Constructor for class ambit2.similarity.stats.SelfBin
 
SelfIterable(T) - Constructor for class ambit2.core.groups.AbstractGroup.SelfIterable
 
selfTest - Variable in class ambit2.groupcontribution.GCMTestConfig
 
selfTest - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
selfwriter - Variable in class ambit2.db.processors.DescriptorsCalculator
 
send(Model, boolean) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
send(Representation, MediaType, boolean) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
send(URL, String) - Method in class ambit2.search.chemidplus.AbstractSearchRequest
 
sep - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
separator - Variable in class ambit2.db.reporters.CSVReporter
 
sequence - Variable in class ambit2.smarts.ChemObjectFactory
 
sequence - Variable in class ambit2.smarts.IsomorphismTester
 
sequence - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
sequencedAtoms - Variable in class ambit2.smarts.IsomorphismTester
 
sequencedAtoms - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
sequencedBondAt1 - Variable in class ambit2.smarts.IsomorphismTester
 
sequencedBondAt1 - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
sequencedBondAt2 - Variable in class ambit2.smarts.IsomorphismTester
 
sequencedBondAt2 - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
SequenceElement - Class in ambit2.smarts
 
SequenceElement() - Constructor for class ambit2.smarts.SequenceElement
 
sequenceElNum - Variable in class ambit2.smarts.Node
 
sequences - Static variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
serializeModel(Object, Instances, ModelQueryResults) - Method in class ambit2.rest.model.builder.CoverageModelBuilder
 
serializeModel(Object, List<BitSet>, ModelQueryResults) - Method in class ambit2.rest.model.builder.FingerprintsModelBuilder
 
serializeModel(Form, ModelQueryResults) - Method in class ambit2.rest.model.builder.SMSDModelBuilder
 
serializeModel(Object, Instances, ModelQueryResults) - Method in class ambit2.rest.task.weka.FilteredWekaModelBuilder
 
serializeModel(Object, Instances, ModelQueryResults) - Method in class ambit2.rest.task.weka.WekaModelBuilder
 
server - Variable in class ambit2.pubchem.DepictRequest
 
ServerError - Exception in ambit2.pubchem
 
ServerError() - Constructor for exception ambit2.pubchem.ServerError
 
service - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
service_ontology - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
session - Variable in class ambit2.db.processors.ProcessorCreateQuery
 
sessionID - Variable in class ambit2.db.processors.DBProcessorsChain
 
SessionID - Class in ambit2.db
Session ID
SessionID() - Constructor for class ambit2.db.SessionID
 
SessionID(int) - Constructor for class ambit2.db.SessionID
 
set(int, T) - Method in class ambit2.core.data.ArrayResult
 
set(int, T) - Method in class ambit2.core.groups.FilteredList
 
set(Result, Property, Object) - Method in class ambit2.db.readers.ValuesByTemplateReader
 
set(IStructureRecord, Property, Object) - Method in class ambit2.db.search.property.ValuesReader
 
set - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
set(ITaskResult) - Method in class ambit2.rest.task.ExecutableTask
 
setA(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setActiveRules(ArrayList<String>) - Method in class ambit2.tautomers.KnowledgeBase
 
setActivityThreshold(double) - Method in class ambit2.db.simiparity.space.QMap
 
setAddEexplicitHydrogens(boolean) - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor
 
setAddGenericTypes(boolean) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
setAdditionalConfig(GroupContributionModel.GCMConfigInfo) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setAdditionalFiles(String[]) - Method in class ambit2.base.external.Command
 
setAddNew(boolean) - Method in class ambit2.db.readers.RetrieveField
 
setAddNew(boolean) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setAddNew(boolean) - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
setAddress(String) - Method in class ambit2.base.data.AmbitUser
 
setAddSMILEScolumn(boolean) - Method in class ambit2.core.io.FilesWithHeaderWriter
 
setAdminPass(String) - Method in class ambit2.db.processors.DbCreateDatabase
 
setAffiliation(String) - Method in class ambit2.base.data.AmbitUser
 
setAlgorithm(String) - Method in class ambit2.core.data.model.ModelWrapper
 
setAlgorithmReporter(AlgorithmURIReporter) - Method in class ambit2.rest.model.builder.ModelBuilder
 
setAllowedValues(List<Comparable>) - Method in class ambit2.base.data.Property
 
setAllowGroupRegistration(boolean) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setANDOperation(boolean) - Method in class ambit2.rules.conditions.ConditionExpression
 
setAnnotation(String) - Method in interface ambit2.base.data.study.IValue
 
setAnnotation(String) - Method in class ambit2.base.data.study.Value
 
setAnnotations(PropertyAnnotations) - Method in class ambit2.base.data.Property
 
setAnswer(WizardPanel.ANSWER_MODE) - Method in class ambit2.ui.WizardPanel
 
setAppDomainMethodType(ADomainMethodType) - Method in class ambit2.model.numeric.DataCoverage
 
setAppDomainMethodType(ADomainMethodType) - Method in interface ambit2.model.numeric.IDataCoverage
 
setApplicable(boolean) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setApplicationConditions(List<ICondition>) - Method in class ambit2.reactions.GenericReaction
 
setApplicationRootReference(Reference) - Method in class ambit2.rest.model.builder.ModelBuilder
 
setAromaticAtomsFromBondFlagInfo(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
setArray(int, Array) - Method in class ambit2.db.results.AmbitRows
 
setAsciiStream(int, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
setAssayUUID(UUID) - Method in class ambit2.base.data.study.ProtocolApplication
 
setAssayUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setAssignProperties(boolean) - Method in class ambit2.db.processors.AbstractDescriptorCalculator
 
setAtm(IAtomTypeMatcher) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
setAtom(int, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setAtom_environment(int[]) - Method in class ambit2.descriptors.AtomEnvironment
 
setAtomColorer(RendererModel, IAtomColorer) - Static method in class ambit2.rendering.RendererModelWrapper
 
setAtomComplexities(List<Double>) - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
setAtomComplexityCalculator(AtomComplexity) - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
setAtomContainer(IAtomContainer, boolean) - Method in class ambit2.ui.Panel2D
 
setAtomContainer(IAtomContainer) - Method in class ambit2.ui.Panel2D
 
setAtomDesignation(String) - Method in class ambit2.groupcontribution.groups.AtomGroup
 
setAtomHNeighbours(IAtom, IAtomContainer, int, SmartsConst.HandleHAtoms) - Static method in class ambit2.smarts.smirks.Transformations
 
setAtomID(SLNAtom, int) - Static method in class ambit2.sln.SLNHelper
 
setAtomno(int) - Method in class ambit2.descriptors.AtomEnvironment
 
setAtomNumbers(boolean) - Method in class ambit2.ui.Panel2D
 
setAtomNums(IQueryAtomContainer) - Method in class ambit2.smarts.QuerySequenceElement
 
setAtomNums(IAtomContainer) - Method in class ambit2.smarts.SequenceElement
 
setAtomRadius(RendererModel, Double) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setAtomRadius()
setAtomRingIndices(List<int[]>) - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
setAtoms(IAtom[]) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setAtoms(List<IAtom>) - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
setAtoms(List<IAtom>) - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
setAtoms(List<IAtom>) - Method in class ambit2.structure2name.components.AbstractComponent
 
setAtomSequence(IAtomContainer, IAtom) - Method in class ambit2.smarts.ChemObjectFactory
 
setAtomTopLayers(IAtomContainer) - Static method in class ambit2.smarts.TopLayer
 
setAtomTopLayers(IAtomContainer, Object) - Static method in class ambit2.smarts.TopLayer
 
setAtomtypeasproperties(boolean) - Method in class ambit2.core.processors.AbstractStructureProcessor
Assign atomtypes as atomcontainer properties
setAtomtypingonsmiles(boolean) - Method in class ambit2.core.processors.structure.MoleculeReader
 
setAttributes(SLNContainerAttributes) - Method in class ambit2.sln.SLNContainer
 
setAttributeSelection(IAttributeSelection<Features>) - Method in class ambit2.model.AbstractModel
 
setAttributeSelection(IAttributeSelection<Features>) - Method in interface ambit2.model.IModelDefinition
 
setAutosizeColumns(boolean) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
setAverageSimilarity(double) - Method in interface ambit2.similarity.ISimilarityResultType
 
setAvg(T) - Method in class ambit2.base.data.PropertyStats
 
setB(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setBackColor(RendererModel, Color) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setBackColor()
setBackground(Color) - Method in interface ambit2.core.io.ICompoundImageTools
 
setBackground(Color) - Method in class ambit2.rendering.CompoundImageTools
 
setBackground(Color) - Method in class ambit2.ui.ImageCellRenderer
 
setBaseReference(Reference) - Method in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
setBaseReference(Reference) - Method in class ambit2.rest.rdf.RDFObjectIterator
This is mainly used to create Template to match record uris and determine if they originate from this service
setBaseReference(Reference) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
setBaseReference(Reference) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
setBaseReference(Reference) - Method in class ambit2.rest.rdf.sparql.RDFSparqlIterator
 
setBaseReference(String) - Method in class ambit2.rest.RDFBatchParser
 
setBasicScore(double) - Method in class ambit2.reactions.GenericReaction
 
setBigDecimal(int, BigDecimal) - Method in class ambit2.db.results.AmbitRows
 
setBinaryStream(int, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
setBinWidth(double) - Method in class ambit2.db.chart.XTabChartGenerator
 
setBits(Content) - Method in class ambit2.db.update.fp.Fingerprint
 
setBits(Content) - Method in interface ambit2.db.update.fp.IFingerprint
 
setBlob(int, Blob) - Method in class ambit2.db.results.AmbitRows
 
setBondDesignation(String) - Method in class ambit2.groupcontribution.groups.BondGroup
 
setBonds(IBond[]) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setBoolean(int, boolean) - Method in class ambit2.db.results.AmbitRows
 
setBorderColor(Color) - Method in interface ambit2.core.io.ICompoundImageTools
 
setBorderColor(Color) - Method in class ambit2.rendering.CompoundImageTools
Creates gradient border of this color.
setBorderWidth(int) - Method in class ambit2.rendering.CompoundImageTools
 
setBoxcox(boolean) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
setBrowserMode(IBrowserMode.BrowserMode) - Method in class ambit2.ui.table.BrowsableTableModel
 
setBrowserMode(IBrowserMode.BrowserMode) - Method in interface ambit2.ui.table.IBrowserMode
 
setBuild2D(boolean) - Method in class ambit2.core.processors.StructureNormalizer
 
setBuild2D(boolean) - Method in class ambit2.db.processors.RepositoryWriter
 
setBuilder(Builder) - Method in class ambit2.rest.model.task.CallableModelCreator
 
setBuilder(IChemObjectBuilder) - Method in class ambit2.smarts.ChemObjectFactory
 
setBuilder(IChemObjectBuilder) - Method in class ambit2.smarts.SmartsToChemObject
 
setBundle(SubstanceEndpointsBundle) - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
setBundle(SubstanceEndpointsBundle) - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
setBundle(SubstanceEndpointsBundle) - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
setBundle(SubstanceEndpointsBundle) - Method in class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
setBundle(SubstanceEndpointsBundle) - Method in class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
setBundle_number(UUID) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setBundleRole(BundleRoleFacet) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
setBundles(SubstanceEndpointsBundle[]) - Method in class ambit2.db.reporters.CSVReporter
 
setByte(int, byte) - Method in class ambit2.db.results.AmbitRows
 
setBytes(int, byte[]) - Method in class ambit2.db.results.AmbitRows
 
setC(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setCacheHeaders() - Method in class ambit2.rest.ProtectedResource
 
setCallback(IProcessor<IAtomContainer, IAtomContainer>) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setCallback(IProcessor<IAtomContainer, IAtomContainer>) - Method in class ambit2.tautomers.processor.TautomerProcessor
 
setCancelled(boolean) - Method in class ambit2.pubchem.HTTPRequest
 
setCanonicTautomerMethod(TautomerConst.CanonicTautomerMethod) - Method in class ambit2.tautomers.TautomerManager
 
setCaseSensitive(boolean) - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
setCaseSensitive(boolean) - Method in class ambit2.db.search.structure.QueryFieldMultiple
 
setCategory(String) - Method in class ambit2.base.data.study.Protocol
 
setCategory(String) - Method in class ambit2.db.cache.QueryCachedResults
 
setCategory(String) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
setCategoryType(ICategory.CategoryType) - Method in interface ambit2.base.interfaces.ICategory
 
setCdkDescrMan(CDKDescriptorManager) - Method in class ambit2.groupcontribution.GCMParser
 
setCellEditor(TableCellEditor) - Method in class ambit2.ui.EditableHeader
 
setCellSize(JTable) - Method in class ambit2.ui.QueryBrowser
 
setCellSize(Dimension, int, int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
setCentral_atom(String) - Method in class ambit2.descriptors.AtomEnvironment
 
setChanged() - Method in class ambit2.base.data.Profile
 
setChangeLineSeparators(boolean) - Method in class ambit2.db.reporters.SDFReporter
 
setCharacterStream(int, Reader, int) - Method in class ambit2.db.results.AmbitRows
 
setChemicalsOnly(boolean) - Method in class ambit2.db.readers.RetrieveField
 
setChemicalsOnly(boolean) - Method in class ambit2.db.readers.RetrieveModelTemplates
 
setChemicalsOnly(boolean) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setChemicalsOnly(Boolean) - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
setChemicalsOnly(boolean) - Method in class ambit2.db.readers.RetrieveTemplate
 
setChemicalsOnly(boolean) - Method in class ambit2.db.results.StoredQueryTableModel
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.property.AbstractPropertyRetrieval
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
setChemicalsOnly(boolean) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setChunkSize(int) - Method in class ambit2.db.reporters.QueryPacketReporter
 
setCitation(ProtocolApplication<Protocol, IParams, String, IParams, String>) - Method in class ambit2.core.io.StringArrayHeader
 
setCity(String) - Method in class ambit2.base.data.AmbitUser
 
setClassifier(Classifier) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
setClassifier(Classifier) - Method in class ambit2.rest.task.weka.WekaPredictor
 
setClassUnknown(boolean) - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
setClazz(String) - Method in class ambit2.base.data.ClassHolder
 
setClazz(Class) - Method in class ambit2.base.data.Property
 
setCleanKekuleBonds(boolean) - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
setClearComposition(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setClearIsotopes(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setClearMeasurements(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setClob(int, Clob) - Method in class ambit2.db.results.AmbitRows
 
setCloseConnection(boolean) - Method in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
setCloseModel(boolean) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
setClusterer(Clusterer) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
setClusterer(Clusterer) - Method in class ambit2.rest.task.weka.WekaPredictor
 
setCMLSMARTSProperties(IAtomContainer) - Method in class ambit2.smarts.CMLUtilities
Generates attributes and sets atom & bond attributes for every atom as atom properties
setCmode(DatasetCenterPoint) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
setCode(int) - Method in exception ambit2.base.exceptions.HttpException
 
setColorAtomsByType(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setColorAtomsByType()
setColStatPercentageThreshold(Double) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setColumnModel(TableColumnModel) - Method in class ambit2.ui.EditableHeader
 
setColumns(String[]) - Method in class ambit2.ui.editors.BeanEditor
 
setCombine(String) - Method in class ambit2.db.search.QueryInfo
 
setCombine_as_and(boolean) - Method in class ambit2.db.search.QueryCombined
 
setCombine_queries(QueryCombined.COMBINE) - Method in class ambit2.db.search.QueryCombined
 
setCommand(ICommand.COMMAND) - Method in interface ambit2.db.processors.ICommand
 
setCommand(String) - Method in class ambit2.db.results.AmbitRows
 
setCommand(StructureEditorProcessor._commands) - Method in class ambit2.rendering.StructureEditorProcessor
 
setCommentChar(String) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
setComments(String) - Method in class ambit2.db.version.AmbitDBVersion
 
setCompactShape(RendererModel, BasicAtomGenerator.Shape) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setCompactShape()
setCompanyName(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setCompanyUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setCompleted(boolean) - Method in class ambit2.ui.table.BrowsableTableModel
 
setCompleted(boolean) - Method in interface ambit2.ui.table.IFindNavigator
 
setComponentInCombination(int, int[]) - Method in class ambit2.smarts.ComponentMapping
 
setComponentLevelGrouping(boolean) - Method in class ambit2.smarts.SmartsParser
 
setComponents(List<ISGroup>) - Method in class ambit2.core.groups.ContainerGroup
 
setCompositionName(String) - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
setCompositionRelation(CompositionRelation) - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
setCompositionUUID(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setCompositionUUID(String) - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
setCompound(IStructureRecord) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
setCompoundIDS(IStructureRecord, int, int) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
setCompoundReporter(CompoundURIReporter<IQueryRetrieval<IStructureRecord>>) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setConcurrency(int) - Method in class ambit2.db.results.AmbitRows
 
setCondition(C) - Method in class ambit2.db.search.AbstractQuery
 
setCondition(NumberCondition) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setCondition(IQueryCondition) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setCondition1(String) - Method in class ambit2.db.search.QueryInfo
 
setCondition2(String) - Method in class ambit2.db.search.QueryInfo
 
setCondition3(String) - Method in class ambit2.db.search.QueryInfo
 
setConditions(CONDITIONS) - Method in class ambit2.base.data.study.EffectRecord
 
setConditions(ArrayList<IMoleculeFilterCondition>) - Method in class ambit2.core.filter.MoleculeFilter
 
setConditions(List<ICondition>) - Method in class ambit2.reactions.GenericReaction
 
setConditions(ArrayList<ICondition>) - Method in class ambit2.rules.conditions.ConditionExpression
 
setConditionScores(List<Double>) - Method in class ambit2.reactions.GenericReaction
 
setConditionType(ReactionGroupCondition.RGConditionType) - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
setConfig(String) - Method in class ambit2.vega.VegaShell
 
setConfiguration(Configuration) - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
setConnection(Connection) - Method in class ambit2.db.DbReaderStructure
 
setConnection(Connection) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
setConnection(Connection) - Method in class ambit2.db.processors.DBProcessorsChain
 
setConnection(Connection) - Method in class ambit2.db.processors.DbStructureWriter
 
setConnection(Connection) - Method in class ambit2.db.processors.DescriptorsCalculator
 
setConnection(Connection) - Method in class ambit2.db.processors.PropertyImporter
 
setConnection(Connection) - Method in class ambit2.db.processors.RepositoryWriter
 
setConnection(Connection) - Method in class ambit2.db.processors.ValueWriterNew
 
setConnection(Connection) - Method in class ambit2.db.readers.ValuesByTemplateReader
 
setConnection(Connection) - Method in class ambit2.db.reporters.AbstractImageReporter
 
setConnection(Connection) - Method in class ambit2.db.reporters.QueryPacketReporter
 
setConnection(Connection) - Method in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
setConnection(Connection) - Method in class ambit2.db.RepositoryReader
 
setConnection(Connection) - Method in class ambit2.db.results.StoredQueryTableModel
 
setConnection(Connection) - Method in class ambit2.db.search.property.ValuesReader
 
setConnection(Connection) - Method in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
setConnection(Connection) - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
setConnection(Connection) - Method in class ambit2.db.StatementExecutor
 
setConnection(Connection) - Method in class ambit2.db.substance.processor.DBBundleStudyWriter
 
setConnection(Connection) - Method in class ambit2.db.substance.processor.DBMatrixValueMarker
 
setConnection(Connection) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setConnection(Connection) - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
setConnection(Connection) - Method in class ambit2.dbui.dictionary.OntologyEditor
query[side.ordinal()].setValue(((Dictionary)selected).getTemplate()); rows[side.ordinal()].setQuery(query[side.ordinal()]);
setConnection(Connection) - Method in class ambit2.dbui.ProfileEditor
 
setConnection(Connection) - Method in class ambit2.dbui.QueryDatasetEditor
 
setConnection(Connection) - Method in class ambit2.dbui.QueryFieldEditor
 
setConnection(Connection) - Method in class ambit2.dbui.QueryFieldNumericEditor
 
setConnection(Connection) - Method in class ambit2.dbui.QueryStoredResultsEditor
 
setConnection(Connection) - Method in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
setConnection(Connection) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
setContent(String) - Method in class ambit2.base.data.StructureRecord
 
setContent(String) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setContent(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setContent(T) - Method in class ambit2.core.data.model.Algorithm
 
setContent(Content) - Method in interface ambit2.core.data.model.IEvaluation
 
setContent(Content) - Method in class ambit2.core.data.model.ModelWrapper
 
setContent(String) - Method in interface ambit2.db.search.IStoredQuery
 
setContent(String) - Method in class ambit2.db.search.StoredQuery
 
setContent(Content) - Method in class ambit2.model.evaluation.EvaluationStats
 
setContentColumn(int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
setContentMediaType(String) - Method in class ambit2.core.data.model.ModelWrapper
 
setContext(Context) - Method in class ambit2.rest.DBConnection
 
setContribution(double) - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
setContribution(double) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
setContribution(double) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
setContribution(double) - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
setContribution(double) - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
setContribution(double) - Method in interface ambit2.groupcontribution.groups.IGroup
 
setContribution(double) - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
setControlsVisible(boolean) - Method in class ambit2.ui.DelimitersPanel
 
setConvertToString(boolean) - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
 
setCopied(boolean) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setCopied(boolean) - Method in class ambit2.base.data.study.ValueAnnotated
 
setCopy(boolean) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setCorrectionFactors(List<ICorrectionFactor>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setCount(long) - Method in class ambit2.base.data.PropertyStats
 
setCount(int) - Method in class ambit2.base.facet.AbstractFacet
 
setCountry(String) - Method in class ambit2.base.data.AmbitUser
 
setCreated(long) - Method in class ambit2.base.data.Bookmark
 
setCreated(long) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setCreated(long) - Method in class ambit2.db.version.AmbitDBVersion
 
setCreateSubLevels(boolean) - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
setCreator(String) - Method in class ambit2.base.data.Bookmark
 
setCreator(String) - Method in class ambit2.core.data.model.ModelWrapper
 
setCreator(String) - Method in class ambit2.db.facets.bookmarks.BookmarksByTopicFacet
 
setCredentials(C) - Method in class ambit2.rest.wrapper.WrappedService
 
setCurIncrStep(TautomerIncrementStep) - Method in class ambit2.tautomers.TautomerManager
 
setCurrentRecord(long) - Method in interface ambit2.base.interfaces.IInputOutputState
 
setCurrentRecord(long) - Method in class ambit2.core.io.FileState
 
setCurrentRecord(long) - Method in class ambit2.core.processors.batch.DefaultIOState
 
setCurrentSide(ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
setCustomExcludeRegionsSmarts(List<String>) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setCustomGroupLocalDescriptors(List<List<ILocalDescriptor>>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setCustomGroups(List<IGroup.Type>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setD(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setDatabase(String) - Method in class ambit2.db.LoginInfo
 
setDatabase(String) - Method in class ambit2.dbui.LoginInfoBean
 
setDataEntryID(int) - Method in class ambit2.base.data.StructureRecord
 
setDataEntryID(int) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setDataEntryID(int) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setDataModel(TableModel) - Method in class ambit2.ui.table.BrowsableTableModel
 
setDataset(DATASET) - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.DbStructureWriter
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.PropertyImporter
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.PropertyValuesWriter
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.RepositoryWriter
 
setDataset(SourceDataset) - Method in class ambit2.db.processors.ValueWriterNew
 
setDataset(SourceDataset) - Method in class ambit2.db.search.QueryInfo
 
setDataset(SourceDataset) - Method in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
setDataset(SourceDataset) - Method in class ambit2.db.search.structure.QueryDataset
 
setDataset(ISourceDataset) - Method in class ambit2.db.simiparity.space.QMap
 
setDatasetCenterPoint(DatasetCenterPoint) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
setDatasetID(int) - Method in class ambit2.base.data.StructureRecord
 
setDatasetID(int) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setDatasetID(int) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setDatasetIndividual(String) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setDatasetReportRef(Reference) - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
setDatasets(SourceDataset[]) - Static method in class ambit2.db.search.QueryInfo
 
setDataSourceName(String) - Method in class ambit2.db.results.AmbitRows
 
setDate(long) - Method in class ambit2.base.data.Bookmark
 
setDate(int, Date) - Method in class ambit2.db.results.AmbitRows
 
setDate(int, Date, Calendar) - Method in class ambit2.db.results.AmbitRows
 
setDbname(String) - Method in class ambit2.db.version.AmbitDBVersion
 
setDefaultColumnIndices() - Method in class ambit2.groupcontribution.dataset.LocalPropertiesIterator
 
setDefaultImage(BufferedImage) - Method in class ambit2.rendering.CompoundImageTools
 
setDelete(boolean) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setDeleted(boolean) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setDeleted(boolean) - Method in class ambit2.base.data.study.ValueAnnotated
 
setDeleteMatrix(boolean) - Method in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
setDelimiter(String) - Method in class ambit2.core.io.QuotedTokenizer
Set the delimiter for the next token.
setDelimiter(String) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
setDelimiter(String) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
setDependent(Template) - Method in class ambit2.core.data.model.ModelWrapper
 
setDescription(String) - Method in class ambit2.base.data.Bookmark
 
setDescription(String) - Method in class ambit2.base.data.ClassHolder
 
setDescription(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setDescription(String) - Method in class ambit2.core.data.model.Algorithm
 
setDescriptor(DESCRIPTOR) - Method in class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor
 
setDescriptor(IMolecularDescriptor) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
setDescriptorName(String) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
setDescriptorName(String) - Method in interface ambit2.rules.conditions.IDescriptorValueCondition
 
setDescriptorNames(String[]) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
setDescriptors(Profile<Property>) - Method in class ambit2.db.processors.AbstractDescriptorCalculator
 
setDescriptors(Object[]) - Method in class ambit2.dragon.DragonShell
Descriptor or block names expected
setDescriptors() - Method in class ambit2.dragon.DragonShell
 
setDescriptors(List<DescriptorInfo>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setDescriptorSolver(IDescriptorSolver) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
setDescriptorSolver(IDescriptorSolver) - Method in interface ambit2.rules.conditions.IDescriptorValueCondition
 
setDescriptorSolver(IDescriptorSolver) - Method in interface ambit2.rules.conditions.INeedsDescriptorSolver
 
setDescriptoSolverForReactDB() - Method in class ambit2.reactions.reactor.Reactor
 
setDetails(String) - Method in exception ambit2.rest.exception.ImportSubstanceException
 
setDetailsCaption(String) - Method in class ambit2.ui.editors.BeanEditor
 
setDisposition(Representation) - Method in class ambit2.rest.RemoteStreamConvertor
 
setDistance(double) - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
setDistance(IDistanceFunction<T>) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
setDistance(Float) - Method in class ambit2.similarity.measure.DistanceComparable
 
setDistanceFunction(IDistanceFunction<T>) - Method in interface ambit2.similarity.knn.INearestNeighborsSearch
 
setDistanceFunction(IDistanceFunction<T>) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
setDistanceFunction(IDistanceFunction<T>) - Method in interface ambit2.similarity.stats.INearestNeighborsSearch
 
setDocumentType(String) - Method in class ambit2.db.substance.CreateSubstance
 
setDocumentUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setDocumentUUID(String) - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
setDomainName(String) - Method in class ambit2.model.numeric.DataCoverage
 
setDouble(int, double) - Method in class ambit2.db.results.AmbitRows
 
setDrawNumbers(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setDrawNumbers(atomNumbers);
setDropHydrogens(boolean) - Method in class ambit2.smi23d.ShellSmi2SDF
 
setEditable(boolean) - Method in interface ambit2.base.interfaces.IAmbitEditor
 
setEditable(boolean) - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
setEditable(boolean) - Method in class ambit2.dbui.dictionary.OntologyEditor
 
setEditable(boolean) - Method in class ambit2.dbui.ProfileEditor
 
setEditable(boolean) - Method in class ambit2.dbui.QueryCombinedEditor
 
setEditable(boolean) - Method in class ambit2.dbui.QueryEditor
 
setEditable(boolean) - Method in class ambit2.dbui.QueryInfoEditor
 
setEditable(boolean) - Method in class ambit2.dbui.QueryScopeEditor
 
setEditable(boolean) - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
setEditable(boolean) - Method in class ambit2.ui.editors.BeanEditor
 
setEditable(boolean) - Method in class ambit2.ui.editors.EditorPanel
 
setEditable(boolean) - Method in class ambit2.ui.editors.FileSelector
 
setEditable(boolean) - Method in class ambit2.ui.editors.ListEditor
 
setEditable(boolean) - Method in class ambit2.ui.editors.PreferencesPanel
 
setEditable(boolean) - Method in class ambit2.ui.editors.SelectFieldsPanel
 
setEditable(boolean) - Method in class ambit2.ui.editors.TemplateEditor
 
setEditable(boolean) - Method in class ambit2.ui.jmol.Panel3D
 
setEditable(boolean) - Method in class ambit2.ui.Panel2D
 
setEditable(boolean) - Method in class ambit2.ui.QueryBrowser
 
setEditingColumn(int) - Method in class ambit2.ui.EditableHeader
 
setEditor(IAmbitEditor) - Method in class ambit2.ui.editors.EditorPanel
 
setEffects(List<EffectRecord<ENDPOINT, CONDITIONS, UNIT>>) - Method in class ambit2.base.data.study.ProtocolApplication
 
setEmail(String) - Method in class ambit2.base.data.AmbitUser
 
setEnabled(boolean) - Method in class ambit2.base.data.Property
 
setEnabled(boolean) - Method in class ambit2.base.external.CommandShell
 
setEnabled(boolean) - Method in class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty
 
setEnabled(boolean) - Method in class ambit2.core.processors.AbstractStructureProcessor
 
setEnabled(boolean) - Method in class ambit2.descriptors.FunctionalGroup
 
setEnabled(boolean) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
setEnabled(boolean) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setEnabled(boolean) - Method in interface ambit2.ml.io.IMLOutput
 
setEnabled(boolean) - Method in class ambit2.ml.io.OutputARFF
 
setEnabled(boolean) - Method in class ambit2.ml.io.OutputVW
 
setEnabled(boolean) - Method in class ambit2.ml.io.OutputVW_LDA
 
setEnabled(boolean) - Method in class ambit2.rest.model.predictor.ExternalModel
 
setEnabled(boolean) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setEnabled(boolean) - Method in class ambit2.some.SOMEVisualizer
 
setEnableFeatures(boolean) - Method in class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle
 
setEnableFeatures(boolean) - Method in class ambit2.db.update.bundle.substance.ReadSubstancesByBundle
 
setEndpoint(ENDPOINT) - Method in class ambit2.base.data.study.EffectRecord
 
setEndpoint(String) - Method in class ambit2.base.data.study.Protocol
 
setEndpoint(String) - Method in class ambit2.core.data.model.Algorithm
 
setEndpoint(String) - Method in class ambit2.core.data.model.ModelQueryResults
 
setEndpoint(String) - Method in class ambit2.db.substance.QueryCountEndpoints
 
setEndpointBundle(SubstanceEndpointsBundle) - Method in class ambit2.export.isa.json.ISAJsonExporter
 
setEndpointcategory(String) - Method in class ambit2.base.data.substance.SubstanceProperty
 
setEndpointGroup(Integer) - Method in class ambit2.base.data.study.EffectRecord
 
setEndpointName(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
setEndpointType(String) - Method in class ambit2.base.data.study.EffectRecord
 
setEndpointURI(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
setEnergyRanking(EnergyRanking) - Method in class ambit2.tautomers.TautomerManager
 
setError(AbstractPropertyWriter.mode) - Method in class ambit2.db.readers.PropertyValue
 
setError(Exception) - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
setError(ResourceException) - Method in class ambit2.rest.task.Task
 
setErrorHandler(IChemObjectReaderErrorHandler) - Method in class ambit2.core.io.IteratingFileReader
setErrorHandler(IChemObjectReaderErrorHandler) - Method in class ambit2.core.io.RawIteratingWrapper
setErrorHandler(IChemObjectReaderErrorHandler) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
setErrorIfDisconnected(boolean) - Method in class ambit2.mopac.AbstractMopacShell
 
setErrorIfDisconnected(boolean) - Method in class ambit2.mopac.DescriptorMopacShell
 
setErrors(List<String>) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
setErrorValue(double) - Method in class ambit2.base.data.study.EffectRecord
 
setErrQualifier(String) - Method in class ambit2.base.data.study.EffectRecord
 
setEscapeProcessing(boolean) - Method in class ambit2.db.results.AmbitRows
 
setEvaluated(boolean) - Method in class ambit2.featureselection.AbstractAttributeSelection
 
setEvaluated(boolean) - Method in interface ambit2.featureselection.IAttributeSelection
 
setEvaluation(List<IEvaluation<EVCONTENT>>) - Method in class ambit2.core.data.model.ModelWrapper
 
setExample(String) - Method in class ambit2.descriptors.FunctionalGroup
 
setExample(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setException(Throwable) - Method in class ambit2.rest.task.ExecutableTask
 
setExcludeAromaticSystems(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeAtomIndices(List<Integer>) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeAzideGroups(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeHidden(boolean) - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
setExcludeNitroGroup(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeNitroGroupPartially(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeNitroxides(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExcludeSulfonylGroups(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setExe(String) - Method in class ambit2.base.external.Command
 
setExitCode(int) - Method in class ambit2.base.external.CommandShell
 
setExpanded(boolean) - Method in interface ambit2.core.groups.IExpandable
 
setExpanded(boolean) - Method in class ambit2.core.groups.MultipleGroup
 
setExpanded(boolean) - Method in class ambit2.core.groups.SuperAtom
 
setExperimentalConditionsInfo(String) - Method in class ambit2.reactions.GenericReaction
 
setExperimentalConditionsScore(double) - Method in class ambit2.reactions.GenericReaction
 
setExplicitH(boolean) - Method in class ambit2.ui.Panel2D
 
setExplicitHAtomData(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
setExportJsonConfig(File) - Method in class ambit2.export.isa.json.ISAJsonExporter
 
setExportJsonConfig(File) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setExtendedURI(boolean) - Method in class ambit2.base.data.substance.SubstanceProperty
 
setExtension(String) - Method in class ambit2.base.io.MolFileFilter
 
setExternalDataFile(File) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setExternalDataSet(DataSet) - Method in class ambit2.groupcontribution.Learner
 
setExternalids(List<ExternalIdentifier>) - Method in class ambit2.base.data.SubstanceRecord
 
setExternId(String) - Method in class ambit2.reactions.GenericReaction
 
setFactory(String) - Method in class ambit2.core.data.HashIntDescriptorResult
 
setFactory(AtomTypeFactory) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
setFamily(String) - Method in class ambit2.descriptors.FunctionalGroup
 
setFeatureValue(Item, Feature, RDFNode) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
setFeatureValue(Instance, Attribute, RDFNode) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
setFeatureValue(IStructureRecord, Property, RDFNode) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
setFetchDirection(int) - Method in class ambit2.db.results.AmbitRows
 
setFetchSize(int) - Method in class ambit2.db.results.AmbitRows
 
setFieldFormat(String) - Method in class ambit2.core.groups.DataGroup
 
setFieldname(SubstanceByCategoryFacet) - Method in class ambit2.db.facets.bundle.EndpointRoleByBundle
 
setFieldname(IStructureRecord) - Method in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
setFieldname(Template) - Method in class ambit2.db.readers.RetrieveTemplateStructure
 
setFieldname(F) - Method in class ambit2.db.search.AbstractQuery
 
setFieldname(String) - Method in class ambit2.db.search.property.RetrieveFieldNamesByType
 
setFieldname(String) - Method in class ambit2.db.search.property.RetrieveProfile
 
setFieldname(String) - Method in class ambit2.db.search.property.TemplateQuery
 
setFieldname(Property) - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
setFieldname(List<PropertyTemplateStats>) - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
setFieldname(ClassHolder) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setFieldname(String) - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
setFieldname(SCOPE) - Method in class ambit2.db.search.structure.ScopeQuery
 
setFieldname(SubstanceRecord) - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
setFieldname(String) - Method in class ambit2.db.substance.ReadByReliabilityFlags
 
setFieldname(String) - Method in class ambit2.db.substance.ReadSubstanceByName
 
setFieldname(SubstanceRecord) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setFieldname(String) - Method in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
setFieldname1(String) - Method in class ambit2.db.search.QueryInfo
 
setFieldname2(String) - Method in class ambit2.db.search.QueryInfo
 
setFieldname3(String) - Method in class ambit2.db.search.QueryInfo
 
setFieldnames(String[]) - Static method in class ambit2.db.search.QueryInfo
 
setFields(TypedListModel<Property>) - Method in class ambit2.base.data.PropertiesTableModel
 
setFieldType(String) - Method in class ambit2.core.groups.DataGroup
 
setFile(File) - Method in class ambit2.core.io.FileState
 
setFile(File, IChemFormat) - Method in class ambit2.core.io.FileState
 
setFileExtension(String) - Method in class ambit2.rest.RemoteStreamConvertor
 
setFileFormat(IChemFormat) - Method in class ambit2.core.processors.batch.DefaultInputState
 
setFileHeader(ExternalDataFileHeader) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
setFilename(String) - Static method in class ambit2.base.config.Preferences
 
setFilename(String) - Method in class ambit2.base.data.study.StructureRecordValidator
 
setFilename(String) - Method in class ambit2.core.io.FileState
 
setFileNamePrefix(String) - Method in class ambit2.rest.RemoteStreamConvertor
 
setFiles(File[]) - Method in class ambit2.core.io.IteratingFolderReader
 
setFiles(File[]) - Method in class ambit2.core.io.RawIteratingFolderReader
 
setFilter(int, Object) - Method in interface ambit2.base.data.IFilteredColumns
 
setFilter(int, Object) - Method in class ambit2.db.results.StoredQueryTableModel
 
setFilter(int, Object) - Method in class ambit2.ui.table.BrowsableTableModel
 
setFilterConfig(String) - Method in class ambit2.rest.wrapper.WrappedService
 
setFiltered(boolean) - Method in class ambit2.core.groups.FilteredList
 
setFiltered(boolean) - Method in interface ambit2.core.groups.IFiltered
 
setFiltered(boolean) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setFingerPrintLength(int) - Method in class ambit2.model.structure.DataCoverageFingerprints
 
setFirstName(String) - Method in class ambit2.base.data.AmbitUser
 
setFirstStructure(FIRSTSTRUC) - Method in interface ambit2.base.interfaces.IStructureRelation
 
setFirstStructure(FIRSTSTRUC) - Method in class ambit2.base.relation.AbstractRelation
 
setFirstValue(int) - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
setFirstValue(int) - Method in class ambit2.core.filter.RecordIntervalCondition
 
setFisher(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setFixErrors(boolean) - Method in class ambit2.base.data.study.StructureRecordValidator
 
setFlag(T, boolean) - Method in class ambit2.domain.stats.datastructures.Histogram
 
setFlag(T, boolean) - Method in class ambit2.similarity.stats.Histogram
 
setFlag(boolean) - Method in class ambit2.similarity.stats.MutableInt
 
setFlagAddImplicitHAtomsOnResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagAllowBondExpressionInRingClosure(boolean) - Method in class ambit2.sln.SLNParser
 
setFlagApplyDuplicationCheckInChI(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagApplyDuplicationCheckIsomorphism(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagApplyDuplicationFilter(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagApplyExcludeFilter(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagApplyStereoTransformation(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagApplyWarningFilter(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagAromaticityTransformation(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagCheckAromaticityOnResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagCheckResultStereo(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagCheckStereoElements(boolean) - Method in class ambit2.smarts.IsomorphismTester
 
setFlagCheckStereoElements(boolean) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
setFlagClearAromaticityBeforeResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
Typically this flag should be true since some aromatic atoms may have lost their aromaticity
setFlagClearExcplicitHAtomsBeforeResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagClearHybridizationBeforeResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules
setFlagClearImplicitHAtomsBeforeResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules
setFlagConvertAddedImplicitHToExplicitOnResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
Typically if this flag is true it is expected that FlagAddImplicitHAtomsOnResultProcess = false
setFlagConvertExplicitHToImplicitOnResultProcess(boolean) - Method in class ambit2.smarts.SMIRKSManager
Typically if this flag is true it is expected that FlagAddImlicitHAtomsOnResultProcess= false
setFlagExcludeWarningTautomers(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagExplicitHAtoms(boolean) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setFlagFilterEquivalentMappings(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagFilterIncorrectHAtomsStructures(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagFilterIncorrectValencySumStructures(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagHAtomsTransformation(boolean) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagHAtomsTransformationMode(SmartsConst.HandleHAtoms) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagPrepareTarget(boolean) - Method in class ambit2.smarts.groups.GroupMatch
 
setFlagProcessResultStructures(boolean) - Method in class ambit2.smarts.SMIRKSManager
Triggers an optional (pre)processing for further use of reaction result
setFlagReactRecursively(boolean) - Method in class ambit2.reactions.reactor.Reactor
 
setFlagSSMode(SmartsConst.SSM_MODE) - Method in class ambit2.smarts.groups.GroupMatch
 
setFlagSSMode(SmartsConst.SSM_MODE) - Method in class ambit2.smarts.SMIRKSManager
 
setFlagStoreCACTVSRank(boolean) - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
setFlagStoreRemovedByFilterTautomers(boolean) - Method in class ambit2.tautomers.FilterTautomers
 
setFlagTolerateSpaces(boolean) - Method in class ambit2.sln.SLNParser
 
setFlagUse(boolean) - Method in class ambit2.reactions.GenericReaction
 
setFlagUse(boolean) - Method in class ambit2.reactions.Reaction
 
setFlagUseAbsolutePathForFileLocation(boolean) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
setFloat(int, float) - Method in class ambit2.db.results.AmbitRows
 
setFolders(String[]) - Method in class ambit2.db.reporters.CSVReporter
 
setFontManager(IFontManager) - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
The font manager must be set by any renderer that uses this class! This manager is needed to keep track of fonts of the right size.
setForceOrdering(boolean) - Method in class ambit2.db.search.structure.QuerySimilarity
 
setForceOrdering(boolean) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setForceReadRDFLocalObjects(boolean) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
setForceStructureDelete(boolean) - Method in class ambit2.db.update.chemical.DeleteChemical
 
setFormat(String) - Method in class ambit2.base.data.StructureRecord
 
setFormat(String) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setFormat(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setFormat(Algorithm.AlgorithmFormat) - Method in class ambit2.core.data.model.Algorithm
 
setFormula(String) - Method in class ambit2.base.data.StructureRecord
 
setFormula(String) - Method in interface ambit2.base.interfaces.IChemical
 
setFormula(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setFormula(String) - Method in class ambit2.db.search.QueryInfo
 
setFp1024_screening(boolean) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setFpmode(FPTable) - Method in class ambit2.descriptors.processors.BitSetGenerator
 
setFptable(FPTable) - Method in class ambit2.db.update.fp.CreateFingerprintChemical
 
setFptable(FPTable) - Method in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
setFragmenationRules(ArrayList<FragmentationRule>) - Method in class ambit2.reactions.fragmentation.Fragmentation
 
setFrameOptions(String) - Method in class ambit2.rest.ProtectedResource
 
setFrequency(int) - Method in class ambit2.db.update.fp.Fingerprint
 
setFrequency(int) - Method in interface ambit2.db.update.fp.IFingerprint
 
setFrequency(int) - Method in class ambit2.descriptors.AtomEnvironment
 
setFunction(String) - Method in class ambit2.base.relation.composition.Proportion
 
setFunctions(List<IFunction>) - Method in class ambit2.rules.functions.NestedFunctions
 
setG2(double) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setGenerate2D(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateInChI(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateSmiles(boolean) - Method in class ambit2.smi23d.ShellSmi2SDF
 
setGenerateSMILES(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateSMILES_Aromatic(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateSMILES_Canonical(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateStereofrom2D(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGenerateTautomers(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setGlobalDictionary(SLNDictionary) - Method in class ambit2.sln.SLNContainer
 
setGroundTruth(IAtomContainer) - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck
 
setGroup(SubstanceEndpointsBundle) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
setGroup(SourceDataset) - Method in class ambit2.db.update.dataset.DatasetAddStructure
 
setGroup(Dictionary) - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
setGroup(SessionID) - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
setGroup(String) - Method in class ambit2.reactions.sets.ReactionData
 
setGroupByInterpretationResult(boolean) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
setGroupDesignation(String) - Method in class ambit2.groupcontribution.groups.DGroup
 
setGroupDesignation(String) - Method in class ambit2.groupcontribution.groups.GGroup
 
setGroupMatch(GroupMatch) - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
setGroupProperties(Profile) - Method in class ambit2.db.reporters.QueryHeaderReporter
 
setGroupProperties(Profile) - Method in class ambit2.db.reporters.SDFReporter
 
setGroupProperties(Profile) - Method in class ambit2.db.reporters.SmilesReporter
 
setGroupProperties(Profile) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setGroups(List<FunctionalGroup>) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
setGroups(Map<String, IGroup>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setGroupVisible(IChemObject, boolean) - Static method in class ambit2.core.groups.AbstractGroup
 
setGuidance(String) - Method in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
setGuideline(List<String>) - Method in class ambit2.base.data.study.Protocol
 
setHandlePrescreen(boolean) - Method in class ambit2.db.DbReader
 
setHandler(String) - Method in class ambit2.rest.wrapper.WrappedService
 
setHashCode(int) - Method in class ambit2.core.io.FileState
 
setHasTopic(String) - Method in class ambit2.base.data.Bookmark
 
setHeader(Map) - Method in class ambit2.core.io.FilesWithHeaderWriter
Creates header from Hashtable keys Used for default header - created from properties of the first molecule written
setHeader(ArrayList) - Method in class ambit2.core.io.FilesWithHeaderWriter
 
setHeader(ArrayList) - Method in class ambit2.core.io.FileWithHeaderWriter
 
setHeader(Map) - Method in class ambit2.core.io.FileWithHeaderWriter
Creates header from Hashtable keys Used for default header - created from properties of the first molecule written
setHeader(ArrayList<StringArrayHeader>) - Method in class ambit2.core.io.StringArrayHeader
 
setHeader(ResultSet, Bucket) - Method in class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
setHeaderColumn(int, String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
setHeaderEditable(boolean) - Method in class ambit2.ui.EditableHeaderTableColumn
 
setHeaderEditor(TableCellEditor) - Method in class ambit2.ui.EditableHeaderTableColumn
 
setHeaders(String[]) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
setHeight(int) - Method in class ambit2.db.chart.ChartGenerator
 
setHeight(int) - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
setHeight(int) - Method in class ambit2.search.csls.CSLSImageRequest
 
setHelp(String) - Method in class ambit2.ui.editors.SelectFieldsPanel
 
setHidden(boolean) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setHidden(boolean) - Method in class ambit2.core.data.model.ModelQueryResults
 
setHigh(T) - Method in class ambit2.similarity.stats.Bin
 
setHint(String) - Method in class ambit2.descriptors.FunctionalGroup
 
setHint(String) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
setHint(String) - Method in interface ambit2.smarts.query.ISmartsPattern
 
setHiRelation(IValue.Relation) - Method in interface ambit2.rules.conditions.value.IValueInterval
 
setHiRelation(IValue.Relation) - Method in class ambit2.rules.conditions.value.ValueInterval
 
setHiValue(double) - Method in interface ambit2.rules.conditions.value.IValueInterval
 
setHiValue(double) - Method in class ambit2.rules.conditions.value.ValueInterval
 
setHost(String) - Method in class ambit2.pubchem.NCISearchProcessor
 
setHostname(String) - Method in class ambit2.db.LoginInfo
 
setHostname(String) - Method in class ambit2.dbui.LoginInfoBean
 
setHtmlbyTemplate(boolean) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
setHtmlbyTemplate(boolean) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
setHtmlbyTemplate(boolean) - Method in class ambit2.rest.freemarker.FreeMarkerSupport
 
setHttpMethod(String) - Method in class ambit2.pubchem.HTTPRequest
 
setHydrogens(boolean) - Method in class ambit2.balloon.ShellBalloon
 
setHydrogens(boolean) - Method in class ambit2.core.processors.structure.FingerprintGenerator
 
setHydrogens(boolean) - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
setI5mode(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setIcon(String) - Method in class ambit2.base.data.ClassHolder
 
setID(int) - Method in class ambit2.base.data.AbstractDataset
 
setId(int) - Method in class ambit2.base.data.Bookmark
 
setId(int) - Method in interface ambit2.base.data.ILiteratureEntry
 
setID(int) - Method in interface ambit2.base.data.ISourceDataset
 
setId(int) - Method in class ambit2.base.data.LiteratureEntry
 
setId(int) - Method in class ambit2.base.data.Property
 
setId(int) - Method in class ambit2.base.data.SourceDataset
 
setID(int) - Method in class ambit2.base.data.SourceDataset
 
setId(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setID(int) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setId(int) - Method in class ambit2.base.data.Template
 
setId(String) - Method in class ambit2.core.data.model.Algorithm
 
setId(Integer) - Method in class ambit2.core.data.model.ModelWrapper
 
setID(int, int) - Method in class ambit2.db.chemrelation.DeleteStructureRelation
 
setID(int, int) - Method in class ambit2.db.chemrelation.UpdateStructureRelation
 
setId(int) - Method in class ambit2.db.readers.PropertyValue
 
setId(Integer) - Method in class ambit2.db.search.AbstractQuery
 
setId(Integer) - Method in class ambit2.db.search.property.FilteredCount
 
setId(Integer) - Method in class ambit2.db.search.QueryCombined
 
setId(Integer) - Method in class ambit2.db.search.StoredQuery
 
setID(int) - Method in class ambit2.db.search.StoredQuery
 
setId(Integer) - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
setId(Integer) - Method in class ambit2.db.search.structure.QueryFunctionalGroups
 
setId(Integer) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setId(Integer) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setId(Integer) - Method in class ambit2.db.search.structure.ScopeQuery
 
setId(Integer) - Method in class ambit2.db.SessionID
 
setId(int) - Method in class ambit2.db.simiparity.space.QMap
 
setID(int, int) - Method in class ambit2.db.substance.CreateSubstance
 
setID(int, int) - Method in class ambit2.db.substance.DeleteSubstance
 
setID(int, int) - Method in class ambit2.db.substance.ids.UpdateSubstanceIdentifiers
 
setID(int, int) - Method in class ambit2.db.substance.relation.DeleteSubstanceRelation
 
setID(int, int) - Method in class ambit2.db.substance.relation.UpdateSubstanceRelation
 
setID(int, int) - Method in class ambit2.db.substance.study.DeleteEffectRecords
 
setID(int, int) - Method in class ambit2.db.substance.study.DeleteStudy
 
setId(Integer) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setID(int, int) - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
setID(int, int) - Method in class ambit2.db.substance.study.UpdateSubstanceStudy
 
setID(int, int) - Method in class ambit2.db.substance.UpdateSubstance
 
setID(int, int) - Method in class ambit2.db.update.bookmark.CreateBookmark
 
setID(int, int) - Method in class ambit2.db.update.bookmark.DeleteBookmark
 
setID(int, int) - Method in class ambit2.db.update.bookmark.UpdateBookmark
 
setID(int, int) - Method in class ambit2.db.update.bundle.chemicals.AddAllChemicalsperSubstanceToBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.chemicals.AddChemicalToBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.chemicals.DeleteChemicalsFromBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.CreateBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.CreateBundleCopy
 
setID(int, int) - Method in class ambit2.db.update.bundle.CreateBundleVersion
 
setID(int, int) - Method in class ambit2.db.update.bundle.DeleteBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.endpoints.AddEndpointToBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.endpoints.DeleteEndpointFromBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.matrix.CreateMatrixFromBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixFromBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixProtocolApplicationValue
 
setID(int, int) - Method in class ambit2.db.update.bundle.matrix.DeleteMatrixValue
 
setID(int, int) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.substance.AddSubstanceToBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.substance.DeleteSubstanceFromBundle
 
setID(int, int) - Method in class ambit2.db.update.bundle.UpdateBundle
 
setID(int, int) - Method in class ambit2.db.update.chemical.CreateChemical
 
setID(int, int) - Method in class ambit2.db.update.chemical.DeleteChemical
 
setID(int, int) - Method in class ambit2.db.update.chemical.UpdateChemical
 
setID(int, int) - Method in class ambit2.db.update.dataset.CreateDataset
 
setID(int, int) - Method in class ambit2.db.update.dataset.DatasetAddStructure
 
setID(int, int) - Method in class ambit2.db.update.dataset.DatasetDeleteStructure
 
setID(int, int) - Method in class ambit2.db.update.dataset.DeleteDataset
 
setID(int, int) - Method in class ambit2.db.update.dataset.UpdateDataset
 
setID(int, int) - Method in class ambit2.db.update.dictionary.CreateDictionary
 
setID(int, int) - Method in class ambit2.db.update.dictionary.DatasetTemplateAddProperty
 
setID(int, int) - Method in class ambit2.db.update.dictionary.DeleteDictionary
 
setID(int, int) - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
setID(int, int) - Method in class ambit2.db.update.dictionary.TemplateDeleteProperty
 
setID(int, int) - Method in class ambit2.db.update.fp.CreateFingerprintChemical
 
setID(int, int) - Method in class ambit2.db.update.fp.CreateFingerprintStructure
 
setID(int, int) - Method in class ambit2.db.update.fpae.CreateAtomEnvironment
 
setID(int, int) - Method in class ambit2.db.update.fpae.CreateAtomEnvironmentMatrix
 
setID(int, int) - Method in class ambit2.db.update.fpae.DeleteAtomEnvironment
 
setID(int, int) - Method in class ambit2.db.update.model.CreateModel
 
setID(int, int) - Method in class ambit2.db.update.model.DeleteModel
 
setID(int, int) - Method in class ambit2.db.update.model.UpdateModel
 
setID(int, int) - Method in class ambit2.db.update.property.CreateProperty
 
setID(int, int) - Method in class ambit2.db.update.property.CreatePropertyReferenceID
 
setID(int, int) - Method in class ambit2.db.update.property.DeleteProperty
 
setID(int, int) - Method in class ambit2.db.update.property.UpdateProperty
 
setID(int, int) - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
setID(int, int) - Method in class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
setID(int, int) - Method in class ambit2.db.update.propertyannotations.DeletePropertyAnnotation
 
setID(int, int) - Method in class ambit2.db.update.propertyannotations.UpdatePropertyAnnotation
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateQLabelCAS
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateQLabelEINECS
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateQLabelFingerprints
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateQLabelPair
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateStructureQLabel
 
setID(int, int) - Method in class ambit2.db.update.qlabel.CreateValueQLabel
 
setID(int, int) - Method in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
setID(int, int) - Method in class ambit2.db.update.qlabel.DeleteValueQLabel
 
setID(int, int) - Method in class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
setID(int, int) - Method in class ambit2.db.update.qlabel.SmilesUniquenessCheck
 
setID(int, int) - Method in class ambit2.db.update.qlabel.ValuesQualityCheck
 
setID(int, int) - Method in class ambit2.db.update.queryfolder.CreateQueryFolder
 
setID(int, int) - Method in class ambit2.db.update.queryfolder.DeleteQueryFolder
 
setID(int, int) - Method in class ambit2.db.update.queryfolder.UpdateQueryFolder
 
setID(int, int) - Method in class ambit2.db.update.reference.CreateReference
 
setID(int, int) - Method in class ambit2.db.update.reference.DeleteReference
 
setID(int, int) - Method in class ambit2.db.update.reference.UpdateReference
 
setID(int, int) - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
setID(int, int) - Method in class ambit2.db.update.storedquery.DeleteStoredQuery
 
setID(int, int) - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
setID(int, int) - Method in class ambit2.db.update.storedquery.QueryAddTemplate
 
setID(int, int) - Method in class ambit2.db.update.storedquery.QueryDeleteStructure
 
setID(int, int) - Method in class ambit2.db.update.storedquery.QueryDeleteTemplate
 
setID(int, int) - Method in class ambit2.db.update.storedquery.SelectStoredQuery
 
setID(int, int) - Method in class ambit2.db.update.storedquery.UpdateSelectedRecords
 
setID(int, int) - Method in class ambit2.db.update.storedquery.UpdateStoredQuery
 
setID(int, int) - Method in class ambit2.db.update.structure.CreateStructure
 
setID(int, int) - Method in class ambit2.db.update.structure.CreateStrucType
 
setID(int, int) - Method in class ambit2.db.update.structure.DeleteStructure
 
setID(int, int) - Method in class ambit2.db.update.structure.UpdateStructure
 
setID(int, int) - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
setID(int, int) - Method in class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
setID(int, int) - Method in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
setID(int, int) - Method in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
setId(int) - Method in class ambit2.descriptors.PKANode
 
setId(int) - Method in class ambit2.reactions.GenericReaction
 
setId(int) - Method in class ambit2.reactions.Reaction
 
setID(int) - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
setID(int) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setId(int) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setIdchemical(int) - Method in class ambit2.base.data.StructureRecord
 
setIdchemical(int) - Method in interface ambit2.base.interfaces.IChemical
 
setIdchemical(int) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setIDChemical(int) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
setIDChemical(int) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
setIDChemical(int) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
setIDColumn(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
setIDColumn(int) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
setIDConformer(int) - Method in class ambit2.rest.rdf.RDFDataEntryIterator
 
setIDConformer(int) - Method in class ambit2.rest.rdf.RDFInstancesIterator
 
setIDConformer(int) - Method in class ambit2.rest.rdf.RDFStructuresIterator
 
setIdentifier(String) - Method in class ambit2.base.data.substance.SubstanceProperty
 
setIdentifier1(String) - Method in class ambit2.db.search.QueryInfo
 
setIdentifier2(String) - Method in class ambit2.db.search.QueryInfo
 
setIdentifier3(String) - Method in class ambit2.db.search.QueryInfo
 
setIdentifiers(Hashtable<String, String>) - Method in class ambit2.rest.legacy.OTCompound
Deprecated.
 
setIdproperty(int) - Method in class ambit2.base.data.PropertyAnnotation
 
setIdresult(int) - Method in class ambit2.base.data.study.EffectRecord
 
setIdresult(IDRESULT) - Method in class ambit2.base.data.study.ValueAnnotated
 
setIdstructure(int) - Method in class ambit2.base.data.StructureRecord
 
setIdstructure(int) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setIdstructure(int) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setIdsubstance(int) - Method in class ambit2.base.data.SubstanceRecord
 
setImage(ImageIcon) - Method in class ambit2.base.data.ClassHolder
 
setImage(BufferedImage) - Method in class ambit2.rendering.CachedImage
 
setImage(JTable, boolean, Image) - Method in class ambit2.ui.ImageCellRenderer
 
setImageMap(String) - Method in class ambit2.rendering.CachedImage
 
setImageMap(StringBuilder) - Method in class ambit2.rendering.CompoundImageTools
 
setImageSize(Dimension) - Method in interface ambit2.core.data.IStructureDiagramDepiction
 
setImageSize(Dimension) - Method in interface ambit2.core.io.ICompoundImageTools
 
setImageSize(Dimension) - Method in class ambit2.db.processors.DescriptorsCalculator
 
setImageSize(Dimension) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
setImageSize(PUGRestImageRequest.IMAGE_SIZE) - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
setImageSize(Dimension) - Method in class ambit2.rendering.CompoundImageTools
 
setImageSize(Dimension) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
setImageSize(Dimension) - Method in class ambit2.some.DescriptorSOMEShell
 
setImageSize(Dimension) - Method in class ambit2.some.SOMEVisualizer
 
setImplementationOf(String) - Method in class ambit2.core.data.model.Algorithm
 
setImplicitHydrogens(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setImportBundles(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setImportedRecord(SubstanceRecord) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setInchi(String) - Method in class ambit2.base.data.StructureRecord
 
setInchi(String) - Method in interface ambit2.base.interfaces.IChemical
 
setInchi(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setInchi(String) - Method in class ambit2.db.search.QueryInfo
 
setInchiKey(String) - Method in class ambit2.base.data.StructureRecord
 
setInchiKey(String) - Method in interface ambit2.base.interfaces.IChemical
 
setInchiKey(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setInchiKeyTag(String) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setInchiOptions(List<INCHI_OPTION>) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setInchiOptions(List<INCHI_OPTION>) - Method in class ambit2.tautomers.FilterTautomers
 
setInchiTag(String) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setIncludeImplicitHAtoms(boolean) - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
setIncludeParent(boolean) - Method in class ambit2.db.search.property.QueryOntology
 
setIndex(int...) - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
setIndex(int) - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
 
setInfo(String) - Method in class ambit2.reactions.GenericReaction
 
setInfo(String) - Method in class ambit2.reactions.Reaction
 
setInfo(String) - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
setInfo(String) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setInfo(String) - Method in class ambit2.reactions.sets.ReactionData
 
setInfo(String) - Method in class ambit2.reactions.sets.ReactionGroup
 
setInfo(String) - Method in class ambit2.reactions.sets.ReactionSet
 
setInfo(String) - Method in interface ambit2.rules.miscellaneous.IProgress
 
setInput(Template) - Method in class ambit2.core.data.model.Algorithm
 
setInput(PUGRestRequest.COMPOUND_DOMAIN_INPUT) - Method in class ambit2.pubchem.rest.PUGRestRequest
 
setInputFile(String) - Method in class ambit2.base.external.CommandShell
 
setInputMolecule(IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
setInt(int, int) - Method in class ambit2.db.results.AmbitRows
 
setInternal(boolean) - Method in class ambit2.rest.task.Task
 
setInterpretation_result(String) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
setInterpretation_result(String) - Method in class ambit2.db.substance.QueryCountInterpretationResults
 
setInterpretation_result(String) - Method in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
setInterpretationCriteria(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setInterpretationResult(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setInterpretationResult(String) - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
setInvestigationUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setInvestigationUUID(UUID) - Method in class ambit2.base.data.study.ProtocolApplication
 
setIsNegated(boolean) - Method in class ambit2.reactions.rules.conditions.ReactionGroupCondition
 
setIsNegated(boolean) - Method in class ambit2.rules.conditions.ConditionExpression
 
setIsNegated(boolean) - Method in class ambit2.rules.conditions.DescriptorExpression
 
setIsNegated(boolean) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
setIsNegated(boolean) - Method in interface ambit2.rules.conditions.ICondition
 
setIsNegated(boolean) - Method in class ambit2.rules.conditions.ValueCondition
 
setIsomorphismTesterFlagCheckStereoElements(boolean) - Method in class ambit2.smarts.SmartsManager
 
setIsRobustStudy(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setIsStructureOnly(boolean) - Method in class ambit2.sln.SLNContainer
 
setIsUsed(boolean) - Method in interface ambit2.groupcontribution.descriptors.ILocalDescriptor
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDAtomFormalCharge
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDAtomHeavyNeighbours
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDAtomHybridization
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDAtomSymbol
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDAtomValency
 
setIsUsed(boolean) - Method in class ambit2.groupcontribution.descriptors.LDHNum
 
setIsUsedforClassification(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setIsUsedforMSDS(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setIterateSubjects(boolean) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
setJCPModel() - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
setJenaModel(OntModel) - Method in class ambit2.rest.reporters.CatalogRDFReporter
 
setJenaModel(Model) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
setK(float) - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
setKDE(int, KDensity1D) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
setKDE
setKeepEffectRecordsForDocUUID(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setKeeprawrecord(boolean) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setKey(Object) - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException
 
setKey(Object) - Method in class ambit2.core.processors.structure.key.InchiKey
 
setKey(Property) - Method in class ambit2.core.processors.structure.key.PropertyKey
 
setKey(Object) - Method in class ambit2.core.processors.structure.key.SmilesKey
 
setKeyColumns(int[]) - Method in class ambit2.db.results.AmbitRows
 
setKNN(int) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
setKnowledgeBase(HNMRKnowledgeBase) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
setLabel(LABEL) - Method in class ambit2.base.data.AbstractLabel
 
setLabel(String) - Method in class ambit2.base.data.Property
 
setLambda(double) - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
setLambda(float) - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
setLastModified(long) - Method in class ambit2.core.io.FileState
 
setLastName(String) - Method in class ambit2.base.data.AmbitUser
 
setLastValue(int) - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
setLastValue(int) - Method in class ambit2.core.filter.RecordIntervalCondition
 
setLeft(double...) - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
setLegend(boolean) - Method in class ambit2.db.chart.ChartGenerator
 
setLength(long) - Method in class ambit2.core.io.FileState
 
setLevels(List<ReactionSequenceLevel>) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setLicense(String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
setLicenseURI(String) - Method in class ambit2.base.data.AbstractDataset
 
setLicenseURI(String) - Method in interface ambit2.base.data.ISourceDataset
 
setLicenseURI(String) - Method in class ambit2.base.data.SourceDataset
 
setLicenseURI(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setLicenseURI(String) - Method in class ambit2.base.processors.batch.BatchReporter
 
setLicenseURI(String) - Method in class ambit2.core.processors.ProcessorFileExport
 
setLicenseURI(String) - Method in class ambit2.db.reporters.CSVReporter
 
setLicenseURI(String) - Method in class ambit2.db.search.StoredQuery
 
setLicenseURI(String) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setLicenseURI(String) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
setLicenseURI(String) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setLimitDiffForSwitchToCombinatorial(int) - Method in class ambit2.tautomers.RuleSelector
 
setLoadExamples(boolean) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
setLocalDescriptors(List<ILocalDescriptor>) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setLocalDictionary(SLNDictionary) - Method in class ambit2.sln.SLNContainer
 
setLocale(Locale) - Method in class ambit2.descriptors.processors.DescriptorResultFormatter
 
setLogfile(String) - Method in class ambit2.pubchem.BatchRetrievePubChem
 
setLogger(Logger) - Method in class ambit2.descriptors.simmatrix.SimilarityMatrix
 
setLogX(boolean) - Method in class ambit2.db.chart.ChartGenerator
 
setLogY(boolean) - Method in class ambit2.db.chart.ChartGenerator
 
setLong(int, long) - Method in class ambit2.db.results.AmbitRows
 
setLoQualifier(String) - Method in class ambit2.base.data.study.EffectRecord
 
setLoQualifier(VALUE) - Method in interface ambit2.base.data.study.IParams
 
setLoQualifier(QUALIFIER) - Method in interface ambit2.base.data.study.IValue
 
setLoQualifier(VALUE) - Method in class ambit2.base.data.study.Params
 
setLoQualifier(String) - Method in class ambit2.base.data.study.Value
 
setLoRelation(IValue.Relation) - Method in interface ambit2.rules.conditions.value.IValueInterval
 
setLoRelation(IValue.Relation) - Method in class ambit2.rules.conditions.value.ValueInterval
 
setLoValue(double) - Method in class ambit2.base.data.study.EffectRecord
 
setLoValue(VALUE) - Method in interface ambit2.base.data.study.IParams
 
setLoValue(VALUE) - Method in interface ambit2.base.data.study.IValue
 
setLoValue(VALUE) - Method in class ambit2.base.data.study.Params
 
setLoValue(VALUE) - Method in class ambit2.base.data.study.Value
 
setLoValue(double) - Method in interface ambit2.rules.conditions.value.IValueInterval
 
setLoValue(double) - Method in class ambit2.rules.conditions.value.ValueInterval
 
setLow(T) - Method in class ambit2.similarity.stats.Bin
 
setLowestDistanceIsClosest(boolean) - Method in class ambit2.similarity.knn.NearestNeighborsSearch
 
setLowestDistanceIsClosest(boolean) - Method in class ambit2.similarity.measure.DistanceComparable
 
setMAE(double) - Method in class ambit2.model.evaluation.EvaluationStats
 
setMaintainer(String) - Method in class ambit2.base.data.AbstractDataset
 
setMaintainer(String) - Method in interface ambit2.base.data.ISourceDataset
 
setMaintainer(String) - Method in class ambit2.base.data.SourceDataset
 
setMaintainer(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setMaintainer(String) - Method in class ambit2.db.search.StoredQuery
 
setMajor(int) - Method in class ambit2.db.version.AmbitDBVersion
 
setMapStrategy(ReactionAtomMapping.MappingStrategy) - Method in class ambit2.reactions.mapping.ReactionAtomMapping
 
setMatchColumn(int) - Method in class ambit2.db.results.AmbitRows
 
setMatchColumn(int[]) - Method in class ambit2.db.results.AmbitRows
 
setMatchColumn(String) - Method in class ambit2.db.results.AmbitRows
 
setMatchColumn(String[]) - Method in class ambit2.db.results.AmbitRows
 
setMaterials(Map<String, StartingMaterialsDataBase.StartMaterialData>) - Method in class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
setMatrixDecDig(int) - Method in class ambit2.groupcontribution.Learner
 
setMatrixDig(int) - Method in class ambit2.groupcontribution.Learner
 
setMax(T) - Method in class ambit2.base.data.PropertyStats
 
setMaxAllAtoms(int) - Method in class ambit2.mopac.AbstractMopacShell
 
setMaxFieldSize(int) - Method in class ambit2.db.results.AmbitRows
 
setMaxHeavyAtoms(int) - Method in class ambit2.mopac.AbstractMopacShell
 
setMaxLevel(int) - Method in class ambit2.descriptors.AtomEnvironentMatrix
 
setMaxLevels(int) - Method in class ambit2.core.data.HashIntDescriptorResult
 
setMaxLevels(Integer) - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
setMaxLevels(Integer) - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
setMaxPoints(int) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
setMaxRows(int) - Method in class ambit2.db.results.AmbitRows
 
setMaxValue(T) - Method in class ambit2.base.data.Range
 
setMaxValue(IStructureRecord) - Method in class ambit2.db.search.QuerySmilesByID
 
setMaxValue(Double) - Method in class ambit2.db.search.structure.NumberQuery
 
setMaxValue(Double) - Method in class ambit2.db.search.structure.QueryDistance
 
setMaxValue(Number) - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
setMaxValue(IStructureRecord) - Method in class ambit2.db.search.structure.QueryStructureByID
 
setMaxValue(Double) - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
setMaxX(Double) - Method in class ambit2.db.chart.BarChartGenerator
 
setMeasurements(List<ProtocolApplication>) - Method in class ambit2.base.data.SubstanceRecord
 
setMediaType(MediaType) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
setMetaData(RowSetMetaData) - Method in class ambit2.db.results.AmbitRows
 
setMetaInfo(GenericRuleMetaInfo) - Method in class ambit2.reactions.rules.GenericParserUtils
 
setMethod(String) - Method in class ambit2.db.search.QueryInfo
 
setMethod(ChemicalSpaceQuery.ChemSpaceMethod) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
setMetric(METRIC) - Method in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
setMetric(Range<Double>) - Method in class ambit2.db.search.property.FilteredCount
 
setMetric(int) - Method in class ambit2.db.search.structure.QueryStructureByID
 
setMetric(Range<Double>) - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
setMetricName(String) - Method in class ambit2.model.numeric.DataCoverage
 
setMimeType(String) - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
setMin(T) - Method in class ambit2.base.data.PropertyStats
 
setMinor(int) - Method in class ambit2.db.version.AmbitDBVersion
 
setMinValue(T) - Method in class ambit2.base.data.Range
 
setMinValue(Double) - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
setMinX(Double) - Method in class ambit2.db.chart.BarChartGenerator
 
setMissing(boolean) - Method in class ambit2.groupcontribution.groups.AtomGroup
 
setMissing(boolean) - Method in class ambit2.groupcontribution.groups.BondGroup
 
setMissing(boolean) - Method in class ambit2.groupcontribution.groups.DGroup
 
setMissing(boolean) - Method in class ambit2.groupcontribution.groups.GGroup
 
setMissing(boolean) - Method in interface ambit2.groupcontribution.groups.IGroup
 
setModal(boolean) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
setModal(boolean) - Method in interface ambit2.ui.IMoleculeEditAction
 
setMode(AbstractFinder.MODE) - Method in class ambit2.base.processors.search.AbstractFinder
 
setMode(RawIteratingFolderReader.FileNameMode) - Method in class ambit2.core.io.RawIteratingFolderReader
 
setMode(SmilesReporter.Mode) - Method in class ambit2.db.reporters.SmilesReporter
 
setMode(FPTable) - Method in class ambit2.db.search.structure.QuerySimilarityBitset
 
setMode(QueryCountProtocolApplications._mode_related) - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
setMode(ADomainMethodType) - Method in class ambit2.model.numeric.DataCoverage
 
setMode(ADomainMethodType) - Method in interface ambit2.model.numeric.IDataCoverage
 
setMode(SmartsConst.SSM_MODE) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setMode(IBrowserMode.BrowserMode, IBrowserMode.BrowserMode) - Method in class ambit2.ui.QueryBrowser
 
setModel(GroupContributionModel) - Method in class ambit2.groupcontribution.Learner
 
setModel(M) - Method in class ambit2.rest.model.predictor.ExternalModel
 
setModelDescription(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setModelName(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setModelReporter(ModelURIReporter<IQueryRetrieval<ModelQueryResults>>) - Method in class ambit2.rest.model.builder.ModelBuilder
 
setModelReporter(ModelURIReporter) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
setModelType(GroupContributionModel.Type) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setMolecule(IAtomContainer) - Method in class ambit2.db.search.QueryInfo
 
setMolecule(IAtomContainer) - Method in class ambit2.jchempaint.editor.AbstractMoleculeAction
 
setMolecule(IAtomContainer) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
setMolecule(IAtomContainer) - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
setMolecule(IAtomContainer) - Method in interface ambit2.ui.IMoleculeEditAction
 
setMoleculeFilter(String) - Method in class ambit2.tautomers.tools.TautomerAnalysis
 
setMoleculeInchiKey(IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setMoleculeStatus(IAtomContainer, ReactionSequence.MoleculeStatus) - Static method in class ambit2.reactions.retrosynth.ReactionSequence
 
setMOLONLY(boolean) - Method in class ambit2.db.reporters.SDFReporter
 
setMopac_commands(String) - Method in class ambit2.mopac.AbstractMopacShell
 
setMopac_commands(String) - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
setMopacCommands(String) - Method in class ambit2.mopac.Mopac7Writer
 
setMulticenter(IAtom) - Method in class ambit2.core.groups.DataGroup
 
setMultiplier(int) - Method in class ambit2.core.groups.MultipleGroup
 
setName(String) - Method in class ambit2.base.data.AbstractDataset
 
setName(String) - Method in class ambit2.base.data.AmbitUser
 
setName(String) - Method in interface ambit2.base.data.ISourceDataset
 
setName(String) - Method in class ambit2.base.data.Profile
 
setName(String) - Method in class ambit2.base.data.Property
 
setName(String) - Method in class ambit2.base.data.SourceDataset
 
setName(String) - Method in class ambit2.base.data.StringBean
 
setName(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setName(String) - Method in interface ambit2.base.interfaces.ICategory
 
setName(String) - Method in interface ambit2.base.interfaces.IStructureRelation
 
setName(String) - Method in class ambit2.base.relation.AbstractRelation
 
setName(String) - Method in class ambit2.core.data.model.Algorithm
 
setName(String) - Method in class ambit2.core.data.model.ModelWrapper
 
setName(String) - Method in class ambit2.core.data.model.Parameter
 
setName(String) - Method in class ambit2.core.groups.DataGroup
 
setName(String) - Method in class ambit2.db.search.AbstractQuery
 
setName(String) - Method in interface ambit2.db.search.IStoredQuery
 
setName(String) - Method in class ambit2.db.search.StoredQuery
 
setName(String) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setName(String) - Method in class ambit2.db.SessionID
 
setName(String) - Method in class ambit2.db.substance.study.facet.OwnerFacet
 
setName(String) - Method in class ambit2.descriptors.FunctionalGroup
 
setName(String) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
setName(String) - Method in class ambit2.reactions.GenericReaction
 
setName(String) - Method in class ambit2.reactions.Reaction
 
setName(String) - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
setName(String) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setName(String) - Method in class ambit2.reactions.sets.ReactionData
 
setName(String) - Method in class ambit2.reactions.sets.ReactionGroup
 
setName(String) - Method in class ambit2.reactions.sets.ReactionSet
 
setName(String) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
setName(OTFeature, String) - Method in class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
setName(PROPERTY, String) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
Property name
setName(Property, String) - Method in class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
setName(String) - Method in class ambit2.rest.task.Task
 
setName(String) - Method in class ambit2.rest.wrapper.WrappedService
 
setName(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setName(String) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
setName(String) - Method in interface ambit2.smarts.query.ISmartsPattern
 
setNameCondition(NC) - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
setNamedConfig(String) - Method in class ambit2.rest.DBConnection
 
setNameValuePairs(PROPERTY, RDFNode, String, String, RDFNode, RDFNode) - Method in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
setNanomaterial(boolean) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
setNearestNeighborsSearch(NearestNeighborsSearch<Features>) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
setNeededDataFlags() - Method in class ambit2.smarts.SmartsParser
 
setNegate(boolean) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
setNegate(boolean) - Method in interface ambit2.smarts.query.ISmartsPattern
 
setNeighbourData(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
setNeutralise(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setNewResource(boolean) - Method in class ambit2.rest.task.TaskResult
 
setNoDataText(String) - Method in class ambit2.ui.editors.EditorPanel
 
setNode(boolean, PKANode) - Method in class ambit2.descriptors.PKANode
 
setNoDuplicates(boolean) - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
setNoDuplicates(boolean) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
setNominal(boolean) - Method in class ambit2.base.data.Property
 
setNull(int, int) - Method in class ambit2.db.results.AmbitRows
 
setNull(int, int, String) - Method in class ambit2.db.results.AmbitRows
 
setNumber(int) - Method in class ambit2.core.groups.AbstractGroup
 
setNumber(int) - Method in interface ambit2.core.groups.ISGroup
 
setNumberOfHeaderLines(int) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
setNumberofHeaderLines(int) - Method in class ambit2.db.reporters.CSVReporter
 
setObject(OBJECT) - Method in class ambit2.base.data.PropertyAnnotation
 
setObject(T) - Method in interface ambit2.base.interfaces.IAmbitEditor
 
setObject(T) - Method in class ambit2.db.results.AmbitRows
 
setObject(int, Object) - Method in class ambit2.db.results.AmbitRows
 
setObject(int, Object, int) - Method in class ambit2.db.results.AmbitRows
 
setObject(int, Object, int, int) - Method in class ambit2.db.results.AmbitRows
 
setObject(SubstanceRecord) - Method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
setObject(Property) - Method in class ambit2.db.update.dictionary.TemplateAddProperty
 
setObject(ModelQueryResults) - Method in class ambit2.db.update.model.CreateModel
 
setObject(Property) - Method in class ambit2.db.update.property.CreateProperty
 
setObject(IStructureRecord) - Method in class ambit2.db.update.structure.CreateStructure
 
setObject(Rows) - Method in class ambit2.dbui.dictionary.AmbitRowsPanel
 
setObject(QueryOntology) - Method in class ambit2.dbui.dictionary.OntologyEditor
 
setObject(Profile<Property>) - Method in class ambit2.dbui.ProfileEditor
 
setObject(QueryCombinedStructure) - Method in class ambit2.dbui.QueryCombinedEditor
 
setObject(Q) - Method in class ambit2.dbui.QueryEditor
 
setObject(QueryFunctionalGroups) - Method in class ambit2.dbui.QueryFunctionalGroupsEditor
 
setObject(QueryInfo) - Method in class ambit2.dbui.QueryInfoEditor
 
setObject(ScopeQuery) - Method in class ambit2.dbui.QueryScopeEditor
 
setObject(IAtomContainerSet) - Method in class ambit2.jchempaint.editor.StructureDiagramEditor
 
setObject(T) - Method in class ambit2.similarity.measure.DistanceComparable
 
setObject(L) - Method in class ambit2.ui.editors.BeanEditor
 
setObject(FileState) - Method in class ambit2.ui.editors.FileSelector
 
setObject(ListModel) - Method in class ambit2.ui.editors.ListEditor
 
setObject(Properties) - Method in class ambit2.ui.editors.PreferencesPanel
 
setObject(TypedListModel<Property>) - Method in class ambit2.ui.editors.SelectFieldsPanel
 
setObject(Profile<Property>) - Method in class ambit2.ui.editors.TemplateEditor
 
setObject(IAtomContainer) - Method in class ambit2.ui.jmol.ImageTools3D
 
setObject(IAtomContainer) - Method in class ambit2.ui.jmol.Panel3D
 
setObject(IAtomContainer) - Method in class ambit2.ui.Panel2D
 
setObject(T) - Method in class ambit2.ui.QueryBrowser
IAmbitEditor
setObserved(Comparable) - Method in class ambit2.similarity.stats.ValuePair
 
setOffset(long) - Method in class ambit2.core.io.FileState
 
setOperation(AbstractRepositoryWriter.OP) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
setOperation(ProcessorOntology.OP) - Method in class ambit2.db.processors.ProcessorOntology
 
setOperation(PUGRestRequest.COMPOUND_DOMAIN_OPERATION) - Method in class ambit2.pubchem.rest.PUGRestRequest
 
setOptimize(boolean) - Method in class ambit2.mopac.AbstractMopacShell
 
setOptimize(int) - Method in class ambit2.mopac.Mopac7Writer
 
setOption(GCMPredictCli._option, String) - Method in class ambit2.groupcontribution.cli.GCMPredictCli
 
setOption(GroupContributionCli._option, String) - Method in class ambit2.groupcontribution.cli.GroupContributionCli
 
setOption(HNMRPredictCli._option, String) - Method in class ambit2.groupcontribution.cli.HNMRPredictCli
 
setOption(NCISearchProcessor.METHODS) - Method in class ambit2.pubchem.NCISearchProcessor
 
setOption(AmbitSmirksCli._option, String) - Method in class ambit2.reactions.cli.AmbitSmirksCli
 
setOption(ReactorCli._option, String) - Method in class ambit2.reactions.cli.ReactorCli
 
setOption(SyntheticAccessibilityCli._option, String) - Method in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
setOptionalInChIHeader(String) - Method in class ambit2.core.io.FileInputState
 
setOptionalInChIHeader(String) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setOptionalInChIKeyHeader(String) - Method in class ambit2.core.io.FileInputState
 
setOptionalInChIKeyHeader(String) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setOptionalSMILESHeader(String) - Method in class ambit2.core.io.FileInputState
 
setOptionalSMILESHeader(String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
setOptionalSMILESHeader(String) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setOptions(List<T>) - Method in class ambit2.base.data.SelectionBean
 
setOrder(int) - Method in class ambit2.base.data.Property
 
setOrder(Integer) - Method in class ambit2.core.groups.ComponentGroup
 
setOrder(QueryFingerprints._order) - Method in class ambit2.db.update.fp.QueryFingerprints
 
setOrder(int) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setOrder_descendant(boolean) - Method in class ambit2.db.search.structure.AbstractStructureQuery
 
setOrigin(OTFeature, RDFNode) - Method in class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
setOrigin(PROPERTY, RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
setOrigin(Property, RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
setOriginalRow() - Method in class ambit2.db.results.AmbitRows
 
setOut(OutputStream) - Method in class ambit2.rest.study.BucketJson2CSVConvertor
 
setOutput(Output) - Method in class ambit2.base.processors.batch.BatchReporter
 
setOutput(FileOutputState) - Method in class ambit2.core.processors.ProcessorFileExport
 
setOutput(Writer) - Method in class ambit2.db.reporters.ARFFReporter
 
setOutput(Document) - Method in class ambit2.db.reporters.PDFReporter
 
setOutput(Investigation) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setOutput(PUGRestRequest.COMPOUND_DOMAIN_OUTPUT) - Method in class ambit2.pubchem.rest.PUGRestRequest
 
setOutput(XMLStreamWriter) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
setOutput(XMLStreamWriter) - Method in class ambit2.rest.dataset.DatasetRDFStaxReporter
 
setOutput(XMLStreamWriter) - Method in class ambit2.rest.substance.SubstanceBundleStAXReporter
 
setOutputDir(File) - Method in class ambit2.export.isa.json.ISAJsonExporter
 
setOutputDir(File) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setOutputFile(String) - Method in class ambit2.base.external.CommandShell
 
setOutputMolecules(List<IAtomContainer>) - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
setOwnerName(String) - Method in class ambit2.base.data.SubstanceRecord
 
setOwnerUUID(String) - Method in class ambit2.base.data.SubstanceRecord
 
setPage(int) - Method in class ambit2.db.search.AbstractQuery
 
setPage(int) - Method in class ambit2.db.search.property.FilteredCount
 
setPage(int) - Method in class ambit2.db.search.StoredQuery
 
setPage(int) - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
setPage(int) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setPage(int) - Method in class ambit2.rest.SimpleTaskResource
 
setPage(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
setPage(int) - Method in interface ambit2.ui.table.IPageNavigator
 
setPageSize(int) - Method in class ambit2.db.results.AmbitRows
 
setPageSize(long) - Method in class ambit2.db.search.AbstractQuery
 
setPageSize(long) - Method in class ambit2.db.search.property.FilteredCount
 
setPageSize(long) - Method in class ambit2.db.search.StoredQuery
 
setPageSize(long) - Method in class ambit2.db.search.structure.QueryCombinedStructure
 
setPageSize(long) - Method in class ambit2.db.search.structure.QueryMissingDescriptor
 
setPageSize(long) - Method in class ambit2.db.search.structure.QueryMissingDistances
 
setPageSize(long) - Method in class ambit2.db.search.structure.QueryMissingProperty
 
setPageSize(long) - Method in class ambit2.db.search.structure.QueryStructureByID
 
setPageSize(long) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setPageSize(long) - Method in class ambit2.rest.SimpleTaskResource
 
setPageSize(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
setPageSize(int) - Method in interface ambit2.ui.table.IPageNavigator
 
setPaging(Form) - Method in class ambit2.rest.SimpleTaskResource
 
setPairwiseSimilarity(double) - Method in interface ambit2.similarity.ISimilarityResultType
 
setParam(String) - Method in class ambit2.db.chart.ChartGenerator
 
setParam(String) - Method in class ambit2.db.chart.FingerprintHistogramDataset
 
setParameter(Object, Object) - Method in class ambit2.model.AbstractModel
 
setParameter(Object, Object) - Method in interface ambit2.model.IModelDefinition
 
setParameter(Object, Object) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
setParameters(PARAMS) - Method in class ambit2.base.data.study.ProtocolApplication
 
setParameters(List<Parameter>) - Method in class ambit2.core.data.model.Algorithm
 
setParameters(String[]) - Method in class ambit2.core.data.model.ModelWrapper
 
setParameters(IQueryRetrieval, int, int) - Method in enum ambit2.db.results.StoredQueryTableModel.FIELDS
 
setParameters(PreparedStatement, List<QueryParam>) - Static method in class ambit2.db.StatementExecutor
 
setParameters(Object[]) - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
setParameters(Object[]) - Method in class ambit2.descriptors.AtomEnvironmentDescriptor
Sets the parameters attribute of the AtomEnvironmentDescriptor object
setParameters(Object[]) - Method in class ambit2.descriptors.AtomEnvironmentMatrixDescriptor
Sets the parameters attribute of the AtomEnvironmentDescriptor object
setParameters(Object[]) - Method in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.constitutional.AbstractAtomCountDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.constitutional.AtomCountRelativeDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.constitutional.RotatableBondFractionDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.fingerprints.Fingerprint2DescriptorWrapper
 
setParameters(Object[]) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
3 parameters : Smarts,name,hint; first two are mandatory.
setParameters(Object[]) - Method in class ambit2.descriptors.geometrical.CGIDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.InChI
 
setParameters(Object[]) - Method in class ambit2.descriptors.MolecularWeight
Sets the parameters attribute of the WeightDescriptor object.
setParameters(Object[]) - Method in class ambit2.descriptors.PKASmartsDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.SizeDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.SpherosityDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.topological.BonchevCentricInformationIndicesDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.topological.CTIDescriptor
 
setParameters(Object[]) - Method in class ambit2.descriptors.topological.EccentricBasedMadanIndicesDescriptor
 
setParameters(Object[]) - Method in class ambit2.dragon.DescriptorDragonShell
 
setParameters(Object) - Method in class ambit2.model.numeric.DataCoverage
 
setParameters(Object[]) - Method in class ambit2.mopac.DescriptorMopacShell
 
setParameters(String[]) - Method in class ambit2.rest.model.builder.SimpleModelBuilder
 
setParameters(Object[]) - Method in class ambit2.some.DescriptorSOMEShell
 
setParams(String[], DragonDescriptorDictionary) - Method in enum ambit2.dragon.DragonShell._options
 
setParams(double[]) - Method in interface ambit2.rules.functions.IFunction
 
setParams(double[]) - Method in class ambit2.rules.functions.LinearFunction
 
setParams(double[]) - Method in class ambit2.rules.functions.NestedFunctions
 
setParams(double[]) - Method in class ambit2.rules.functions.ReciprocalFunction
 
setParent(int) - Method in class ambit2.descriptors.PKANode
 
setParentComponent(Component) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
setParentComponent(Component) - Method in interface ambit2.ui.IMoleculeEditAction
 
setParentMoleculeData(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
setParentTemplate(String) - Method in class ambit2.base.data.Dictionary
 
setParser(SmilesParserWrapper.SMILES_PARSER) - Method in class ambit2.core.smiles.SmilesParserWrapper
 
setParser(SmilesParser) - Method in class ambit2.rendering.CompoundImageTools
 
setParserMetaInfoForRetroSynthRule() - Method in class ambit2.reactions.rules.ReactionParser
 
setParserType(SmartsPatternFactory.SmartsParser) - Method in class ambit2.smarts.query.SmartsPatternFactory
 
setPassword(String) - Method in class ambit2.base.data.AmbitUser
 
setPassword(String) - Method in class ambit2.db.LoginInfo
 
setPassword(String) - Method in class ambit2.db.results.AmbitRows
 
setPassword(String) - Method in class ambit2.dbui.LoginInfoBean
 
setPathLenght(int) - Method in class ambit2.reactions.rules.scores.AtomComplexity
 
setPca(boolean) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
setPca(PrincipalComponents) - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
setPca(PrincipalComponents) - Method in class ambit2.rest.task.weka.WekaPredictor
 
setPctCorrect(double) - Method in class ambit2.model.evaluation.EvaluationStats
 
setPctInCorrect(double) - Method in class ambit2.model.evaluation.EvaluationStats
 
setPercentage(double) - Method in interface ambit2.rules.miscellaneous.IProgress
 
setPercentCompleted(float) - Method in class ambit2.rest.task.TaskResult
 
setPka(double) - Method in class ambit2.descriptors.PKANode
 
setPka_range(double) - Method in class ambit2.descriptors.PKANode
 
setPolicy() - Method in class ambit2.rest.task.Task
Does nothing so far, but should register the result URI to the policy server
setPolicyError(Exception) - Method in class ambit2.rest.task.Task
 
setPort(String) - Method in class ambit2.db.LoginInfo
 
setPort(String) - Method in class ambit2.dbui.LoginInfoBean
 
setPredicate(String) - Method in class ambit2.base.data.PropertyAnnotation
 
setPredicted(PredictedVarsTemplate) - Method in class ambit2.core.data.model.ModelWrapper
 
setPredicted(Double) - Method in class ambit2.model.dataset.DoubleArrayDataset
 
setPredicted(ResultType) - Method in interface ambit2.model.IDataset
 
setPredicted(Comparable) - Method in class ambit2.similarity.stats.ValuePair
 
setPredictor(Predictor) - Method in class ambit2.rest.model.task.CallableModelPredictor
 
setPredictors(Template) - Method in class ambit2.core.data.model.ModelWrapper
 
setPreferedStructure(boolean) - Method in class ambit2.db.readers.RetrieveStructure
 
setPrefix(String) - Method in class ambit2.base.data.study.StructureRecordValidator
 
setPrefix(String) - Method in class ambit2.rest.structure.CompoundURIReporter
 
setPresent(boolean) - Method in class ambit2.descriptors.PKANode
 
setPriorityScore(double) - Method in class ambit2.reactions.GenericReaction
 
setProcessorChain(ProcessorsChain<ItemInput, Result, IProcessor>) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
setProcessorChain(ProcessorsChain<Target, IBatchStatistics, IProcessor>) - Method in class ambit2.base.processors.batch.BatchProcessor
 
setProcessors(ProcessorsChain<Item, IBatchStatistics, IProcessor>) - Method in class ambit2.base.processors.batch.BatchReporter
 
setProducts(IAtomContainer) - Method in class ambit2.reactions.Reaction
 
setProfile(Template) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setProfile(String, Profile<Property>) - Method in class ambit2.db.results.StoredQueryTableModel
 
setProfile(Profile<Property>) - Method in class ambit2.db.search.property.ValuesReader
 
setProfile(Profile<Property>) - Method in class ambit2.dbui.dictionary.DictionaryQueryPanel
 
setProfile(RangeProfile) - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
setProfile(String) - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
setProfile(String, Profile<Property>) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
setProperties(Profile) - Method in class ambit2.core.io.SimpleIOListener
 
setProperties(Profile) - Method in class ambit2.ui.AmbitSettingsListener
 
setProperty(String, String) - Static method in class ambit2.base.config.Preferences
 
setProperty(Property) - Method in class ambit2.base.data.PropertyTemplateStats
 
setProperty(Property, Object) - Method in class ambit2.core.io.ToXMLReaderSimple
 
setProperty(Property) - Method in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
setProperty(Property) - Method in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
setProperty(Property) - Method in class ambit2.db.chart.PieChartGenerator
 
setProperty(PROPERTY) - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
setProperty(Property) - Method in class ambit2.db.processors.quality.QualityValueWriter
 
setProperty(Property) - Method in class ambit2.db.readers.PropertyValue
 
setProperty(Property) - Method in class ambit2.db.search.property.FilteredCount
 
setProperty(Property) - Method in class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty
 
setProperty(P) - Method in class ambit2.db.simiparity.space.QMap
 
setProperty(Property) - Method in class ambit2.db.update.qlabel.ValuesQualityCheck
 
setProperty(Property) - Method in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
setProperty(MORE) - Method in class ambit2.rendering.CachedImage
 
setProperty(Object) - Method in class ambit2.similarity.measure.DistanceComparable
Property to be predicted by nearest neighbors (e.g.
setProperty(String, String) - Static method in class ambit2.ui.EditorPreferences
 
setPropertyChangeSupport(PropertyChangeSupport) - Static method in class ambit2.base.config.Preferences
 
setPropertyChangeSupport(PropertyChangeSupport) - Static method in class ambit2.ui.EditorPreferences
 
setPropertyKey(IStructureKey) - Method in class ambit2.db.processors.PropertyImporter
 
setPropertyKey(IStructureKey) - Method in class ambit2.db.processors.RepositoryWriter
 
setPropertyname(String) - Method in class ambit2.db.results.AmbitRows
 
setPropertyQuery(IQueryRetrieval<Property>) - Method in class ambit2.db.readers.ValuesByTemplateReader
 
setPropertyReporter(PropertyURIReporter) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setPropertyReporter(PropertyURIReporter) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
setPropertyType(IntPropertyIntervalCondition.PropertyType) - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
setPropertyX(Property) - Method in class ambit2.db.chart.BarChartGenerator
 
setPropertyX(Property) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
setPropertyX(Property) - Method in class ambit2.db.chart.XTabChartGenerator
 
setPropertyY(Property) - Method in class ambit2.db.chart.BarChartGenerator
 
setPropertyY(Property) - Method in class ambit2.db.chart.PropertiesChartGenerator
 
setPropertyY(Property) - Method in class ambit2.db.chart.XTabChartGenerator
 
setProtocol(PROTOCOL) - Method in class ambit2.base.data.study.ProtocolApplication
 
setProtocol(Protocol) - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
setProtocolapp_copied(boolean) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setProtocolapp_deleted(boolean) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setProtocolapp_remarks(String) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setPThreshold(double) - Method in class ambit2.model.numeric.DataCoverage
 
setPThreshold(double) - Method in interface ambit2.model.numeric.IDataCoverage
The percent of points in-domain from the training set [0 - 1]
percent - 1 means 100% , all points in
setPublicName(String) - Method in class ambit2.base.data.SubstanceRecord
 
setPurposeFlag(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setQmap(QMap) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setQModifier(QueryAtomEnvironment.q_modifier) - Method in class ambit2.db.search.structure.QueryAtomEnvironment
 
setQuery(IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.processors.ProcessorSetQueryScope
 
setQuery(IQueryRetrieval<IStructureRecord>) - Method in class ambit2.db.processors.ProcessorStructureRetrieval
 
setQuery(IQueryRetrieval<T>) - Method in class ambit2.db.results.AmbitRows
 
setQuery(AbstractStructureQuery) - Method in class ambit2.db.results.StoredQueryTableModel
 
setQuery(IQueryObject<IStructureRecord>) - Method in interface ambit2.db.search.IStoredQuery
 
setQuery(IStoredQuery) - Method in class ambit2.db.search.property.FilteredCount
 
setQuery(IQueryObject<IStructureRecord>) - Method in class ambit2.db.search.StoredQuery
 
setQuery(IQueryRetrieval<IStructureRecord[]>) - Method in class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval
 
setQuery(ISmartsPattern<IAtomContainer>) - Method in class ambit2.descriptors.FunctionalGroup
 
setQuery(String) - Method in class ambit2.rest.wrapper.WrappedService
 
setQuery(String) - Method in class ambit2.sln.search.SLNSearchManager
 
setQuery(IQueryAtomContainer) - Method in class ambit2.smarts.IsomorphismTester
 
setQuery(IQueryAtomContainer) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
setQuery(IQueryAtomContainer) - Method in class ambit2.smarts.Screening
obtained by SmartsParser - might not work by other QueryAtomContainer
setQuery(String) - Method in class ambit2.smarts.SmartsManager
 
setQuery(IQueryAtomContainer) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
setQueryCreate(IQueryUpdate<Group, Target>) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
setQueryDelete(IQueryUpdate<Group, Target>) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
setQueryExpansion(boolean) - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
setQueryID(Object) - Method in class ambit2.core.data.model.ModelWrapper
 
setQueryName(String) - Method in class ambit2.db.cache.RetrieveStructureImagePath
 
setQueryName(String) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setQueryOperator(String) - Method in class ambit2.core.groups.DataGroup
 
setQuerySmarts(String) - Method in class ambit2.smarts.smirks.ReactionSearch
 
setQuerySmirks(String) - Method in class ambit2.smarts.smirks.ReactionSearch
 
setQueryTimeout(int) - Method in class ambit2.db.results.AmbitRows
 
setQueryType(String) - Method in class ambit2.core.groups.DataGroup
 
setQueryUpdate(IQueryUpdate<Group, Target>) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
setRank(long) - Method in class ambit2.structure2name.components.AbstractComponent
 
setRank(long) - Method in interface ambit2.structure2name.components.IIUPACComponent
 
setRankTag(String) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setReactants(IAtomContainer) - Method in class ambit2.reactions.Reaction
 
setReactDB(ReactionDataBase) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setReaction(GenericReaction) - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
setReactionCenterIndices(int[]) - Method in class ambit2.reactions.GenericReaction
 
setReactionClass(String) - Method in class ambit2.reactions.GenericReaction
 
setReactionClass(String) - Method in class ambit2.reactions.Reaction
 
setReactionClass(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setReactionDataBase(ReactionDataBase) - Method in class ambit2.reactions.reactor.Reactor
 
setReactionGroups(ArrayList<ReactionGroup>) - Method in class ambit2.reactions.sets.ReactionSet
 
setReactionInstance(List<IAtom>) - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
setReactions(ArrayList<ReactionData>) - Method in class ambit2.reactions.sets.ReactionGroup
 
setReactions(ArrayList<ReactionData>) - Method in class ambit2.reactions.sets.ReactionSet
 
setReactionScore(ReactionScore) - Method in class ambit2.reactions.retrosynth.ReactionSequenceStep
 
setReactionSequence(ReactionSequence) - Method in interface ambit2.reactions.retrosynth.IReactionSequenceHandler
 
setReactionSequenceHandler(IReactionSequenceHandler) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setReactionType(GenericReaction.ReactionType) - Method in class ambit2.reactions.GenericReaction
 
setReader(Reader) - Method in class ambit2.core.io.DelimitedFileReader
 
setReader(InputStream) - Method in class ambit2.core.io.DelimitedFileReader
 
setReader(InputStream) - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
setReader(Reader) - Method in class ambit2.core.io.ECHAPreregistrationListReader
 
setReader(InputStream) - Method in class ambit2.core.io.FilteredMDLReader
 
setReader(Reader) - Method in class ambit2.core.io.FilteredMDLReader
 
setReader(InputStream) - Method in class ambit2.core.io.I5ReaderSimple
 
setReader(Reader) - Method in class ambit2.core.io.I5ReaderSimple
 
setReader(InputStream) - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
setReader(Reader) - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
setReader(InputStream) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
setReader(Reader) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
setReader(Reader) - Method in class ambit2.core.io.IteratingFileReader
 
setReader(InputStream) - Method in class ambit2.core.io.IteratingFileReader
 
setReader(Reader) - Method in class ambit2.core.io.IteratingFolderReader
 
setReader(InputStream) - Method in class ambit2.core.io.IteratingFolderReader
 
setReader(InputStream) - Method in class ambit2.core.io.IteratingXLSReader
 
setReader(Reader) - Method in class ambit2.core.io.IteratingXLSReader
 
setReader(Reader) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
setReader(InputStream) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
setReader(Reader) - Method in class ambit2.core.io.MDLReader
 
setReader(InputStream) - Method in class ambit2.core.io.MDLReader
 
setReader(Reader) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setReader(InputStream) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setReader(InputStream) - Method in class ambit2.core.io.RawIteratingReader
 
setReader(Reader) - Method in class ambit2.core.io.RawIteratingReader
 
setReader(InputStream) - Method in class ambit2.core.io.RawIteratingWrapper
 
setReader(Reader) - Method in class ambit2.core.io.RawIteratingWrapper
 
setReader(Reader) - Method in class ambit2.core.io.ToXMLReaderSimple
 
setReader(InputStream) - Method in class ambit2.core.io.ToXMLReaderSimple
 
setReader(Reader) - Method in class ambit2.mopac.Mopac7Reader
 
setReader(InputStream) - Method in class ambit2.mopac.Mopac7Reader
 
setReader(Reader) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
setReader(InputStream) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
setReaderMode(IChemObjectReader.Mode) - Method in class ambit2.core.io.IteratingFileReader
 
setReaderMode(IChemObjectReader.Mode) - Method in class ambit2.core.io.RawIteratingWrapper
 
setReaderMode(IChemObjectReader.Mode) - Method in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
setReadOnly(boolean) - Method in class ambit2.db.results.AmbitRows
 
setReadOutput(boolean) - Method in class ambit2.core.external.ShellSDFoutput
 
setReady(boolean) - Method in class ambit2.db.results.AmbitRows
 
setReal_lower(String) - Method in class ambit2.base.relation.composition.Proportion
 
setReal_lowervalue(Double) - Method in class ambit2.base.relation.composition.Proportion
 
setReal_unit(String) - Method in class ambit2.base.relation.composition.Proportion
 
setReal_upper(String) - Method in class ambit2.base.relation.composition.Proportion
 
setReal_uppervalue(Double) - Method in class ambit2.base.relation.composition.Proportion
 
setRecalls(String) - Method in class ambit2.base.data.Bookmark
 
setRecord(IStructureRecord) - Method in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
setRecord(IStructureRecord) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setRecord(IStructureRecord) - Method in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
setRecord(IStructureRecord) - Method in class ambit2.db.readers.RetrieveTemplateStructure
 
setRecord(IStructureRecord) - Method in class ambit2.db.simiparity.space.QMapSpace
 
setRecord(IStructureRecord) - Method in class ambit2.db.substance.properties.ReadChemPropertiesByComposition
 
setRecord(CompositionRelation) - Method in class ambit2.db.substance.relation.ReadSubstanceComposition
 
setRecord(SubstanceRecord) - Method in class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
setRecord(SubstanceStudyFacet) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
setRecord(PA) - Method in class ambit2.db.substance.study.ReadSubstanceStudy
 
setRecord(List<ProtocolApplication>) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setRecord(int, int) - Method in class ambit2.ui.QueryBrowser
 
setRecord(int) - Method in class ambit2.ui.table.BrowsableTableModel
 
setRecord(int) - Method in interface ambit2.ui.table.IRecordNavigator
 
setRecordProperty(Property, Object) - Method in class ambit2.base.data.StructureRecord
 
setRecordProperty(Property, Object) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setRecordProperty(Property, Object) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setRecords(List<IStructureRecord>) - Method in class ambit2.base.processors.StructureRecordsAppender
 
setRecords(CachedRowSet) - Method in class ambit2.dbui.CachedRowSetTableModel
 
setRecords(Iterator<SubstanceRecord>) - Method in class ambit2.export.isa.json.ISAJsonExporter
 
setRecords(List<IStructureRecord>) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
setRecords_to_delete(List<ValueAnnotated>) - Method in class ambit2.base.data.study.ProtocolApplicationAnnotated
 
setRecordType(PUGRestImageRequest.RECORD_TYPE) - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
setRef(int, Ref) - Method in class ambit2.db.results.AmbitRows
 
setReference(ILiteratureEntry) - Method in class ambit2.base.data.Property
 
setReference(ILiteratureEntry) - Method in class ambit2.base.data.SourceDataset
 
setReference(ILiteratureEntry) - Method in class ambit2.base.data.StructureRecord
 
setReference(String) - Method in class ambit2.base.data.study.ProtocolApplication
"citation": { "title": "ABCDE", "year": "2014", "owner": "" },
setReference(ILiteratureEntry) - Method in interface ambit2.base.interfaces.ICiteable
 
setReference(ILiteratureEntry) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setReference(ILiteratureEntry) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setReference(ILiteratureEntry) - Method in class ambit2.core.io.I5ReaderSimple
 
setReference(ILiteratureEntry) - Method in class ambit2.core.io.json.SubstanceStudyParser
 
setReference(ILiteratureEntry) - Method in class ambit2.core.io.RawIteratingCSVReader
 
setReference(ILiteratureEntry) - Method in class ambit2.core.io.RawIteratingReader
 
setReference(ILiteratureEntry) - Method in class ambit2.core.io.RawIteratingWrapper
 
setReference(ILiteratureEntry) - Method in class ambit2.db.processors.BatchDBProcessor
 
setReferenceID(int) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setReferenceOwner(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setReferenceSubstanceUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setReferenceSubstanceUUID(String) - Method in class ambit2.base.data.SubstanceRecord
 
setReferenceYear(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setRelatedStructures(List<CompositionRelation>) - Method in class ambit2.base.data.SubstanceRecord
 
setRelation(RELATION_METRIC) - Method in interface ambit2.base.interfaces.IStructureRelation
 
setRelation(RELATION_METRIC) - Method in class ambit2.base.relation.AbstractRelation
 
setRelation(RELATION) - Method in class ambit2.db.chemrelation.AbstractUpdateStructureRelation
 
setRelation(IValue.Relation) - Method in interface ambit2.rules.conditions.value.IValue
 
setRelation(IValue.Relation) - Method in class ambit2.rules.conditions.value.Value
 
setRelationship(String) - Method in class ambit2.base.data.Dictionary
 
setRelationType(RELATION_TYPE) - Method in interface ambit2.base.interfaces.IStructureRelation
 
setRelationType(RELATION_TYPE) - Method in class ambit2.base.relation.AbstractRelation
 
setRelevance(double) - Method in class ambit2.base.data.Bookmark
 
setReliability(ReliabilityParams) - Method in class ambit2.base.data.study.ProtocolApplication
 
setReliabilityScore(double) - Method in class ambit2.reactions.GenericReaction
 
setRemark(String) - Method in class ambit2.base.data.study.ValueAnnotated
 
setRemarks(String) - Method in class ambit2.base.data.study.ProtocolEffectRecordMatrix
 
setRemarks(String) - Method in class ambit2.base.facet.BundleRoleFacet
 
setRemoveCDKTitle(boolean) - Method in class ambit2.core.processors.structure.MoleculeReader
 
setRendererModel(RendererModel) - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
setReportConfig(GCMReportConfig) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setRepresentation(NCISearchProcessor.METHODS) - Method in class ambit2.search.csls.CSLSRequest
 
setRequest(Request) - Method in class ambit2.rest.reporters.CatalogURIReporter
 
setRequestref(Reference) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
setRequestref(Reference) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
setRequirement(Algorithm.requires) - Method in class ambit2.core.data.model.Algorithm
 
setResolutionStep(double) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
setResponseType(String) - Method in interface ambit2.base.interfaces.IInputOutputState
 
setResponseType(String) - Method in class ambit2.core.io.FileState
 
setResponseType(String) - Method in class ambit2.core.processors.batch.DefaultIOState
 
setResult(E) - Method in class ambit2.db.substance.study.facet.ResultsCountFacet
 
setResult(IAmbitResult) - Method in class ambit2.similarity.AbstractSimilarityModel
 
setResultDir(String) - Method in class ambit2.pubchem.BatchRetrievePubChem
 
setResults(Map<String, V>) - Method in class ambit2.core.data.HashDescriptorResult
 
setResultSet(ResultSet) - Method in class ambit2.db.DbReader
 
setResultSet(ResultSet) - Method in class ambit2.db.results.ResultSetTableModel
 
setResultType(int) - Method in class ambit2.db.search.QueryExecutor
 
setResultTypeConcurency(int) - Method in class ambit2.db.search.QueryExecutor
 
setRetrieve_conformers(boolean) - Method in class ambit2.pubchem.EntrezSearchProcessor
 
setRetrieve_sdf(boolean) - Method in class ambit2.pubchem.EntrezSearchProcessor
If true (default) retrieves SDF via two stage query (Entrez + PUG).
setRetrieveConformers(boolean) - Method in class ambit2.pubchem.PUGProcessor
 
setRetrieveProperties(boolean) - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
setReuseRecord(boolean) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
setRight(double...) - Method in class ambit2.db.search.structure.pairwise.ChemSpaceCell
 
setrightsHolder(String) - Method in class ambit2.base.data.AbstractDataset
 
setrightsHolder(String) - Method in interface ambit2.base.data.ISourceDataset
 
setrightsHolder(String) - Method in class ambit2.base.data.SourceDataset
 
setrightsHolder(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setrightsHolder(String) - Method in class ambit2.db.search.StoredQuery
 
setRingData(IAtomContainer, boolean, boolean) - Static method in class ambit2.smarts.SmartsParser
 
setRingInfo(IAtomContainer) - Static method in class ambit2.descriptors.utils.RingInfo
 
setRingSet(IRingSet) - Method in class ambit2.structure2name.components.MoleculeAnalysis
 
setRMSE(double) - Method in class ambit2.model.evaluation.EvaluationStats
 
setRows(int) - Method in interface ambit2.db.search.IStoredQuery
 
setRows(int) - Method in class ambit2.db.search.StoredQuery
 
setRule(IRetroSynthRule) - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
setRule(IRetroSynthRule) - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
setRuleActive(boolean) - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
setRuleActive(boolean) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setRuleNumberLimit(int) - Method in class ambit2.tautomers.RuleSelector
 
setRuleSelector(RuleSelector) - Method in class ambit2.tautomers.TautomerManager
 
setSameas(String) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
setSameAs(OTFeature, RDFNode) - Method in class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
setSameAs(PROPERTY, RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
URI of an individual in an ontology, owl:sameAs this property e.g.
setSameAs(Property, RDFNode) - Method in class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
setSampleID(String) - Method in class ambit2.base.data.study.EffectRecord
 
setScale(boolean) - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
setScheme(String) - Method in class ambit2.db.LoginInfo
 
setScheme(String) - Method in class ambit2.dbui.LoginInfoBean
 
setScope(Parameter.ParameterScope) - Method in class ambit2.core.data.model.Parameter
 
setScope(IQueryObject<T>) - Method in class ambit2.db.search.QueryCombined
 
setScope(String) - Method in class ambit2.db.search.QueryInfo
 
setScope(IQueryRetrieval<IStructureRecord>) - Method in class ambit2.dbui.QueryCombinedEditor
 
setScore(double) - Method in interface ambit2.reactions.rules.IRetroSynthRuleInstance
 
setScore(double) - Method in class ambit2.reactions.rules.RetroSynthRuleInstance
 
setSD(double) - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
setSD(double) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
setSD(double) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
setSD(double) - Method in interface ambit2.groupcontribution.correctionfactors.ICorrectionFactor
 
setSD(double) - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
setSD(double) - Method in interface ambit2.groupcontribution.groups.IGroup
 
setSD(double) - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
setSearchByAlias(boolean) - Method in class ambit2.db.readers.RetrieveField
 
setSearchByAlias(boolean) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setSearchByAlias(boolean) - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
setSearchByAlias(boolean) - Method in class ambit2.db.search.structure.QueryFieldAbstract
 
setSearchByAlias(boolean) - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
setSearchByID(boolean) - Method in class ambit2.db.readers.RetrieveField
 
setSearchByID(boolean) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setSearchMode(AbstractPropertyRetrieval.SearchMode) - Method in class ambit2.db.readers.RetrieveField
 
setSearchMode(RetrieveProfileValues.SearchMode) - Method in class ambit2.db.readers.RetrieveProfileValues
 
setSecondStructure(SECONDSTRUC) - Method in interface ambit2.base.interfaces.IStructureRelation
 
setSecondStructure(SECONDSTRUC) - Method in class ambit2.base.relation.AbstractRelation
 
setSeeAlso(String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
setSelected(int) - Method in class ambit2.base.data.SelectionBean
 
setSelected(T) - Method in class ambit2.base.data.SelectionBean
 
setSelected(boolean) - Method in class ambit2.base.data.StructureRecord
 
setSelected(boolean) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setSelected(boolean) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setSelected(boolean) - Method in class ambit2.db.search.AbstractQuery
 
setSelected(boolean) - Method in class ambit2.db.update.storedquery.SelectStoredQuery
 
setSelected(Object[]) - Method in class ambit2.dragon.DragonDescriptorDictionary
 
setSelected(boolean) - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
setSelected(boolean) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
setSelected(boolean) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
setSelectedColor(Color) - Method in class ambit2.ui.ImageCellRenderer
 
setSelectedItem(Object) - Method in class ambit2.ui.HeaderComboBoxModel
 
setSelectedPartColor(RendererModel, Color) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setSelectedPartColor()
setSelection(ISelectableRecords.SELECTION_MODE) - Method in interface ambit2.base.data.ISelectableRecords
 
setSelection(ISelectableRecords.SELECTION_MODE) - Method in class ambit2.db.results.StoredQueryTableModel
 
setSelection(ISelectableRecords.SELECTION_MODE) - Method in class ambit2.ui.table.BrowsableTableModel
 
setSelectionMode(TautomerConst.RSM) - Method in class ambit2.tautomers.RuleSelector
 
setSelectionOrder(int) - Method in class ambit2.tautomers.RuleSelector
 
setSelectionRadius(RendererModel, Double) - Static method in class ambit2.rendering.RendererModelWrapper
 
setSelectionShape(RendererModel, BasicAtomGenerator.Shape) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setSelectionShape
setSelector(IAtomContainerHighlights) - Method in class ambit2.ui.Panel2D
 
setSeparator(String) - Method in class ambit2.db.reporters.CSVReporter
 
setSequence(IQueryAtomContainer, List<QuerySequenceElement>) - Method in class ambit2.smarts.IsomorphismTester
 
setSequence(IQueryAtomContainer, List<QuerySequenceElement>) - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
setServer(String) - Method in class ambit2.pubchem.DepictRequest
 
setSession(SessionID) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setSheet(Sheet) - Method in class ambit2.core.io.XLSFileWriter
 
setShift(double) - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
setShort(int, short) - Method in class ambit2.db.results.AmbitRows
 
setShowAromaticity(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
setShowAromaticity()
setShowAtomTypeNames(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
 
setShowDeleted(boolean) - Method in class ambit2.db.results.AmbitRows
 
setShowExplicitHydrogens(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setShowImplicitHydrogens() (?)
setSimilarityColumn(Property) - Method in class ambit2.db.reporters.CSVReporter
 
setSimilarityThreshold(double) - Method in class ambit2.db.simiparity.space.QMap
 
setSize(int) - Method in class ambit2.core.smiles.OpenBabelDepiction
 
setSk1024_screening(boolean) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setSmarts(String) - Method in class ambit2.descriptors.FunctionalGroup
 
setSmarts(String) - Method in class ambit2.descriptors.PKANode
 
setSmarts(String) - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
setSmarts(String) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
setSmarts(String) - Method in interface ambit2.smarts.query.ISmartsPattern
 
setSmarts(String) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
setSmarts(String) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
setSMARTSData(IAtomContainer) - Method in class ambit2.smarts.SmartsParser
 
setSmartsDataForTarget(boolean) - Method in class ambit2.smarts.SmartsManager
 
setSmartsKeys(List<String>) - Method in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
setSmiles(String) - Method in class ambit2.base.data.StructureRecord
 
setSmiles(String) - Method in interface ambit2.base.interfaces.IChemical
 
setSmiles(String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setSmiles(String) - Method in class ambit2.db.search.QueryInfo
 
setSMILESTag(String) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setSmirks(String) - Method in class ambit2.reactions.GenericReaction
 
setSmirks(String) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setSmirks(String) - Method in class ambit2.reactions.sets.ReactionData
 
setSMIRKS(String) - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
setSmirksFlag(Map<SmirksTransformationFlag, Boolean>) - Method in class ambit2.reactions.GenericReaction
 
setSmirksReaction(SMIRKSReaction) - Method in class ambit2.reactions.GenericReaction
 
setSMIRKSReaction() - Method in class ambit2.smarts.SMIRKSTransform
 
setSmrkMan(SMIRKSManager) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setSolvers(List<IDescriptorSolver>) - Method in class ambit2.rules.conditions.DescriptorSolverSet
 
setSortingOrder(int) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
setSource(String) - Method in class ambit2.base.data.AbstractDataset
 
setSource(String) - Method in interface ambit2.base.data.ISourceDataset
 
setSource(String) - Method in class ambit2.base.data.SourceDataset
 
setSource(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setSource(String) - Method in class ambit2.db.search.StoredQuery
 
setSource(String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
setSparseproperties(boolean) - Method in class ambit2.core.processors.AbstractStructureProcessor
if true assigns empty properties
setSplitFragments(boolean) - Method in class ambit2.tautomers.processor.StructureStandardizer
 
setSplitRecord(boolean) - Method in class ambit2.db.substance.processor.DBSubstanceWriter
 
setSql(String[]) - Method in class ambit2.db.processors.ConnectionStatisticsProcessor
 
setSQLFile(String) - Method in class ambit2.db.processors.DbCreateDatabase
 
setSSMode(SmartsConst.SSM_MODE) - Method in class ambit2.smarts.SMIRKSManager
 
setStarNode(Node) - Method in class ambit2.smarts.NodeExplorer
 
setStars(int) - Method in class ambit2.base.data.AbstractDataset
 
setStars(int) - Method in interface ambit2.base.data.ISourceDataset
 
setStars(int) - Method in class ambit2.base.data.SourceDataset
 
setStars(int) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setStars(int) - Method in class ambit2.core.data.model.ModelWrapper
 
setStars(int) - Method in class ambit2.db.search.StoredQuery
 
setStartingMaterialsDataBase(StartingMaterialsDataBase) - Method in class ambit2.reactions.SimilarityManager
 
setStartMatDB(StartingMaterialsDataBase) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setState(IIUPACComponent.CompState) - Method in class ambit2.structure2name.components.AbstractComponent
 
setState(IIUPACComponent.CompState) - Method in interface ambit2.structure2name.components.IIUPACComponent
 
setState(IBasicCenter.State) - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
setState(IAcidicCenter.State) - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
setState(IAcidicCenter.State) - Method in interface ambit2.tautomers.zwitterion.IAcidicCenter
 
setState(IBasicCenter.State) - Method in interface ambit2.tautomers.zwitterion.IBasicCenter
 
setState(IAcidicCenter.State) - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
setState(IAcidicCenter.State) - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
setState(IAcidicCenter.State) - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
setState(IAcidicCenter.State) - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
setStats(IModelStatistics<ResultType>) - Method in class ambit2.model.AbstractModel
 
setStatus(String) - Method in class ambit2.base.data.AbstractDataset
 
setStatus(String) - Method in interface ambit2.base.data.ISourceDataset
 
setStatus(String) - Method in class ambit2.base.data.SourceDataset
 
setStatus(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setStatus(String) - Method in class ambit2.db.search.StoredQuery
 
setStatus(Set<UpdateBundle._published_status>) - Method in class ambit2.db.update.bundle.ReadBundle
 
setStatus(int) - Method in class ambit2.descriptors.AtomEnvironment
 
setStatus(IModelStatistics.ModelStatus) - Method in interface ambit2.model.IModelStatistics
 
setStatus(int) - Method in exception ambit2.pubchem.ServerError
 
setStatus(TaskStatus) - Method in class ambit2.rest.task.Task
 
setStatus(IModelStatistics.ModelStatus) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
setStdDev(double) - Method in class ambit2.base.data.study.EffectRecord
 
setStdDev(double, String) - Method in class ambit2.base.data.study.EffectRecord
 
setStereoElements(List<IStereoElement>) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setStereoElementType(IStereoElement) - Method in class ambit2.smarts.StereoChange
 
setStereoInfo(DoubleBondStereoInfo) - Method in class ambit2.smarts.DoubleBondAromaticityNotSpecified
 
setStereoInfo(DoubleBondStereoInfo) - Method in class ambit2.smarts.DoubleNonAromaticBond
 
setStereoInfo(DoubleBondStereoInfo) - Method in class ambit2.smarts.SmartsBondExpression
 
setSteroElementsAsProperties(IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
setStorageMode(ExternalDataFileManager.StorageMode) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
setStoredQuery(IStoredQuery) - Method in class ambit2.db.processors.ProcessorCreateQuery
 
setStoredQuery(IStoredQuery) - Method in class ambit2.db.search.QueryInfo
 
setStrategy(ReactorStrategy) - Method in class ambit2.reactions.reactor.Reactor
 
setStrategy(SyntheticStrategy) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setStrategy(SyntheticAccessibilityStrategy) - Method in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
setString(int, String) - Method in class ambit2.db.results.AmbitRows
 
setStructure(IStructureRecord) - Method in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
setStructure(IStructureRecord) - Method in class ambit2.db.processors.ValueWriter
 
setStructure(IAtomContainer) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setStructure(IStructureRecord) - Method in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
setStructure(IStructureRecord) - Method in class ambit2.descriptors.processors.DescriptorValue2Property
 
setStructure(IAtomContainer) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
setStructure(IAtomContainer) - Method in class ambit2.reactions.retrosynth.RetroSynthesis
 
setStructure(IAtomContainer) - Method in class ambit2.tautomers.TautomerManager
 
setStructure(IAtomContainer) - Method in class ambit2.tautomers.zwitterion.ZwitterionManager
 
setStructureRequired(boolean) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
setStudyResultType(String) - Method in class ambit2.base.data.study.ProtocolEffectRecord
 
setStudyResultType(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setStudyResultType(ReliabilityParams._r_flags) - Method in class ambit2.base.data.substance.SubstanceProperty
 
setSubcategoryTitle(String) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
setSubcategoryTitle(String) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
setSubGroup(String) - Method in class ambit2.reactions.sets.ReactionData
 
setSublevel(int) - Method in class ambit2.descriptors.AtomEnvironment
 
setSubscript(String) - Method in class ambit2.core.groups.AbstractGroup
 
setSubscript(String) - Method in interface ambit2.core.groups.ISGroup
text of Sgroup subscript.
setSubscript(String) - Method in class ambit2.core.groups.SuperAtom
 
setSubstanceName(String) - Method in class ambit2.base.data.SubstanceRecord
Substance name, as assigned by the owner
setSubstancesCount(int) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
setSubstancetype(String) - Method in class ambit2.base.data.SubstanceRecord
 
setSubstanceUUID(String) - Method in class ambit2.base.data.study.ProtocolApplication
 
setSubstanceUUID(String) - Method in class ambit2.base.data.SubstanceRecord
Substance UUID as assigned by the substance owner
setSubstanceUUID(String) - Method in class ambit2.db.substance.study.UpdateEffectRecords
 
setSubSubGroup(String) - Method in class ambit2.reactions.sets.ReactionData
 
setSummary(boolean) - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
setSupportedExtDescriptions(String[]) - Method in class ambit2.core.io.FileState
 
setSupportedExtensions(String[]) - Method in class ambit2.core.io.FileState
 
setSupportsPredictedVarURI(boolean) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
setSyncProvider(String) - Method in class ambit2.db.results.AmbitRows
 
setSystemDesignator(String) - Method in class ambit2.base.data.substance.ExternalIdentifier
 
setSystemIdentifier(String) - Method in class ambit2.base.data.substance.ExternalIdentifier
 
setT(double) - Method in class ambit2.tautomers.TautomerRanking
 
setTableName(String) - Method in class ambit2.db.results.AmbitRows
 
setTag(String) - Method in class ambit2.base.facet.BundleRoleFacet
 
setTag(Boolean) - Method in class ambit2.db.processors.ProcessorCreateProfileQuery
 
setTag(Comparable) - Method in class ambit2.domain.stats.datastructures.SubcategoryBin
 
setTarget(Target) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
setTarget(IAtomContainer) - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
setTarget(IAtomContainer) - Method in class ambit2.reactions.rules.scores.MolecularComplexity
 
setTarget(Object) - Method in interface ambit2.rules.actions.IAction
 
setTarget(IAtomContainer) - Method in class ambit2.smarts.EquivalenceTester
 
setTargetDataObject(Object) - Method in interface ambit2.export.isa.base.IISADataMapper
 
setTargetDataObject(Object) - Method in class ambit2.export.isa.v1_0.ISAJsonMapper1_0
 
setTargetProperty(String) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setTargetURI(String[]) - Method in class ambit2.model.builder.AbstractModelBuilder
 
setTask(ITask<ITaskResult, USERID>) - Method in class ambit2.rest.task.ExecutableTask
 
setTaskStorage(ITaskStorage<USERID>) - Method in class ambit2.rest.TaskApplication
 
setTautomerManager(TautomerManager) - Method in class ambit2.tautomers.processor.TautomerProcessor
 
setTemplate(String) - Method in class ambit2.base.data.Dictionary
 
setTemplate(String) - Method in class ambit2.base.data.PropertyTemplateStats
 
setTemplate(Template) - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException
 
setTemplate(Dictionary, ProcessorOntology.SIDE) - Method in class ambit2.db.processors.ProcessorOntology
 
setTemplate(Template) - Method in class ambit2.db.reporters.AbstractStructureRecordReporter
 
setTemplate(Template) - Method in class ambit2.db.reporters.QueryHeaderReporter
 
setTemplate(Template) - Method in class ambit2.db.reporters.SDFReporter
 
setTemplate(Template) - Method in class ambit2.db.reporters.SmilesReporter
 
setTemplate(Template) - Method in interface ambit2.db.search.IStoredQuery
 
setTemplate(Template) - Method in class ambit2.db.search.StoredQuery
 
setTemplate(Template) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
setTerm(String) - Method in class ambit2.pubchem.EntrezSearchOptions
 
setTerm(String, String) - Method in class ambit2.pubchem.EntrezSearchOptions
 
setTerminal(boolean) - Method in class ambit2.descriptors.PKANode
 
setTestInstances(TestInstances) - Method in class ambit2.core.data.model.ModelWrapper
 
setText(String) - Method in class ambit2.base.data.AbstractLabel
 
setText(String) - Method in class ambit2.db.search.structure.QueryStructureByID
 
setTextValue(Object) - Method in class ambit2.base.data.study.EffectRecord
 
setTextValue(String) - Method in class ambit2.base.data.study.ValueAnnotated
 
setThreshold(double) - Method in class ambit2.db.search.property.QueryPairwiseTanimoto
 
setThreshold(Double) - Method in class ambit2.db.search.QueryInfo
 
setThreshold(double) - Method in class ambit2.db.search.structure.QuerySimilarity
 
setThreshold(double) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setThreshold(double) - Method in class ambit2.featureselection.RRelieFFAttributeSelection
 
setThreshold_a(int) - Method in class ambit2.db.simiparity.space.QueryQMapSpace
 
setThreshold_dactivity(double) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
setThreshold_similarity(double) - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
setThumbnail(boolean) - Method in class ambit2.db.chart.ChartGenerator
 
setTime(int, Time) - Method in class ambit2.db.results.AmbitRows
 
setTime(int, Time, Calendar) - Method in class ambit2.db.results.AmbitRows
 
setTime_elapsed(long) - Method in class ambit2.descriptors.AtomEnvironment
 
setTimeCompleted(long) - Method in class ambit2.rest.task.Task
 
setTimeout(long) - Method in interface ambit2.base.interfaces.IBatchProcessor
 
setTimeout(long) - Method in class ambit2.base.processors.batch.BatchProcessor
 
setTimeout(long) - Method in class ambit2.base.processors.batch.BatchReporter
 
setTimeout(long) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
setTimeout(long) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setTimeout(int) - Method in class ambit2.pubchem.HTTPRequest
 
setTimeout(int) - Method in class ambit2.pubchem.SearchApplication
 
setTimestamp(int, Timestamp) - Method in class ambit2.db.results.AmbitRows
 
setTimestamp(int, Timestamp, Calendar) - Method in class ambit2.db.results.AmbitRows
 
setTitle(String) - Method in class ambit2.base.data.AmbitUser
 
setTitle(String) - Method in class ambit2.base.data.Bookmark
 
setTitle(String) - Method in class ambit2.base.data.ClassHolder
 
setTitle(String) - Method in class ambit2.base.data.SelectionBean
 
setTitle(String) - Method in class ambit2.base.data.SourceDataset
 
setTitle(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setTitle(String) - Method in interface ambit2.base.processors.IAmbitResult
 
setTitle(String) - Method in class ambit2.core.groups.SuppleAtomContainer
 
setTitle(String) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
setTitle(String) - Method in interface ambit2.model.IModelStatistics
 
setTitle(String) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
setTman(TautomerManager) - Method in class ambit2.tautomers.ranking.CanonicTautomer
 
setTokenCookies(Variant, boolean) - Method in class ambit2.rest.ProtectedResource
 
setTopCategory(String) - Method in class ambit2.base.data.study.Protocol
 
setTopcategory(String) - Method in class ambit2.base.data.substance.SubstanceProperty
 
setTopcategory(String) - Method in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
setTrainDataSet(DataSet) - Method in class ambit2.groupcontribution.Learner
 
setTrainingData(DATA) - Method in class ambit2.model.builder.AbstractModelBuilder
 
setTrainingInstances(TrainingInstances) - Method in class ambit2.core.data.model.ModelWrapper
 
setTransactionIsolation(int) - Method in class ambit2.db.results.AmbitRows
 
setTransformationasproperties(boolean) - Method in class ambit2.smarts.processors.SMIRKSProcessor
 
setTransformations(SimilarityManager.SimilarityTransformation[]) - Method in class ambit2.reactions.SimilarityManager
 
setTransformedMaterials(Map<String, SimilarityManager.TransformedStartMaterialData>) - Method in class ambit2.reactions.SimilarityManager
 
setTransformType(GenericReaction.TransformType) - Method in class ambit2.reactions.GenericReaction
 
setType(AmbitUser.USER_TYPE) - Method in class ambit2.base.data.AmbitUser
 
setType(String) - Method in class ambit2.base.data.Bookmark
 
setType(ILiteratureEntry._type) - Method in interface ambit2.base.data.ILiteratureEntry
 
setType(ILiteratureEntry._type) - Method in class ambit2.base.data.LiteratureEntry
 
setType(String) - Method in class ambit2.base.data.PropertyAnnotation
 
setType(IStructureRecord.STRUC_TYPE) - Method in class ambit2.base.data.StructureRecord
 
setType(IStructureRecord.STRUC_TYPE) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setType(IStructureRecord.STRUC_TYPE) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setType(String[]) - Method in class ambit2.core.data.model.Algorithm
 
setType(IEvaluation.EVType) - Method in interface ambit2.core.data.model.IEvaluation
 
setType(ContainerGroup.SGROUP_MIXTURE) - Method in class ambit2.core.groups.ContainerGroup
 
setType(int) - Method in class ambit2.db.results.AmbitRows
 
setType(Type) - Method in class ambit2.db.update.fp.Fingerprint
 
setType(Type) - Method in interface ambit2.db.update.fp.IFingerprint
 
setType(IEvaluation.EVType) - Method in class ambit2.model.evaluation.EvaluationStats
 
setType(IRetroSynthRule.Type) - Method in interface ambit2.reactions.rules.IRetroSynthRule
 
setType(IRetroSynthRule.Type) - Method in class ambit2.reactions.rules.RetroSynthRule
 
setType(String) - Method in class ambit2.reactions.sets.ReactionData
 
setTypeMap(Map<String, Class<?>>) - Method in class ambit2.db.results.AmbitRows
 
setTypical(String) - Method in class ambit2.base.relation.composition.Proportion
 
setTypical_unit(String) - Method in class ambit2.base.relation.composition.Proportion
 
setTypical_value(Double) - Method in class ambit2.base.relation.composition.Proportion
 
setUnit(UNIT) - Method in class ambit2.base.data.study.EffectRecord
 
setUnitMatrix() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
setUnits(String) - Method in class ambit2.base.data.Property
 
setUnits(VALUE) - Method in interface ambit2.base.data.study.IParams
 
setUnits(UNITS) - Method in interface ambit2.base.data.study.IValue
 
setUnits(VALUE) - Method in class ambit2.base.data.study.Params
 
setUnits(String) - Method in class ambit2.base.data.study.Value
 
setUnits(String) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
setUnits(OTFeature, String) - Method in class ambit2.rest.legacy.RDFFeaturesIterator
Deprecated.
 
setUnits(PROPERTY, String) - Method in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
Property units
setUnits(Property, String) - Method in class ambit2.rest.rdf.sparql.RDFFeatureIterator
 
setUp() - Method in class ambit2.mopac.MopacUtilities
 
setup() - Method in class ambit2.reactions.reactor.ReactorDescriptorSolver
 
setup(IAtomContainer) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
setup(IAtomContainer, IRingSet) - Method in class ambit2.tautomers.tools.CustomTautomerFilters
 
setUpdated(Date) - Method in class ambit2.base.data.study.ProtocolApplication
 
setUpdated(long) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setupDescriptoSolver() - Method in class ambit2.reactions.reactor.Reactor
 
setupInchiGenerator() - Method in class ambit2.reactions.reactor.Reactor
 
setUpQualifier(String) - Method in class ambit2.base.data.study.EffectRecord
 
setUpQualifier(VALUE) - Method in interface ambit2.base.data.study.IParams
 
setUpQualifier(QUALIFIER) - Method in interface ambit2.base.data.study.IValue
 
setUpQualifier(VALUE) - Method in class ambit2.base.data.study.Params
 
setUpQualifier(String) - Method in class ambit2.base.data.study.Value
 
setUpValue(double) - Method in class ambit2.base.data.study.EffectRecord
 
setUpValue(VALUE) - Method in interface ambit2.base.data.study.IParams
 
setUpValue(VALUE) - Method in interface ambit2.base.data.study.IValue
 
setUpValue(VALUE) - Method in class ambit2.base.data.study.Params
 
setUpValue(VALUE) - Method in class ambit2.base.data.study.Value
 
setURI(URI) - Method in class ambit2.db.LoginInfo
 
setURI(Connection) - Method in class ambit2.db.LoginInfo
 
setURI(URI) - Method in class ambit2.dbui.LoginInfoBean
 
setURI(Connection) - Method in class ambit2.dbui.LoginInfoBean
 
setUri(REFERENCE) - Method in class ambit2.rest.task.Task
 
setUri(String) - Method in class ambit2.rest.task.TaskResult
 
setURI(URI) - Method in class ambit2.rest.wrapper.WrappedService
 
setUriReporter(QueryURIReporter<INPUT, IQueryRetrieval<INPUT>>) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
setUriReporter(QueryURIReporter<T, IQueryRetrieval<T>>) - Method in class ambit2.rest.QueryStaXReporter
 
setURL(String) - Method in interface ambit2.base.data.ILiteratureEntry
 
setURL(String) - Method in class ambit2.base.data.LiteratureEntry
 
setURL(String) - Method in class ambit2.base.data.SourceDataset
 
setURL(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setUrl(String) - Method in exception ambit2.base.exceptions.HttpException
 
setUrl(String) - Method in class ambit2.db.results.AmbitRows
 
setUrl(String) - Method in class ambit2.pubchem.HTTPRequest
 
setUrlPrefix(String) - Method in class ambit2.db.reporters.ARFFReporter
 
setUrlPrefix(String) - Method in class ambit2.db.reporters.CSVReporter
 
setUseAntiAliasing(RendererModel, boolean) - Static method in class ambit2.rendering.RendererModelWrapper
r2dm.setUseAntiAliasing();
setUseCache(boolean) - Method in class ambit2.db.StatementExecutor
Deprecated.
setUseCDKIsomorphism(boolean) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
setUseCDKIsomorphismTester(boolean) - Method in class ambit2.smarts.SmartsManager
 
setUseExistingDatabase(boolean) - Method in class ambit2.db.processors.DbCreateDatabase
 
setUseExistingStructure(boolean) - Method in class ambit2.db.processors.RepositoryWriter
 
setUseHydrogens(boolean) - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
setUseOriginalStructure(boolean) - Method in class ambit2.mopac.AbstractMopacShell
 
setUseOriginalStructure(boolean) - Method in class ambit2.some.SOMEShell
 
setUsePrecalculatedAtomProperties(boolean) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setUsePreferedStructure(boolean) - Method in class ambit2.base.data.StructureRecord
 
setUsePreferedStructure(boolean) - Method in interface ambit2.base.interfaces.IChemical
 
setUsePreferedStructure(boolean) - Method in interface ambit2.base.interfaces.IStructureRecord
 
setUsePreferedStructure(boolean) - Method in class ambit2.base.relation.composition.CompositionRelation
 
setUser(AmbitUser) - Method in class ambit2.base.data.AbstractLabel
 
setUser(String) - Method in class ambit2.db.LoginInfo
 
setUser(AmbitUser) - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
setUser(AmbitUser) - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
setUser(AmbitUser) - Method in class ambit2.db.update.storedquery.CreateStoredQuery
 
setUser(String) - Method in class ambit2.dbui.LoginInfoBean
 
setUseRegion(boolean) - Method in class ambit2.tautomers.rules.TautomerRegion
 
setUserid(USERID) - Method in class ambit2.rest.task.Task
 
setUsername(String) - Method in class ambit2.base.data.SourceDataset
 
setUserName(String) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setUsername(String) - Method in class ambit2.db.results.AmbitRows
 
setUserPass(String) - Method in class ambit2.db.processors.DbCreateDatabase
 
setUuid(String) - Method in class ambit2.base.data.Bookmark
 
setUuid(UUID) - Method in class ambit2.rest.task.CallableMockup
 
setUuid(UUID) - Method in class ambit2.rest.task.CallableProtectedTask
 
setUuid(UUID) - Method in class ambit2.rest.task.Task
 
setValenceData(IAtomContainer) - Static method in class ambit2.smarts.SmartsParser
 
setValidationConfig(ValidationConfig) - Method in class ambit2.groupcontribution.GroupContributionModel
 
setValue(VALUE) - Method in class ambit2.base.data.study.ReliabilityParams
 
setValue(T) - Method in class ambit2.base.facet.AbstractFacet
 
setValue(T) - Method in class ambit2.core.data.model.Parameter
 
setValue(int, int, String) - Method in class ambit2.core.io.StringArrayHeader
 
setValue(T) - Method in class ambit2.db.readers.PropertyValue
 
setValue(IStructureRecord) - Method in class ambit2.db.readers.RetrieveAtomContainer
 
setValue(IStructureRecord) - Method in class ambit2.db.readers.RetrieveStructure
 
setValue(T) - Method in class ambit2.db.search.AbstractQuery
 
setValue(PropertyAnnotation<String>, String) - Method in enum ambit2.db.search.property.AbstractPropertyRetrieval.ANNOTATIONS_TABLE
 
setValue(Range<T>) - Method in class ambit2.db.search.property.FilteredCount
 
setValue(String) - Method in class ambit2.db.search.property.ModelTemplates
 
setValue(ObjectNode) - Method in class ambit2.db.search.SQLFileQueryParams
 
setValue(IAtomContainer) - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
setValue(Number) - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
setValue(IStructureRecord) - Method in class ambit2.db.search.structure.QueryLookupStructure
 
setValue(IAtomContainerSet) - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
setValue(FunctionalGroup) - Method in class ambit2.db.search.structure.QuerySMARTS
 
setValue(ExternalIdentifier) - Method in class ambit2.db.substance.ids.ReadSubstanceIdentifiers
 
setValue(String) - Method in class ambit2.db.substance.QueryCountProtocolApplications
 
setValue(String) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
setValue(List<ProtocolApplication>) - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
setValue(String) - Method in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
setValue(Range) - Method in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
setValue(Object) - Method in class ambit2.rest.model.predictor.ExpertModelpredictor
 
setValue(COMPOUND, PROPERTY, double) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
setValue(COMPOUND, PROPERTY, float) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
setValue(COMPOUND, PROPERTY, int) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
setValue(COMPOUND, PROPERTY, String) - Method in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
setValue(IStructureRecord, Property, double) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
setValue(IStructureRecord, Property, float) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
setValue(IStructureRecord, Property, int) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
setValue(IStructureRecord, Property, String) - Method in class ambit2.rest.rdf.sparql.RDFCompoundIterator
 
setValue(IValue) - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
setValue(IValue) - Method in interface ambit2.rules.conditions.IValueCondition
 
setValue(double) - Method in interface ambit2.rules.conditions.value.IValue
 
setValue(double) - Method in class ambit2.rules.conditions.value.Value
 
setValue(IValue) - Method in class ambit2.rules.conditions.ValueCondition
 
setValue(int) - Method in class ambit2.similarity.stats.MutableInt
 
setValue(Object) - Method in class ambit2.ui.NumberCellRenderer
 
setValue(Object) - Method in class ambit2.ui.table.BrowsableTableModel
 
setValue(E) - Method in interface ambit2.ui.table.IFindNavigator
 
setValueAt(Object, int, int) - Method in class ambit2.base.data.PropertiesTableModel
 
setValueAt(Object, int, int) - Method in class ambit2.db.results.StoredQueryTableModel
 
setValueAt(Object, int, int) - Method in class ambit2.dbui.CachedRowSetTableModel
 
setValueAt(Object, int, int) - Method in class ambit2.ui.table.BrowsableTableModel
 
setValueAt(Object, int, int) - Method in class ambit2.ui.table.StructureRecordsTableModel
 
setValueInterval(IValueInterval) - Method in interface ambit2.rules.conditions.IValueIntervalCondition
 
setValuesRequired(boolean) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
setValueTransformation(IValueTransformation) - Method in class ambit2.groupcontribution.correctionfactors.AtomPairCorrectionFactor
 
setValueTransformation(IValueTransformation) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorCorrectionFactor
 
setValueTransformation(IValueTransformation) - Method in class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
setValueTransformation(IValueTransformation) - Method in interface ambit2.groupcontribution.groups.IGroup
 
setValueTransformation(IValueTransformation) - Method in class ambit2.groupcontribution.groups.ValueTransformedGroup
 
setValueTransformation(IValueTransformation) - Method in interface ambit2.groupcontribution.transformations.IHasValueTransformation
 
setVariant(Variant) - Method in exception ambit2.rest.exception.RResourceException
The variant
setVerbose(boolean) - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
setVerboseMatch(boolean) - Method in class ambit2.descriptors.FunctionalGroup
 
setVersion(int) - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
setVersionLong(String) - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
setVersionShort(String) - Method in class ambit2.rest.freemarker.FreeMarkerApplication
 
setVisible(Boolean) - Method in class ambit2.base.data.ProfileListModel
 
setVisible(boolean) - Method in class ambit2.jchempaint.editor.JChemPaintDialog
 
setWait_ms(long) - Method in class ambit2.pubchem.NCISearchProcessor
 
setWarnings(List<String>) - Method in class ambit2.groupcontribution.nmr.HNMRShifts
 
setWeight(double) - Method in class ambit2.reactions.generator.score.components.DescriptorRangeScore
 
setWeight(double) - Method in class ambit2.reactions.generator.score.components.KnimeWorkflowScore
 
setWeight(double) - Method in interface ambit2.reactions.generator.score.IScoreComponent
 
setWidth(int) - Method in class ambit2.db.chart.ChartGenerator
 
setWidth(int) - Method in class ambit2.pubchem.rest.PUGRestImageRequest
 
setWidth(int) - Method in class ambit2.search.csls.CSLSImageRequest
 
setWorkFolder(String) - Method in class ambit2.base.external.CommandShell
 
setWriteCompoundURI(boolean) - Method in class ambit2.db.reporters.CSVReporter
 
setWriter(Writer) - Method in class ambit2.core.io.ArffWriter
 
setWriter(OutputStream) - Method in class ambit2.core.io.ArffWriter
 
setWriter(OutputStream) - Method in class ambit2.core.io.DelimitedFileWriter
 
setWriter(Writer) - Method in class ambit2.core.io.DelimitedFileWriter
 
setWriter(Writer) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
setWriter(OutputStream) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
setWriter(Writer) - Method in class ambit2.core.io.PDFWriter
 
setWriter(OutputStream) - Method in class ambit2.core.io.PDFWriter
 
setWriter(Writer) - Method in class ambit2.core.io.XLSFileWriter
 
setWriter(OutputStream) - Method in class ambit2.core.io.XLSFileWriter
 
setWriter(OutputStream) - Method in class ambit2.mopac.Mopac7Writer
 
setWriter(Writer) - Method in class ambit2.mopac.Mopac7Writer
 
setWww(String) - Method in class ambit2.base.data.AmbitUser
 
setXmlISAConfig(File) - Method in class ambit2.export.isa.json.ISAJsonExporter
 
setXmlISAConfig(File) - Method in class ambit2.export.isa.v1_0.ISAJsonExporter1_0
 
setYieldHi(double) - Method in class ambit2.reactions.GenericReaction
 
setYieldLo(double) - Method in class ambit2.reactions.GenericReaction
 
sg - Variable in class ambit2.core.io.DelimitedFileWriter
 
sg - Variable in class ambit2.core.io.FileWithHeaderWriter
 
SGROUP_CONNECTIVITY - Static variable in interface ambit2.core.groups.ISGroup
 
SGROUP_VISIBLE - Static variable in interface ambit2.core.groups.ISGroup
 
SGroupMDL2000Helper - Class in ambit2.core.io
Helper for MDL SGroups
SGroupMDL2000Helper() - Constructor for class ambit2.core.io.SGroupMDL2000Helper
 
SGroupMDL2000Helper.SGROUP_CONNECTIVITY - Enum in ambit2.core.io
 
SGroupMDL2000Helper.SGROUP_LINE - Enum in ambit2.core.io
 
SGroupMDL2000Helper.SGROUP_POLYMER_TYPE - Enum in ambit2.core.io
 
SGroupMDL2000Helper.SGROUP_TYPE - Enum in ambit2.core.io
 
shannonEntropy(Map<String, Integer>) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
shannonEntropy(Map<String, Integer>, int) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
shannonEntropy(int[]) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
shannonEntropy(int[], int) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
sheet - Variable in class ambit2.core.io.IteratingXLSReader
 
sheet - Variable in class ambit2.core.io.XLSFileWriter
 
sheet - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
sheetIndex - Variable in class ambit2.core.io.IteratingXLSReader
 
shell - Variable in exception ambit2.base.external.ShellException
 
shell - Variable in class ambit2.dragon.DescriptorDragonShell
 
shell - Variable in class ambit2.mopac.MopacShellOB
 
shell - Variable in class ambit2.mopac.MopacUtilities
 
ShellBalloon - Class in ambit2.balloon
A wrapper for Balloon http://users.abo.fi/mivainio/balloon
ShellBalloon() - Constructor for class ambit2.balloon.ShellBalloon
 
shellBalloon - Variable in class ambit2.mopac.MopacShellBalloon
 
ShellBalloonWeb - Class in ambit2.balloon
Same as ShellBalloon, but gets the BALOON_HOME var from config file Used in web services.
ShellBalloonWeb() - Constructor for class ambit2.balloon.ShellBalloonWeb
 
ShellException - Exception in ambit2.base.external
 
ShellException(CommandShell) - Constructor for exception ambit2.base.external.ShellException
 
ShellException(CommandShell, String) - Constructor for exception ambit2.base.external.ShellException
 
ShellException(CommandShell, String, Throwable) - Constructor for exception ambit2.base.external.ShellException
 
ShellException(CommandShell, Throwable) - Constructor for exception ambit2.base.external.ShellException
 
ShellMengine - Class in ambit2.smi23d
A wrapper for Mengine
ShellMengine() - Constructor for class ambit2.smi23d.ShellMengine
 
ShellSDFoutput<INPUT> - Class in ambit2.core.external
 
ShellSDFoutput() - Constructor for class ambit2.core.external.ShellSDFoutput
 
ShellSmi2SDF - Class in ambit2.smi23d
 
ShellSmi2SDF() - Constructor for class ambit2.smi23d.ShellSmi2SDF
 
SHIFT_ATOM_ELEMENT - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_BOND_TYPE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_INNER_BOND_TYPE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_ISOTOPE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_LAYER_AT1 - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_LAYER_AT2 - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_NEG_CHARGE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_POS_CHARGE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_TOP_DEGREE - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
SHIFT_TOP_LAYER - Static variable in class ambit2.smarts.AtomEquivalenceInfo
 
shiftDesignations - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
shiftsAssociation - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
shiftState() - Method in class ambit2.tautomers.zwitterion.AminoGroup
 
shiftState() - Method in class ambit2.tautomers.zwitterion.CarboxylicGroup
 
shiftState() - Method in interface ambit2.tautomers.zwitterion.IAcidicCenter
 
shiftState() - Method in interface ambit2.tautomers.zwitterion.IBasicCenter
 
shiftState() - Method in class ambit2.tautomers.zwitterion.PhosphoricGroup
 
shiftState() - Method in class ambit2.tautomers.zwitterion.SulfGroup
 
shiftState() - Method in class ambit2.tautomers.zwitterion.SulfinicGroup
 
shiftState() - Method in class ambit2.tautomers.zwitterion.SulfonicGroup
 
SHOW_AROMATICITY - Static variable in class ambit2.base.config.Preferences
 
SHOW_AROMATICITY - Static variable in class ambit2.core.config.Resources
show aromaticity
showEndpoints - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
showFeatures - Variable in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
showGridHorizontal() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
showGridVertical() - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
shutdown(long, TimeUnit) - Method in class ambit2.rest.task.TaskStorage
 
SIMILARITY_ORDER - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
similarityColumn - Variable in class ambit2.db.reporters.CSVReporter
 
SimilarityManager - Class in ambit2.reactions
 
SimilarityManager() - Constructor for class ambit2.reactions.SimilarityManager
 
SimilarityManager.SimilarityTransformation - Enum in ambit2.reactions
 
SimilarityManager.TransformedStartMaterialData - Class in ambit2.reactions
 
SimilarityMatrix<T> - Class in ambit2.descriptors.simmatrix
 
SimilarityMatrix() - Constructor for class ambit2.descriptors.simmatrix.SimilarityMatrix
 
SimilarityMatrixBitset - Class in ambit2.descriptors.simmatrix
 
SimilarityMatrixBitset() - Constructor for class ambit2.descriptors.simmatrix.SimilarityMatrixBitset
 
SimilarityMatrixDouble - Class in ambit2.descriptors.simmatrix
 
SimilarityMatrixDouble() - Constructor for class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
SimilarityRelation - Class in ambit2.base.relation
 
SimilarityRelation(IStructureRecord, IStructureRecord) - Constructor for class ambit2.base.relation.SimilarityRelation
 
SimilarityRelation(IStructureRecord, IStructureRecord, Double) - Constructor for class ambit2.base.relation.SimilarityRelation
 
SimpleErrorHandler - Class in ambit2.base.io
 
SimpleErrorHandler(String) - Constructor for class ambit2.base.io.SimpleErrorHandler
 
SimpleIOListener - Class in ambit2.core.io
 
SimpleIOListener(IOSetting.Importance) - Constructor for class ambit2.core.io.SimpleIOListener
 
SimpleModelBuilder - Class in ambit2.rest.model.builder
Builds a model from ModelQueryResults.
SimpleModelBuilder(Reference, ModelURIReporter, AlgorithmURIReporter, String) - Constructor for class ambit2.rest.model.builder.SimpleModelBuilder
 
SimpleModelBuilder(Reference, ModelURIReporter, AlgorithmURIReporter, boolean, String) - Constructor for class ambit2.rest.model.builder.SimpleModelBuilder
 
simpleStoreData(Object) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
SimpleTaskResource<USERID> - Class in ambit2.rest
http://opentox.org/wiki/opentox/Asynchronous_jobs Provide (read)access to running tasks under URL http://host/application/task.
SimpleTaskResource() - Constructor for class ambit2.rest.SimpleTaskResource
 
SingleBondAromaticityNotSpecified - Class in ambit2.smarts
 
SingleBondAromaticityNotSpecified(IChemObjectBuilder) - Constructor for class ambit2.smarts.SingleBondAromaticityNotSpecified
 
singleElectrons - Variable in class ambit2.core.groups.SuppleAtomContainer
Internal array of single electrons.
singleElectrons() - Method in class ambit2.core.groups.SuppleAtomContainer
 
singleJSONFile - Variable in class ambit2.export.isa.json.ISAJsonExportConfig
 
SingleNonAromaticBond - Class in ambit2.smarts
 
SingleNonAromaticBond(IChemObjectBuilder) - Constructor for class ambit2.smarts.SingleNonAromaticBond
 
SingleOrAromaticBond - Class in ambit2.smarts
 
SingleOrAromaticBond(IChemObjectBuilder) - Constructor for class ambit2.smarts.SingleOrAromaticBond
 
singleSQLName - Static variable in class ambit2.db.search.property.FreeTextPropertyQuery
 
singleSQLName - Static variable in class ambit2.db.search.structure.FreeTextQuery
 
singleSQLValue - Static variable in class ambit2.db.search.property.FreeTextPropertyQuery
 
singleSQLValue - Static variable in class ambit2.db.search.structure.FreeTextQuery
 
SingleTaskIterator<USERID> - Class in ambit2.rest.task
Iterator for a single task
SingleTaskIterator(UUID) - Constructor for class ambit2.rest.task.SingleTaskIterator
 
sio_uri - Static variable in class ambit2.rest.substance.SubstanceRecordStaxWriter
 
siqr(double[], int) - Static method in class ambit2.domain.stats.Tools
 
size() - Method in class ambit2.base.data.Profile
 
size() - Method in class ambit2.base.data.study.Params
 
size() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader
 
size() - Method in class ambit2.core.data.ArrayResult
 
size - Variable in class ambit2.core.groups.FilteredList
 
size() - Method in class ambit2.core.groups.FilteredList
 
size - Variable in class ambit2.core.smiles.OpenBabelDepiction
 
size() - Method in class ambit2.db.results.AmbitRows
 
size() - Method in class ambit2.db.search.QueryCombined
 
size() - Method in class ambit2.model.dataset.DoubleArrayDataset
 
size() - Method in interface ambit2.model.IDataset
 
size() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
size() - Method in class ambit2.rest.legacy.OTRemoteTaskPool
Deprecated.
 
SizeDescriptor - Class in ambit2.descriptors
Size descriptor.
SizeDescriptor() - Constructor for class ambit2.descriptors.SizeDescriptor
 
sizeDescriptor - Variable in class ambit2.descriptors.SpherosityDescriptor
 
sk1024_screening - Variable in class ambit2.db.search.structure.QuerySMARTS
 
sk_prescreen - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
skGenerator - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
skGenerator - Variable in class ambit2.db.search.structure.QuerySMARTS
 
skip(Resource) - Method in class ambit2.rest.rdf.RDFObjectIterator
 
skipLines(int) - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
sleepInterval(long, boolean, int) - Method in class ambit2.rest.legacy.OTFibonacciSequence
Deprecated.
Calculates sleep interval
SLN2ChemObject - Class in ambit2.sln.io
 
SLN2ChemObject() - Constructor for class ambit2.sln.io.SLN2ChemObject
 
sln2ChemObject - Variable in class ambit2.sln.io.SLN2Substance
 
SLN2SMARTS - Class in ambit2.sln.io
 
SLN2SMARTS() - Constructor for class ambit2.sln.io.SLN2SMARTS
 
SLN2Substance - Class in ambit2.sln.io
 
SLN2Substance() - Constructor for class ambit2.sln.io.SLN2Substance
 
SLN2SubstanceConfig - Class in ambit2.sln.io
 
SLN2SubstanceConfig() - Constructor for class ambit2.sln.io.SLN2SubstanceConfig
 
SLN2SubstanceConfig.ConversionFlags - Class in ambit2.sln.io
 
SLN2SubstanceConfig.JsonFlags - Class in ambit2.sln.io
 
SLNAtom - Class in ambit2.sln
Abstract sln atom.
SLNAtom(IChemObjectBuilder) - Constructor for class ambit2.sln.SLNAtom
 
SLNAtomExpression - Class in ambit2.sln
 
SLNAtomExpression() - Constructor for class ambit2.sln.SLNAtomExpression
 
slnAtomToAtom(SLNAtom) - Method in class ambit2.sln.io.SLN2ChemObject
 
slnAtomToQueryAtom(SLNAtom) - Method in class ambit2.sln.io.SLN2ChemObject
 
SLNBond - Class in ambit2.sln
 
SLNBond(IChemObjectBuilder) - Constructor for class ambit2.sln.SLNBond
 
SLNBondExpression - Class in ambit2.sln
 
SLNBondExpression() - Constructor for class ambit2.sln.SLNBondExpression
 
slnBondToBond(SLNBond) - Method in class ambit2.sln.io.SLN2ChemObject
 
slnBondToQueryBond(SLNBond) - Method in class ambit2.sln.io.SLN2ChemObject
 
SLNCharToBondTypeAttr(char) - Static method in class ambit2.sln.SLNConst
 
SLNCompositeObject - Class in ambit2.sln
 
SLNCompositeObject() - Constructor for class ambit2.sln.SLNCompositeObject
 
SLNConst - Class in ambit2.sln
 
SLNConst() - Constructor for class ambit2.sln.SLNConst
 
SLNContainer - Class in ambit2.sln
 
SLNContainer(IChemObjectBuilder) - Constructor for class ambit2.sln.SLNContainer
 
SLNContainer.SLNObjectType - Enum in ambit2.sln
 
SLNContainerAttributes - Class in ambit2.sln
 
SLNContainerAttributes() - Constructor for class ambit2.sln.SLNContainerAttributes
 
slnContainerToAtomContainer(SLNContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
slnContainerToCompositionRelation(SLNContainer) - Method in class ambit2.sln.io.SLN2Substance
 
slnContainerToQueryAtomContainer(SLNContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
slnContainerToSMIRKSReaction(SLNContainer) - Method in class ambit2.sln.io.SLN2ChemObject
 
slnContainerToStructureRecord(SLNContainer) - Method in class ambit2.sln.io.SLN2Substance
 
SLNDictionary - Class in ambit2.sln.dictionary
 
SLNDictionary() - Constructor for class ambit2.sln.dictionary.SLNDictionary
 
SLNExpressionToken - Class in ambit2.sln
 
SLNExpressionToken(int) - Constructor for class ambit2.sln.SLNExpressionToken
 
SLNExpressionToken(int, int) - Constructor for class ambit2.sln.SLNExpressionToken
 
SLNExpressionToken(int, double) - Constructor for class ambit2.sln.SLNExpressionToken
 
SLNExpressionToken(int, String) - Constructor for class ambit2.sln.SLNExpressionToken
 
SLNExpressionToken(String, String) - Constructor for class ambit2.sln.SLNExpressionToken
 
SLNHelper - Class in ambit2.sln
 
SLNHelper() - Constructor for class ambit2.sln.SLNHelper
 
SLNIOHelpers - Class in ambit2.sln.io
 
SLNIOHelpers() - Constructor for class ambit2.sln.io.SLNIOHelpers
 
SLNLogicalExpression - Class in ambit2.sln
 
SLNLogicalExpression() - Constructor for class ambit2.sln.SLNLogicalExpression
 
SLNParser - Class in ambit2.sln
 
SLNParser() - Constructor for class ambit2.sln.SLNParser
 
SLNParser(SLNDictionary) - Constructor for class ambit2.sln.SLNParser
 
SLNParserError - Class in ambit2.sln
 
SLNParserError(String, String, int, String) - Constructor for class ambit2.sln.SLNParserError
 
SLNReaction - Class in ambit2.sln.reaction
 
SLNReaction() - Constructor for class ambit2.sln.reaction.SLNReaction
 
SLNRingClosure - Class in ambit2.sln
 
SLNRingClosure() - Constructor for class ambit2.sln.SLNRingClosure
 
SLNSearchManager - Class in ambit2.sln.search
 
SLNSearchManager() - Constructor for class ambit2.sln.search.SLNSearchManager
 
SLNStringToAtomStereoChemAttr(String) - Static method in class ambit2.sln.SLNConst
 
SLNStringToBondStereoChemAttr(String) - Static method in class ambit2.sln.SLNConst
 
SLNStringToBondTypeAttr(String) - Static method in class ambit2.sln.SLNConst
 
SLNStringToComparisonOperation(String) - Static method in class ambit2.sln.SLNConst
 
SLNStringToCoverageQueryAttr(String) - Static method in class ambit2.sln.SLNConst
 
SLNStringToSpinAttr(String) - Static method in class ambit2.sln.SLNConst
 
SLNSubstance - Class in ambit2.sln
 
SLNSubstance() - Constructor for class ambit2.sln.SLNSubstance
 
slnToSmarts(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
slnToSmiles(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
slnToSmirks(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
slnToSubstanceComposition(SLNSubstance) - Method in class ambit2.sln.io.SLN2Substance
 
slogger - Static variable in class ambit2.descriptors.FuncGroupsDescriptorFactory
 
sman - Variable in class ambit2.smarts.query.SmartsPatternAmbit
 
SMARTS - Static variable in class ambit2.db.search.structure.QuerySMARTS
 
smarts - Variable in class ambit2.descriptors.PKANode
 
smarts - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
smarts - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule2J
 
smarts - Variable in class ambit2.groupcontribution.nmr.Substituent
 
smarts - Variable in class ambit2.reactions.fragmentation.FragmentationRule
 
smarts - Variable in class ambit2.smarts.query.AbstractSmartsPattern
 
smarts - Variable in class ambit2.tautomers.rules.AtomCondition
 
smarts - Variable in class ambit2.tautomers.rules.CustomTautomerRegion
 
smarts1 - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
smarts2 - Variable in class ambit2.groupcontribution.nmr.nmr_1h.Rule3J
 
SMARTS_UNDEFINED - Static variable in class ambit2.core.config.Resources
Undefined smarts
SMARTSAcceleratorWriter - Class in ambit2.db.update.qlabel.smarts
 
SMARTSAcceleratorWriter() - Constructor for class ambit2.db.update.qlabel.smarts.SMARTSAcceleratorWriter
 
SmartsAtomExpression - Class in ambit2.smarts
 
SmartsAtomExpression(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsAtomExpression
 
SmartsBondExpression - Class in ambit2.smarts
 
SmartsBondExpression(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsBondExpression
 
SmartsConst - Class in ambit2.smarts
 
SmartsConst() - Constructor for class ambit2.smarts.SmartsConst
 
SmartsConst.HandleHAtoms - Enum in ambit2.smarts
 
SmartsConst.SSM_MODE - Enum in ambit2.smarts
 
SmartsCorrectionFactor - Class in ambit2.groupcontribution.correctionfactors
 
SmartsCorrectionFactor(String, SmartsParser, IsomorphismTester) - Constructor for class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
SmartsCorrectionFactor(String, SmartsParser, IsomorphismTester, IValueTransformation) - Constructor for class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
SmartsCorrectionFactor(String, SmartsParser, IsomorphismTester, SmartsConst.SSM_MODE, IValueTransformation) - Constructor for class ambit2.groupcontribution.correctionfactors.SmartsCorrectionFactor
 
SMARTSException - Exception in ambit2.smarts.query
Exception , throwsn on SMARTS processing
SMARTSException() - Constructor for exception ambit2.smarts.query.SMARTSException
 
SMARTSException(String) - Constructor for exception ambit2.smarts.query.SMARTSException
 
SMARTSException(String, Throwable) - Constructor for exception ambit2.smarts.query.SMARTSException
 
SMARTSException(Throwable) - Constructor for exception ambit2.smarts.query.SMARTSException
 
smartsExpressionToAtom(SmartsAtomExpression) - Method in class ambit2.smarts.SmartsToChemObject
This function tries to convert the SmartsAtomExpression to a IAtom with defined atom type.
smartsExpressionToBond(SmartsBondExpression) - Method in class ambit2.smarts.SmartsToChemObject
 
SmartsExpressionToken - Class in ambit2.smarts
 
SmartsExpressionToken(int, int) - Constructor for class ambit2.smarts.SmartsExpressionToken
 
SmartsFingerprinter - Class in ambit2.smarts
 
SmartsFingerprinter(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsFingerprinter
 
SmartsFlags - Class in ambit2.smarts
 
SmartsFlags() - Constructor for class ambit2.smarts.SmartsFlags
 
SmartsHelper - Class in ambit2.smarts
 
SmartsHelper(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsHelper
 
SmartsIsomorphismTester - Class in ambit2.smarts.smirks
 
SmartsIsomorphismTester() - Constructor for class ambit2.smarts.smirks.SmartsIsomorphismTester
 
smartsKeys - Static variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
SmartsLogicalExpression - Class in ambit2.smarts
 
SmartsLogicalExpression() - Constructor for class ambit2.smarts.SmartsLogicalExpression
 
SmartsManager - Class in ambit2.smarts
Implements utilities needed for handling searching with SMARTS utilizing JDK library.
SmartsManager(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsManager
 
smartsMatch - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
SmartsMatch - Class in ambit2.smarts.smirks
 
SmartsMatch() - Constructor for class ambit2.smarts.smirks.SmartsMatch
 
SmartsMatch.AttributeComparison - Enum in ambit2.smarts.smirks
 
SmartsMatch.MatchMode - Enum in ambit2.smarts.smirks
 
SmartsParser - Class in ambit2.smarts
Implements SMARTS parser
SmartsParser() - Constructor for class ambit2.smarts.SmartsParser
 
SmartsParserError - Class in ambit2.smarts
 
SmartsParserError(String, String, int, String) - Constructor for class ambit2.smarts.SmartsParserError
 
smartsPattern - Static variable in class ambit2.descriptors.PKANode
 
SmartsPatternAmbit - Class in ambit2.smarts.query
Encapsulates Ambit SMARTS parser.
SmartsPatternAmbit() - Constructor for class ambit2.smarts.query.SmartsPatternAmbit
 
SmartsPatternAmbit(IChemObjectBuilder) - Constructor for class ambit2.smarts.query.SmartsPatternAmbit
 
SmartsPatternAmbit(String) - Constructor for class ambit2.smarts.query.SmartsPatternAmbit
 
SmartsPatternAmbit(String, IChemObjectBuilder) - Constructor for class ambit2.smarts.query.SmartsPatternAmbit
 
SmartsPatternAmbit(String, boolean, IChemObjectBuilder) - Constructor for class ambit2.smarts.query.SmartsPatternAmbit
 
SmartsPatternCDK - Class in ambit2.smarts.query
Encapsulates CDK SMARTS parser.
SmartsPatternCDK() - Constructor for class ambit2.smarts.query.SmartsPatternCDK
 
SmartsPatternCDK(String) - Constructor for class ambit2.smarts.query.SmartsPatternCDK
 
SmartsPatternCDK(String, boolean) - Constructor for class ambit2.smarts.query.SmartsPatternCDK
 
SmartsPatternFactory - Class in ambit2.smarts.query
Creates any of SMARTS pattern classes.
SmartsPatternFactory() - Constructor for class ambit2.smarts.query.SmartsPatternFactory
 
SmartsPatternFactory.SmartsParser - Enum in ambit2.smarts.query
 
SMARTSProp - Static variable in class ambit2.smarts.CMLUtilities
 
SMARTSPropertiesGenerator - Class in ambit2.smarts.processors
 
SMARTSPropertiesGenerator() - Constructor for class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
SMARTSPropertiesReader - Class in ambit2.smarts.processors
Expects properties to accelerate smarts search , expected in CMLUtilities.SMARTSProp
SMARTSPropertiesReader() - Constructor for class ambit2.smarts.processors.SMARTSPropertiesReader
 
smartsProperty - Variable in class ambit2.core.processors.structure.MoleculePairProcessor
 
smartsProperty - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
smartsProperty - Variable in class ambit2.db.search.structure.QuerySMARTS
 
smartsProperty - Variable in class ambit2.descriptors.processors.BitSetGenerator
 
smartsQueries - Static variable in class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
smartsQueries - Variable in class ambit2.tautomers.rules.AtomCondition
 
SMARTSQuery - Static variable in class ambit2.core.config.AmbitCONSTANTS
SMARTS Query
smartsQueryFlags - Variable in class ambit2.tautomers.rules.AtomCondition
 
SmartsScreeningKeys - Class in ambit2.smarts
 
SmartsScreeningKeys() - Constructor for class ambit2.smarts.SmartsScreeningKeys
 
smartsStates - Variable in class ambit2.tautomers.Rule
 
smartsToChemObject - Variable in class ambit2.db.search.structure.QuerySMARTS
 
smartsToChemObject - Variable in class ambit2.dbui.QuerySmartsEditor
 
SmartsToChemObject - Class in ambit2.smarts
 
SmartsToChemObject(IChemObjectBuilder) - Constructor for class ambit2.smarts.SmartsToChemObject
 
SmartsToSLN(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
smi2sdf - Variable in class ambit2.mopac.MopacShell
 
SMI2SDF_LINUX - Static variable in class ambit2.base.config.Preferences
 
SMI2SDF_WIN - Static variable in class ambit2.base.config.Preferences
 
smiles - Variable in class ambit2.base.data.StructureRecord
 
SMILES - Static variable in class ambit2.core.config.AmbitCONSTANTS
SMILES
smiles - Variable in class ambit2.db.search.QueryInfo
 
smiles - Variable in class ambit2.db.search.structure.QueryLookupStructure
 
smiles - Variable in class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialData
 
smiles - Variable in class ambit2.reactions.SimilarityManager.TransformedStartMaterialData
 
smiles - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
smiles - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
smiles - Variable in class ambit2.smarts.StructInfo
 
smiles - Variable in class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
SMILES_FIELD - Static variable in class ambit2.base.config.Preferences
 
SMILES_GEN - Static variable in class ambit2.base.config.Preferences
 
smiles_generator - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
smilesBondToString(IBond, boolean) - Static method in class ambit2.smarts.SmartsHelper
 
smilesIndex - Variable in class ambit2.core.io.FilesWithHeaderWriter
 
smilesIndex - Variable in class ambit2.core.io.FileWithHeaderWriter
 
smilesIndex - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
SmilesKey - Class in ambit2.core.processors.structure.key
Returns smiles, given the structure
SmilesKey() - Constructor for class ambit2.core.processors.structure.key.SmilesKey
 
smilesKey - Variable in class ambit2.core.processors.StructureNormalizer
 
smilesKey - Variable in class ambit2.db.processors.quality.QualityLabelWriter
 
smilesKey - Variable in class ambit2.db.search.structure.QueryStructure
 
SMILESPARSER - Static variable in class ambit2.base.config.Preferences
 
SMILESPARSER - Static variable in class ambit2.core.config.Resources
Openbabel or CDK smiles parser
SmilesParserWrapper - Class in ambit2.core.smiles
 
SmilesParserWrapper() - Constructor for class ambit2.core.smiles.SmilesParserWrapper
 
SmilesParserWrapper(SmilesParserWrapper.SMILES_PARSER) - Constructor for class ambit2.core.smiles.SmilesParserWrapper
 
SmilesParserWrapper.SMILES_PARSER - Enum in ambit2.core.smiles
 
SmilesReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters
 
SmilesReporter() - Constructor for class ambit2.db.reporters.SmilesReporter
 
SmilesReporter(boolean, Template) - Constructor for class ambit2.db.reporters.SmilesReporter
 
SmilesReporter(boolean, SmilesReporter.Mode, Template) - Constructor for class ambit2.db.reporters.SmilesReporter
 
SmilesReporter.Mode - Enum in ambit2.db.reporters
 
SmilesToSLN(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
SmilesUniquenessCheck - Class in ambit2.db.update.qlabel
 
SmilesUniquenessCheck() - Constructor for class ambit2.db.update.qlabel.SmilesUniquenessCheck
 
smiParser - Variable in class ambit2.core.processors.structure.MoleculeReader
 
smirks - Variable in class ambit2.reactions.GenericReaction
 
smirks - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
smirks - Variable in class ambit2.reactions.rules.RetroSynthRule
 
smirks - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
smirksArg - Variable in class ambit2.reactions.cli.AmbitSmirksCli
 
smirksFlag - Variable in class ambit2.reactions.GenericReaction
 
SMIRKSManager - Class in ambit2.smarts
 
SMIRKSManager(IChemObjectBuilder) - Constructor for class ambit2.smarts.SMIRKSManager
 
SmirksMatch - Class in ambit2.smarts.smirks
 
SmirksMatch() - Constructor for class ambit2.smarts.smirks.SmirksMatch
 
SMIRKSProcessor - Class in ambit2.smarts.processors
 
SMIRKSProcessor(Logger) - Constructor for class ambit2.smarts.processors.SMIRKSProcessor
 
SMIRKSProcessor(File, Logger) - Constructor for class ambit2.smarts.processors.SMIRKSProcessor
 
SMIRKSProcessor(InputStream, Logger) - Constructor for class ambit2.smarts.processors.SMIRKSProcessor
 
smirksReaction - Variable in class ambit2.reactions.GenericReaction
 
smirksReaction - Variable in class ambit2.smarts.processors.SMIRKSTransformation
 
SMIRKSReaction - Class in ambit2.smarts
 
SMIRKSReaction(IChemObjectBuilder) - Constructor for class ambit2.smarts.SMIRKSReaction
 
SMIRKSReactionToSLNContainer(SMIRKSReaction) - Method in class ambit2.sln.io.SLN2ChemObject
 
SmirksToSLN(String) - Method in class ambit2.sln.io.SLN2SMARTS
 
SMIRKSTransform - Class in ambit2.smarts
 
SMIRKSTransform() - Constructor for class ambit2.smarts.SMIRKSTransform
 
SMIRKSTransformation - Class in ambit2.smarts.processors
Placeholder for set of SMIRKS with additional options
SMIRKSTransformation() - Constructor for class ambit2.smarts.processors.SMIRKSTransformation
 
SmirksTransformationFlag - Enum in ambit2.smarts.smirks
 
SMRK_UNSPEC_ATOM - Static variable in class ambit2.smarts.SmartsConst
 
smrkMan - Variable in class ambit2.reactions.reactor.Reactor
 
smrkMan - Variable in class ambit2.smarts.processors.SMIRKSProcessor
 
SMSDModelBuilder - Class in ambit2.rest.model.builder
 
SMSDModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String) - Constructor for class ambit2.rest.model.builder.SMSDModelBuilder
 
SMSDModelBuilder(Reference, ModelURIReporter<IQueryRetrieval<ModelQueryResults>>, AlgorithmURIReporter, String[], String[], String) - Constructor for class ambit2.rest.model.builder.SMSDModelBuilder
 
solr_basic_password - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
solr_basic_user - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
solr_filter - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
solr_service - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
solr_url - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
solver - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
solver - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
solvers - Variable in class ambit2.rules.conditions.DescriptorSolverSet
 
SOME_HOME - Static variable in class ambit2.some.SOMEShell
 
SOME_RESULT - Static variable in class ambit2.some.SOMEShell
 
some_shell - Variable in class ambit2.some.DescriptorSOMEShell
 
SOMERawReader - Class in ambit2.some
Reads SOME records
SOMERawReader(Reader) - Constructor for class ambit2.some.SOMERawReader
 
SOMERawReader.someindex - Enum in ambit2.some
 
SOMEResultsParser - Class in ambit2.some
Parses SOME text results.
SOMEResultsParser() - Constructor for class ambit2.some.SOMEResultsParser
 
SOMEShell - Class in ambit2.some
Wrapper for Site Of Metabolism Estimator (SOME) http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz.
SOMEShell() - Constructor for class ambit2.some.SOMEShell
 
SOMEVisualizer - Class in ambit2.some
 
SOMEVisualizer() - Constructor for class ambit2.some.SOMEVisualizer
 
sort(int, boolean) - Method in interface ambit2.base.data.ISortableColumns
 
sort(int, boolean) - Method in class ambit2.db.results.StoredQueryTableModel
 
sort(int, boolean) - Method in class ambit2.ui.table.BrowsableTableModel
 
sortConnectionsByRank(List<ComponentConnection>) - Static method in class ambit2.structure2name.components.ComponentUtils
 
sortingOrder - Variable in class ambit2.base.facet.SubstanceStudyFacet
 
sortReactionInstances(List<GenericReactionInstance>) - Static method in class ambit2.reactions.retrosynth.ReactionSequence
 
sortReactionInstances(List<GenericReactionInstance>, ReactionSequence.SortingMethod) - Static method in class ambit2.reactions.retrosynth.ReactionSequence
 
Source - Class in ambit2.export.isa.v1_0.objects
ISA source schema JSON-schema representing a source in the ISA model.
Source() - Constructor for class ambit2.export.isa.v1_0.objects.Source
 
source - Variable in class ambit2.pubchem.EntrezSearchOptions
 
source - Variable in class ambit2.rest.legacy.OTDataset
Deprecated.
 
SourceDataset - Class in ambit2.base.data
A dataset
SourceDataset() - Constructor for class ambit2.base.data.SourceDataset
 
SourceDataset(String) - Constructor for class ambit2.base.data.SourceDataset
 
SourceDataset(String, ILiteratureEntry) - Constructor for class ambit2.base.data.SourceDataset
 
SourceDatasetEditor - Class in ambit2.dbui
 
SourceDatasetEditor() - Constructor for class ambit2.dbui.SourceDatasetEditor
 
SourceDatasetRows<M extends ISourceDataset> - Class in ambit2.db
TODO to be removed
SourceDatasetRows() - Constructor for class ambit2.db.SourceDatasetRows
 
sourceName - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
sourceReference - Variable in class ambit2.rest.task.CallableQueryProcessor
 
sources - Variable in class ambit2.export.isa.v1_0.objects.Materials_
 
sourceSLN - Variable in class ambit2.sln.SLNParserError
 
sourceSmarts - Variable in class ambit2.smarts.SmartsParserError
 
sp - Static variable in class ambit2.core.data.MoleculeTools
 
sp - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
sp - Variable in class ambit2.smarts.query.FastSmartsMatcher
 
sparql - Static variable in class ambit2.rest.legacy.RDFAbstractFeatureIterator
Deprecated.
 
sparql - Variable in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
sparql - Static variable in class ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator
 
sparql - Static variable in class ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator
 
sparqlEndpoint - Static variable in class ambit2.rest.rdf.chembl.ChEMBLRawReader
 
sparseproperties - Variable in class ambit2.core.processors.AbstractStructureProcessor
 
SPECIFIC_SURFACE_AREA - Static variable in class ambit2.base.ro.I5CONSTANTS
 
SpherosityDescriptor - Class in ambit2.descriptors
Spherosity descriptor.
SpherosityDescriptor() - Constructor for class ambit2.descriptors.SpherosityDescriptor
 
spiroAtoms - Variable in class ambit2.structure2name.IUPACNameGenerator
 
splitFragments - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
splitI5UUID(String) - Static method in class ambit2.base.data.I5Utils
 
splitRecord - Variable in class ambit2.db.substance.processor.DBSubstanceWriter
 
splitter - Static variable in class ambit2.export.isa.base.ExternalDataFileLocation
 
splitter - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
splitter - Static variable in class ambit2.export.isa.base.ISALocation
 
splitter - Variable in class ambit2.tautomers.Tautomer2DescriptorUtils
 
SQI - Variable in class ambit2.smarts.StructureSetAnalyzer.CharStructInfo
 
sql - Static variable in class ambit2.db.chart.FuncGroupsChartGenerator
 
sql - Static variable in class ambit2.db.chart.Nominal2SimilarityChartGenerator
 
sql - Static variable in class ambit2.db.chart.Numeric2SimilarityChartGenerator
 
sql - Static variable in class ambit2.db.chart.XTabChartGenerator
 
sql - Static variable in class ambit2.db.chemrelation.ReadStructureRelation
 
sql - Variable in class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery
 
sql - Static variable in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
sql - Static variable in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
sql - Static variable in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
sql - Static variable in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
sql - Static variable in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
sql - Variable in class ambit2.db.processors.ConnectionStatisticsProcessor
 
sql - Variable in class ambit2.db.processors.processorCloseSession
 
sql - Static variable in class ambit2.db.readers.AbstractStructureRetrieval
 
sql - Static variable in class ambit2.db.readers.RetrieveDescriptor
 
sql() - Method in class ambit2.db.readers.RetrieveField
 
sql() - Method in class ambit2.db.readers.RetrieveProfileValues
 
SQL - Static variable in class ambit2.db.search.DictionaryQuery
 
sql - Variable in class ambit2.db.search.property.FilteredCountNominal
 
sql - Variable in class ambit2.db.search.property.FilteredCountNumeric
 
sql - Static variable in class ambit2.db.search.property.FreeTextPropertyQuery
 
sql - Variable in class ambit2.db.search.property.ModelTemplates
 
SQL - Static variable in class ambit2.db.search.property.PropertyCount
 
sql - Static variable in class ambit2.db.search.property.PropertyStatsNumeric
 
sql - Static variable in class ambit2.db.search.property.PropertyStatsString
 
sql - Static variable in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
sql - Static variable in class ambit2.db.search.property.RetrieveFieldNamesByType
 
SQL - Static variable in class ambit2.db.search.property.TemplateQuery
 
sql - Static variable in class ambit2.db.search.qlabel.QueryQLabel
 
SQL - Static variable in class ambit2.db.search.QueryUser
 
sql - Static variable in class ambit2.db.search.structure.ChemicalByQueryFolder
 
sql - Static variable in class ambit2.db.search.structure.FingerprintsByStatus
 
sql - Static variable in class ambit2.db.search.structure.FreeTextQuery
 
sql - Static variable in class ambit2.db.search.structure.MissingInChIsQuery
 
sql - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
sql - Variable in class ambit2.db.search.structure.pairwise.QueryStructurePairsDataset
 
sql - Variable in class ambit2.db.search.structure.pairwise.QueryStructurePairsMixed
 
sql - Variable in class ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset
 
sql - Variable in class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback
 
sql - Static variable in class ambit2.db.search.structure.QueryDataset
 
sql - Static variable in class ambit2.db.search.structure.QueryDatasetByID
 
sql - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
sql - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
sql - Static variable in class ambit2.db.search.structure.QueryStructureByValueQuality
 
sql - Static variable in class ambit2.db.search.structure.QueryStructureType
 
sql - Static variable in class ambit2.db.search.structure.QueryStrucType
 
sql - Static variable in class ambit2.db.simiparity.space.QueryQMapStructures
 
sql - Static variable in class ambit2.db.substance.AbstractReadSubstance
 
sql - Static variable in class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
sql - Variable in class ambit2.db.substance.study.facet.OwnerSubstanceStats
 
sql - Static variable in class ambit2.db.substance.study.ReadEffectRecordAbstract
 
sql - Static variable in class ambit2.db.update.bookmark.ReadAnnotation
 
sql - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
sql - Variable in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
sql - Static variable in class ambit2.db.update.fp.CreateFingerprintStructure
 
sql - Variable in class ambit2.db.update.fp.QueryFingerprints
 
sql - Static variable in class ambit2.db.update.fp.ReadStructuresByFingerprint
 
sql - Static variable in class ambit2.db.update.fpae.DeleteAtomEnvironment
 
sql - Static variable in class ambit2.db.update.model.AbstractModelQuery
 
sql - Variable in class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
sql - Variable in class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
sql - Variable in class ambit2.db.update.propertyannotations.DeletePropertyAnnotation
 
sql - Variable in class ambit2.db.update.propertyannotations.ReadPropertyAnnotations
 
sql - Variable in class ambit2.db.update.propertyannotations.UpdatePropertyAnnotation
 
sql - Static variable in class ambit2.db.update.qlabel.CreateQLabelCAS
 
sql - Static variable in class ambit2.db.update.qlabel.CreateQLabelEINECS
 
sql - Static variable in class ambit2.db.update.qlabel.CreateQLabelFingerprints
 
sql - Static variable in class ambit2.db.update.qlabel.CreateQLabelPair
 
sql - Variable in class ambit2.db.update.qlabel.CreateStructureQLabel
 
sql - Variable in class ambit2.db.update.qlabel.CreateValueQLabel
 
sql - Variable in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
sql - Variable in class ambit2.db.update.qlabel.DeleteValueQLabel
 
sql - Static variable in class ambit2.db.update.qlabel.smarts.CreateSMARTSData
 
sql - Static variable in class ambit2.db.update.qlabel.SmilesUniquenessCheck
 
sql - Static variable in class ambit2.db.update.qlabel.ValuesQualityCheck
 
sql - Static variable in class ambit2.db.update.queryfolder.CreateQueryFolder
 
sql - Static variable in class ambit2.db.update.queryfolder.DeleteQueryFolder
 
sql - Static variable in class ambit2.db.update.queryfolder.ReadQueryFolder
 
sql - Static variable in class ambit2.db.update.queryfolder.UpdateQueryFolder
 
sql - Static variable in class ambit2.db.update.reference.ReadReference
 
sql - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql - Static variable in class ambit2.db.update.structure.ChemicalByDataset
 
sql - Variable in class ambit2.db.update.structure.CreateStrucType
 
sql - Variable in class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
sql - Variable in class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
sql - Variable in class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
sql - Variable in class ambit2.db.update.value.UpdateStructurePropertyIDString
 
sql1 - Variable in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
sql2 - Variable in class ambit2.db.search.structure.pairwise.RetrieveStructurePair
 
sql_alias - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_all - Static variable in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
sql_all - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
sql_by_relation - Static variable in class ambit2.db.update.bookmark.ReadAnnotation
 
sql_byid - Static variable in class ambit2.db.update.storedquery.CreateStoredQuery
 
sql_byname - Static variable in class ambit2.db.update.storedquery.CreateStoredQuery
 
sql_bypropertyname - Variable in class ambit2.db.update.propertyannotations.CreatePropertyAnnotation
 
sql_chemical - Variable in class ambit2.db.readers.RetrieveField
 
sql_chemical - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_chemical - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
sql_chemical - Static variable in class ambit2.db.search.qlabel.QueryConsensus
 
sql_chemical - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
sql_chemical - Static variable in class ambit2.db.search.structure.QueryStructure
 
sql_chemical - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
sql_chemical - Variable in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
sql_chemical_novalue - Variable in class ambit2.db.readers.RetrieveField
 
sql_chemical_novalue - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_chemicals - Variable in class ambit2.db.readers.RetrieveModelTemplates
 
sql_chemicals - Variable in class ambit2.db.readers.RetrieveTemplate
 
sql_chemicals - Static variable in class ambit2.db.update.dataset.QueryCountChemicalInDataset
 
sql_compound - Static variable in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
sql_compounds - Static variable in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds
 
sql_current_user - Static variable in class ambit2.db.update.queryfolder.CreateQueryFolder
 
sql_current_user - Static variable in class ambit2.db.update.queryfolder.DeleteQueryFolder
 
sql_current_user - Static variable in class ambit2.db.update.queryfolder.UpdateQueryFolder
 
sql_dataset - Static variable in class ambit2.db.chart.BarChartGeneratorDataset
 
sql_dataset - Static variable in class ambit2.db.chart.PieChartGenerator
 
sql_dataset - Static variable in class ambit2.db.chart.PropertiesChartGenerator
 
sql_dataset - Static variable in class ambit2.db.chemrelation.ReadDatasetRelation
 
sql_dataset - Static variable in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
sql_dataset - Static variable in class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset
 
sql_dataset_bycompound - Static variable in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
sql_datasetid - Variable in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
sql_datasets - Static variable in class ambit2.db.update.dataset.QueryCountChemicalInDataset
 
sql_datasets - Static variable in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
sql_defaultuser - Variable in class ambit2.db.update.qlabel.CreateStructureQLabel
 
sql_defaultuser - Variable in class ambit2.db.update.qlabel.CreateValueQLabel
 
sql_defaultuser - Variable in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
sql_defaultuser - Variable in class ambit2.db.update.qlabel.DeleteValueQLabel
 
sql_exact - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
sql_grouped - Variable in class ambit2.db.readers.RetrieveGroupedValuesByAlias
 
SQL_INSERT - Static variable in interface ambit2.db.search.IStoredQuery
 
sql_labelsonly - Static variable in class ambit2.db.update.bookmark.ReadAnnotation
 
sql_labelsonly_by_relation - Static variable in class ambit2.db.update.bookmark.ReadAnnotation
 
sql_metric - Variable in class ambit2.db.search.property.FilteredCountNominal
 
sql_metric - Variable in class ambit2.db.search.property.FilteredCountNumeric
 
sql_metric - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_models - Static variable in class ambit2.db.model.QueryCountModels
 
sql_name - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_predicted - Static variable in class ambit2.db.update.model.AbstractModelQuery
 
sql_prefered - Variable in class ambit2.db.readers.RetrieveStructure
 
sql_prefered - Static variable in class ambit2.db.search.structure.QueryStructure
 
sql_prescreen - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
sql_properties - Static variable in class ambit2.db.update.dataset.QueryCountProperties
 
sql_property - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
sql_propery - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_queries - Static variable in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
sql_query - Static variable in class ambit2.db.chart.BarChartGeneratorDataset
 
sql_query - Static variable in class ambit2.db.chart.PieChartGenerator
 
sql_query - Static variable in class ambit2.db.chart.PropertiesChartGenerator
 
sql_query - Static variable in class ambit2.db.chemrelation.ReadDatasetRelation
 
sql_query - Variable in class ambit2.db.search.property.FilteredCountNominal
 
sql_query - Variable in class ambit2.db.search.property.FilteredCountNumeric
 
sql_query - Static variable in class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults
 
sql_query - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_query_and_dataset - Static variable in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
sql_similarity - Variable in class ambit2.db.search.structure.QuerySimilarityBitset
 
sql_size - Variable in class ambit2.db.update.bookmark.CreateBookmark
 
sql_size - Variable in class ambit2.db.update.model.CreateModel
 
sql_struc - Variable in class ambit2.db.search.structure.QueryPrescreenBitSet
 
sql_structure - Static variable in class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery
 
sql_structure - Variable in class ambit2.db.readers.RetrieveField
 
sql_structure - Variable in class ambit2.db.readers.RetrieveModelTemplates
 
sql_structure - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_structure - Variable in class ambit2.db.readers.RetrieveProfileValuesAsRow
 
sql_structure - Variable in class ambit2.db.readers.RetrieveTemplate
 
sql_structure - Static variable in class ambit2.db.search.qlabel.QueryConsensus
 
sql_structure - Variable in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
sql_structure_novalue - Variable in class ambit2.db.readers.RetrieveField
 
sql_structure_novalue - Variable in class ambit2.db.readers.RetrieveProfileValues
 
sql_structures - Static variable in class ambit2.db.update.dataset.QueryCount
 
sql_substances - Static variable in class ambit2.db.substance.QueryCountSubstances
 
sql_substancetype - Static variable in class ambit2.db.substance.QueryCountSubstanceTypes
 
sql_summary - Static variable in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
sql_table_string - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_templateall - Variable in class ambit2.db.readers.RetrieveModelTemplates
 
sql_templateall - Variable in class ambit2.db.readers.RetrieveTemplate
 
sql_value - Variable in class ambit2.db.search.property.FilteredCountNominal
 
sql_value - Variable in class ambit2.db.search.property.FilteredCountNumeric
 
sql_value_numeric - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_value_string - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_values - Static variable in class ambit2.db.substance.QueryCountBundles
 
sql_values - Static variable in class ambit2.db.update.dataset.QueryCountDataset
 
sql_values - Static variable in class ambit2.db.update.dataset.QueryCountValues
 
sql_values - Variable in class ambit2.db.update.propertyannotations.CreatePropertyAnnotations
 
sql_where - Variable in class ambit2.db.readers.RetrieveModelTemplates
 
sql_where - Variable in class ambit2.db.readers.RetrieveTemplate
 
SQL_WHERE - Static variable in class ambit2.db.search.property.TemplateQuery
 
sql_where - Static variable in class ambit2.db.search.qlabel.QueryConsensus
 
sql_where - Static variable in class ambit2.db.search.qlabel.QueryQLabel
 
sql_where_name - Variable in class ambit2.db.readers.RetrieveTemplate
 
sql_where_num - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sql_where_string - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
sqlChild - Variable in class ambit2.db.search.property.QueryOntology
 
sqlDataset - Static variable in class ambit2.db.search.structure.QueryStructureByID
 
sqlField - Static variable in class ambit2.db.cache.QueryCachedResults
 
sqlField - Static variable in class ambit2.db.cache.RetrieveStructureImagePath
 
sqlField - Static variable in class ambit2.db.search.QuerySmilesByID
 
sqlField - Static variable in class ambit2.db.search.structure.MissingFingerprintsQuery
 
sqlField - Static variable in class ambit2.db.search.structure.QueryDistance
 
sqlField - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
 
sqlField - Static variable in class ambit2.db.search.structure.QueryFieldNumeric
 
sqlField - Static variable in class ambit2.db.search.structure.QueryStoredResults
 
sqlField - Static variable in class ambit2.db.search.structure.QueryStoredResultsByName
 
sqlField - Static variable in class ambit2.db.search.structure.QueryStructureByID
 
sqlField - Static variable in class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
sqlField - Static variable in class ambit2.db.update.dataset.DatasetQueryFieldString
 
sqlField - Static variable in class ambit2.db.update.storedquery.ReadStoredQuery
 
sqlField - Static variable in class ambit2.db.update.storedquery.SearchStoredQueries
 
sqlField_ci - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
 
sqlField_Rdatasets - Static variable in class ambit2.db.update.dataset.DatasetQueryFieldNumeric
 
sqlField_Rdatasets - Static variable in class ambit2.db.update.dataset.DatasetQueryFieldString
 
sqlFieldProperties - Static variable in class ambit2.db.search.structure.QueryFieldAbstract
This is faster than the one below, but will work if the summary table exists and for case insensitive searches only
sqlFieldStruc - Static variable in class ambit2.db.search.structure.MissingFingerprintsQuery
 
SQLFile - Variable in class ambit2.db.processors.DbCreateDatabase
 
SQLFileQueryParams - Class in ambit2.db.search
 
SQLFileQueryParams(File, ObjectNode) - Constructor for class ambit2.db.search.SQLFileQueryParams
 
SQLFileQueryParams(String, ObjectNode) - Constructor for class ambit2.db.search.SQLFileQueryParams
 
SQLFileQueryParams._fields - Enum in ambit2.db.search
 
sqlINCHI - Static variable in class ambit2.db.search.structure.MissingFingerprintsQuery
 
sqlParent - Variable in class ambit2.db.search.property.QueryOntology
 
sqlPerChemical - Static variable in class ambit2.db.update.property.ReadProperty
 
sqlPerStructure - Static variable in class ambit2.db.update.property.ReadProperty
 
sqlQuery - Static variable in class ambit2.db.search.structure.QueryStructureByID
 
sqlSMARTS - Static variable in class ambit2.db.search.structure.MissingFingerprintsQuery
 
sqt - Variable in class ambit2.smarts.query.SmartsPatternCDK
 
SquareDistanceDegreeVector(IAtomContainer) - Static method in class ambit2.descriptors.utils.TopologicalUtilities
 
SquareRootMolecularWeightDescriptor - Class in ambit2.descriptors.constitutional
Square root molecular weight.
SquareRootMolecularWeightDescriptor() - Constructor for class ambit2.descriptors.constitutional.SquareRootMolecularWeightDescriptor
 
sres(double, int) - Static method in class ambit2.domain.stats.Tools
 
sresults - Variable in class ambit2.db.search.QueryExecutor
 
srtm - Variable in class ambit2.dbui.dictionary.AmbitRowsPanel
 
sse(double[], double[]) - Static method in class ambit2.domain.stats.Tools
 
stack - Variable in class ambit2.smarts.IsomorphismTester
 
stack - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
standardError(MatrixDouble, MatrixDouble, int) - Static method in class ambit2.groupcontribution.utils.math.Statistics
 
stars - Variable in class ambit2.base.data.AbstractDataset
 
stars - Variable in class ambit2.base.data.SourceDataset
 
stars - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
stars - Variable in class ambit2.core.data.model.ModelWrapper
 
stars - Variable in class ambit2.db.search.StoredQuery
 
START_MYSQL - Static variable in class ambit2.base.config.Preferences
 
started - Variable in class ambit2.rest.task.Task
 
StartingMaterialsDataBase - Class in ambit2.reactions.retrosynth
 
StartingMaterialsDataBase() - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
StartingMaterialsDataBase(String[]) - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
StartingMaterialsDataBase(File) - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
StartingMaterialsDataBase(File, int) - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase
 
StartingMaterialsDataBase.AccessType - Enum in ambit2.reactions.retrosynth
 
StartingMaterialsDataBase.StartMaterialData - Class in ambit2.reactions.retrosynth
 
StartingMaterialsDataBase.StartMaterialStandartization - Class in ambit2.reactions.retrosynth
 
startLineNum - Variable in class ambit2.tautomers.Tautomer2DescriptorUtils
 
StartMaterialData() - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialData
 
startMaterialSimilarityWeight - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
StartMaterialStandartization() - Constructor for class ambit2.reactions.retrosynth.StartingMaterialsDataBase.StartMaterialStandartization
 
state - Variable in class ambit2.structure2name.components.AbstractComponent
 
state - Variable in class ambit2.tautomers.rules.EnergyRule
 
stateBonds - Variable in class ambit2.tautomers.Rule
 
stateChanged(IChemObjectChangeEvent) - Method in class ambit2.core.groups.SuppleAtomContainer
 
stateChanged(EventObject) - Method in class ambit2.ui.Panel2D
 
stateEnergy - Variable in class ambit2.tautomers.rules.EnergyRule
 
stateFlags - Variable in class ambit2.tautomers.Rule
 
stateInfo - Variable in class ambit2.tautomers.rules.EnergyRule
 
statement - Variable in class ambit2.db.search.QueryExecutor
 
StatementExecutor<Q extends net.idea.modbcum.i.IStatement,Results> - Class in ambit2.db
 
StatementExecutor() - Constructor for class ambit2.db.StatementExecutor
 
stateQueries - Variable in class ambit2.tautomers.Rule
 
Statistics - Class in ambit2.groupcontribution.utils.math
 
Statistics() - Constructor for class ambit2.groupcontribution.utils.math.Statistics
 
stats - Variable in class ambit2.dbui.QueryFieldEditor
 
stats - Variable in class ambit2.dbui.QueryFieldNumericEditor
 
stats - Variable in class ambit2.model.AbstractModel
 
stats - Variable in class ambit2.similarity.stats.AbstractModelStatistics
 
statsAdapter - Variable in class ambit2.dbui.QueryFieldNumericEditor
 
statsProcessor - Variable in class ambit2.db.results.StoredQueryTableModel
 
statsQuery - Variable in class ambit2.dbui.QueryFieldNumericEditor
 
status - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
status - Variable in class ambit2.db.update.bundle.ReadBundle
 
status - Variable in class ambit2.descriptors.AtomEnvironment
 
status - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
status - Variable in exception ambit2.pubchem.ServerError
 
status - Variable in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
status - Variable in class ambit2.rest.task.CallablePOST
 
status - Variable in class ambit2.rest.task.Task
 
status - Variable in class ambit2.similarity.stats.ModelValuesHistogram
 
STATUS_FINISHED - Static variable in class ambit2.tautomers.TautomerConst
 
STATUS_NONE - Static variable in class ambit2.tautomers.TautomerConst
 
STATUS_SET_STRUCTURE - Static variable in class ambit2.tautomers.TautomerConst
 
STATUS_STARTED - Static variable in class ambit2.tautomers.TautomerConst
 
STATUS_STOPPED - Static variable in class ambit2.tautomers.TautomerConst
 
stco - Variable in class ambit2.smarts.SMIRKSManager
 
std(double[], int) - Static method in class ambit2.domain.stats.Tools
Standard deviation
steps - Variable in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
steps - Variable in class ambit2.reactions.retrosynth.RetroSynthPath
 
stereoCenterToString(IAtomContainer, ITetrahedralChirality) - Static method in class ambit2.smarts.SmartsHelper
 
StereoChange - Class in ambit2.smarts
 
StereoChange() - Constructor for class ambit2.smarts.StereoChange
 
StereoChange.StereoElementType - Enum in ambit2.smarts
 
StereoChemUtils - Class in ambit2.smarts
 
StereoChemUtils() - Constructor for class ambit2.smarts.StereoChemUtils
 
StereoChiralAtTransformation - Class in ambit2.smarts
 
StereoChiralAtTransformation() - Constructor for class ambit2.smarts.StereoChiralAtTransformation
 
StereoDBTransformation - Class in ambit2.smarts
 
StereoDBTransformation() - Constructor for class ambit2.smarts.StereoDBTransformation
 
stereoElement2String(IStereoElement, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
stereoElements - Variable in class ambit2.core.groups.SuppleAtomContainer
Internal list of atom parities.
stereoElements() - Method in class ambit2.core.groups.SuppleAtomContainer
 
StereoFromSmartsAtomExpression - Class in ambit2.smarts
 
StereoFromSmartsAtomExpression() - Constructor for class ambit2.smarts.StereoFromSmartsAtomExpression
 
stereoInfoToString(IAtomContainer) - Static method in class ambit2.smarts.SmartsHelper
 
stereoLigands - Variable in class ambit2.smarts.SmartsAtomExpression
 
stereoMatch(IAtom, int) - Method in class ambit2.smarts.SmartsAtomExpression
 
stereoRemovedTokens - Variable in class ambit2.smarts.SmartsAtomExpression
 
stereoRemovedToString() - Method in class ambit2.smarts.SmartsAtomExpression
 
stereoTokenIndices - Variable in class ambit2.smarts.SmartsAtomExpression
 
StereoTransformation - Class in ambit2.smarts.smirks
 
StereoTransformation() - Constructor for class ambit2.smarts.smirks.StereoTransformation
 
stochasticAnalysis() - Method in class ambit2.smarts.StructureSetAnalyzer
 
stop() - Method in class ambit2.rest.TaskApplication
 
STOP_AT_UNKNOWNATOMTYPES - Static variable in class ambit2.base.config.Preferences
 
storage - Variable in class ambit2.base.data.study.Params
 
storage - Variable in class ambit2.rest.reporters.TaskRDFReporter
 
storage - Variable in class ambit2.rest.reporters.TaskURIReporter
 
storage - Variable in class ambit2.rest.task.FilteredTasksIterator
 
storageMode - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
storeData(Object) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
storedQuery - Variable in class ambit2.db.search.QueryInfo
 
StoredQuery - Class in ambit2.db.search
StoredQuery (table queries)
StoredQuery() - Constructor for class ambit2.db.search.StoredQuery
 
StoredQuery(Integer) - Constructor for class ambit2.db.search.StoredQuery
 
StoredQueryTableModel - Class in ambit2.db.results
 
StoredQueryTableModel() - Constructor for class ambit2.db.results.StoredQueryTableModel
 
StoredQueryTableModel(boolean) - Constructor for class ambit2.db.results.StoredQueryTableModel
 
StoredQueryTableModel.FIELDS - Enum in ambit2.db.results
 
storedResults - Variable in class ambit2.db.results.StoredQueryTableModel
 
storeRecordNum(String) - Method in class ambit2.export.isa.base.ExternalDataFileManager
 
strategy - Variable in class ambit2.reactions.reactor.Reactor
 
strategy - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
strBuffer - Variable in class ambit2.export.isa.base.ExternalDataFileManager
 
StreamConvertor<T,Q,R extends net.idea.modbcum.i.reporter.Reporter<Q,OutputStream>> - Class in ambit2.rest
 
StreamConvertor(R, MediaType) - Constructor for class ambit2.rest.StreamConvertor
 
StreamConvertor(R, MediaType, String) - Constructor for class ambit2.rest.StreamConvertor
 
StringArrayHeader<CATEGORIES> - Class in ambit2.core.io
 
StringArrayHeader(String, int) - Constructor for class ambit2.core.io.StringArrayHeader
 
StringArrayHeader(String, int, String) - Constructor for class ambit2.core.io.StringArrayHeader
 
StringArrayResult - Class in ambit2.core.data
Array of srings implementing IDescriptorResult.
StringArrayResult() - Constructor for class ambit2.core.data.StringArrayResult
 
StringArrayResult(String[]) - Constructor for class ambit2.core.data.StringArrayResult
 
StringBean - Class in ambit2.base.data
 
StringBean(String) - Constructor for class ambit2.base.data.StringBean
 
StringBeanEditor - Class in ambit2.ui.editors
 
StringBeanEditor() - Constructor for class ambit2.ui.editors.StringBeanEditor
 
StringBeanEditor(StringBean, String) - Constructor for class ambit2.ui.editors.StringBeanEditor
 
StringDescriptorResultType - Class in ambit2.core.data
type left for compatibility
StringDescriptorResultType() - Constructor for class ambit2.core.data.StringDescriptorResultType
 
StringDescriptorResultType(String) - Constructor for class ambit2.core.data.StringDescriptorResultType
 
stringify(T) - Method in class ambit2.db.search.AbstractQuery
 
stringify(SubstanceRecord) - Method in class ambit2.db.substance.ReadSubstance
 
stringify(String[]) - Method in class ambit2.db.substance.ReadSubstances
 
stringParam - Variable in class ambit2.sln.SLNExpressionToken
 
StringQueryFacet - Class in ambit2.db.facets.datasets
 
StringQueryFacet() - Constructor for class ambit2.db.facets.datasets.StringQueryFacet
 
stringToBitSet(String) - Method in class ambit2.smarts.Screening
 
StringValuesHistogram - Class in ambit2.similarity.stats
 
StringValuesHistogram(String) - Constructor for class ambit2.similarity.stats.StringValuesHistogram
 
strKeysToString(BitSet) - Method in class ambit2.smarts.Screening
 
strType - Variable in class ambit2.sln.io.SLN2SubstanceConfig.ConversionFlags
 
strType - Variable in class ambit2.sln.io.SLN2SubstanceConfig.JsonFlags
 
struc_typeProperty - Static variable in class ambit2.db.update.structure.CreateStructure
 
strucQuery - Variable in class ambit2.db.DbReaderStructure
 
strucQuery - Variable in class ambit2.db.reporters.AbstractImageReporter
 
struct - Variable in class ambit2.tautomers.TautomerIncrementStep
 
StructInfo - Class in ambit2.smarts
 
StructInfo() - Constructor for class ambit2.smarts.StructInfo
 
StructuralKey - Static variable in class ambit2.core.config.AmbitCONSTANTS
 
StructuralKey_STATUS - Static variable in class ambit2.core.config.AmbitCONSTANTS
 
StructuralKey_TIME - Static variable in class ambit2.core.config.AmbitCONSTANTS
 
structure - Variable in class ambit2.chebi.ChEBIClient
 
structure - Variable in class ambit2.db.facets.datasets.DatasetPrefixFacet
 
structure - Variable in class ambit2.db.processors.ValueWriter
 
structure - Variable in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
structure - Variable in class ambit2.descriptors.processors.DescriptorValue2Property
 
Structure2DBuilder - Class in ambit2.core.processors
 
Structure2DBuilder() - Constructor for class ambit2.core.processors.Structure2DBuilder
 
Structure2DProcessor - Class in ambit2.rest.model.predictor
 
Structure2DProcessor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.Structure2DProcessor
 
structure2substance(IStructureRecord) - Static method in class ambit2.db.update.bundle.substance.AddCompoundAsSubstanceToBundle
 
STRUCTURE_RELATION - Enum in ambit2.base.relation
 
structure_search_options - Static variable in class ambit2.db.search.QueryInfo
 
StructureDiagramEditor - Class in ambit2.jchempaint.editor
 
StructureDiagramEditor() - Constructor for class ambit2.jchempaint.editor.StructureDiagramEditor
 
StructureEditorProcessor - Class in ambit2.rendering
 
StructureEditorProcessor(String) - Constructor for class ambit2.rendering.StructureEditorProcessor
 
StructureEditorProcessor._commands - Enum in ambit2.rendering
 
StructureFromIUPACName - Class in ambit2.structure2name
 
StructureFromIUPACName() - Constructor for class ambit2.structure2name.StructureFromIUPACName
 
StructureGenerator - Class in ambit2.reactions.generator
Focused libraries and Diverse libraries Filters: -properties -toxicity Scores: -properties
StructureGenerator() - Constructor for class ambit2.reactions.generator.StructureGenerator
 
structureKeys - Variable in class ambit2.smarts.ScreeningData
 
StructureKeysBitSetGenerator - Class in ambit2.smarts.processors
Generates screening fingerprints / structural keys for smarts queries
StructureKeysBitSetGenerator() - Constructor for class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
StructureKeysBitSetGenerator(List<String>) - Constructor for class ambit2.smarts.processors.StructureKeysBitSetGenerator
 
StructureListReporter - Class in ambit2.db.reporters
 
StructureListReporter(Profile, Template) - Constructor for class ambit2.db.reporters.StructureListReporter
 
StructureListReporter(List<IStructureRecord>, Profile, Template) - Constructor for class ambit2.db.reporters.StructureListReporter
 
StructureNormalizer - Class in ambit2.core.processors
 
StructureNormalizer() - Constructor for class ambit2.core.processors.StructureNormalizer
 
StructureProcessor - Class in ambit2.rest.model.predictor
 
StructureProcessor(Reference, ModelQueryResults, ModelURIReporter, PropertyURIReporter, String[]) - Constructor for class ambit2.rest.model.predictor.StructureProcessor
 
StructureRecord - Class in ambit2.base.data
 
StructureRecord() - Constructor for class ambit2.base.data.StructureRecord
 
StructureRecord(int, int, String, String) - Constructor for class ambit2.base.data.StructureRecord
 
structureRecord - Variable in class ambit2.core.io.RawIteratingCSVReader
 
StructureRecordReporter - Class in ambit2.db.reporters
 
StructureRecordReporter(Profile, Template) - Constructor for class ambit2.db.reporters.StructureRecordReporter
 
StructureRecordReporter(IStructureRecord, Profile, Template) - Constructor for class ambit2.db.reporters.StructureRecordReporter
 
StructureRecordsAppender - Class in ambit2.base.processors
 
StructureRecordsAppender() - Constructor for class ambit2.base.processors.StructureRecordsAppender
 
StructureRecordsTableModel - Class in ambit2.ui.table
 
StructureRecordsTableModel() - Constructor for class ambit2.ui.table.StructureRecordsTableModel
 
structureRecordToSLNContainer(IStructureRecord) - Method in class ambit2.sln.io.SLN2Substance
 
StructureRecordValidator - Class in ambit2.base.data.study
 
StructureRecordValidator() - Constructor for class ambit2.base.data.study.StructureRecordValidator
 
StructureRecordValidator(String, boolean, String) - Constructor for class ambit2.base.data.study.StructureRecordValidator
 
StructureRecordXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters.xlsx
 
StructureRecordXLSXReporter(String, boolean, Template, Profile, SubstanceEndpointsBundle[], String, boolean, String) - Constructor for class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
StructureRelation - Class in ambit2.base.relation
 
StructureRelation() - Constructor for class ambit2.base.relation.StructureRelation
 
StructureRelation(IStructureRecord, IStructureRecord, Double) - Constructor for class ambit2.base.relation.StructureRelation
 
StructureRepeatingUnit - Class in ambit2.core.groups
 
StructureRepeatingUnit(String, int) - Constructor for class ambit2.core.groups.StructureRepeatingUnit
 
structureRequired - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
structures - Variable in class ambit2.smarts.StructureSetAnalyzer
 
StructureSetAnalyzer - Class in ambit2.smarts
 
StructureSetAnalyzer(IChemObjectBuilder) - Constructor for class ambit2.smarts.StructureSetAnalyzer
 
StructureSetAnalyzer.CharStructInfo - Class in ambit2.smarts
 
StructureStandardizer - Class in ambit2.tautomers.processor
 
StructureStandardizer() - Constructor for class ambit2.tautomers.processor.StructureStandardizer
 
StructureStandardizer(Logger) - Constructor for class ambit2.tautomers.processor.StructureStandardizer
 
StructureStatisticsProcessor - Class in ambit2.db.processors
 
StructureStatisticsProcessor() - Constructor for class ambit2.db.processors.StructureStatisticsProcessor
 
STRUCTURETYPE - Static variable in class ambit2.core.config.AmbitCONSTANTS
Structure tyoe
StructureTypeProcessor - Class in ambit2.core.processors.structure
 
StructureTypeProcessor() - Constructor for class ambit2.core.processors.structure.StructureTypeProcessor
 
structureWriter - Variable in class ambit2.db.processors.RepositoryWriter
 
strucType - Variable in class ambit2.core.processors.StructureNormalizer
 
studies - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
study - Variable in class ambit2.core.io.json.SubstanceStudyParser
 
study - Variable in class ambit2.core.io.ToXMLReaderSimple
 
Study - Class in ambit2.export.isa.v1_0.objects
Study JSON Schema JSON Schema describing an Study
Study() - Constructor for class ambit2.export.isa.v1_0.objects.Study
 
studyDesignDescriptors - Variable in class ambit2.export.isa.v1_0.objects.Study
 
studyFilePrefix - Static variable in class ambit2.export.isa.base.ISAConst
 
StudyFormatter - Class in ambit2.core.io.study
 
StudyFormatter() - Constructor for class ambit2.core.io.study.StudyFormatter
 
StudyFormatter(String) - Constructor for class ambit2.core.io.study.StudyFormatter
 
studyHeaders - Variable in class ambit2.rest.study.BucketJson2CSVConvertor
 
studyResultType - Variable in class ambit2.base.data.study.ProtocolEffectRecord
 
studyResultType - Variable in class ambit2.base.data.substance.SubstanceProperty
 
style - Variable in class ambit2.core.io.XLSFileWriter
 
style - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
style - Variable in class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter
 
stype - Variable in class ambit2.rest.model.predictor.Structure2DProcessor
 
stype - Variable in class ambit2.rest.model.predictor.StructureProcessor
 
subBlocks - Variable in class ambit2.dragon.DragonDescriptorDictionary
 
subcategory - Variable in class ambit2.base.facet.SubstanceStudyFacet
 
subcategory - Variable in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
SubcategoryBin<T extends Comparable> - Class in ambit2.domain.stats.datastructures
 
SubcategoryBin(T, Comparable) - Constructor for class ambit2.domain.stats.datastructures.SubcategoryBin
 
subElementIndex - Variable in class ambit2.export.isa.base.ISALocation
 
subElementName - Variable in class ambit2.export.isa.base.ISALocation
 
sublevel - Variable in class ambit2.descriptors.AtomEnvironment
 
subList(int, int) - Method in class ambit2.core.groups.FilteredList
 
submissionDate - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
submissionDate - Variable in class ambit2.export.isa.v1_0.objects.Study
 
subsetWithoutPredictedValues(OTDataset) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
 
subsetWithoutPredictedValues(OTDataset) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
substance - Variable in class ambit2.core.io.json.SubstanceStudyParser
 
substanceAttributes - Variable in class ambit2.sln.SLNSubstance
 
SubstanceBundleStAXReporter - Class in ambit2.rest.substance
 
SubstanceBundleStAXReporter(Request) - Constructor for class ambit2.rest.substance.SubstanceBundleStAXReporter
 
SubstanceByCategoryFacet - Class in ambit2.db.substance.study.facet
 
SubstanceByCategoryFacet(String) - Constructor for class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
substanceCompositionToSln(List<CompositionRelation>) - Method in class ambit2.sln.io.SLN2Substance
 
SubstanceDataAvailabilityFacet - Class in ambit2.db.substance.study.facet
 
SubstanceDataAvailabilityFacet(String) - Constructor for class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
SubstanceEndpointsBundle - Class in ambit2.base.data.substance
 
SubstanceEndpointsBundle(int) - Constructor for class ambit2.base.data.substance.SubstanceEndpointsBundle
 
SubstanceEndpointsBundle() - Constructor for class ambit2.base.data.substance.SubstanceEndpointsBundle
 
SubstanceEndpointsBundle(String) - Constructor for class ambit2.base.data.substance.SubstanceEndpointsBundle
 
SubstanceEndpointsBundle(String, ILiteratureEntry) - Constructor for class ambit2.base.data.substance.SubstanceEndpointsBundle
 
substanceIndex - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
SubstanceName - Class in ambit2.base.data.substance
 
SubstanceName() - Constructor for class ambit2.base.data.substance.SubstanceName
 
SubstanceOwner - Class in ambit2.base.data.substance
 
SubstanceOwner() - Constructor for class ambit2.base.data.substance.SubstanceOwner
 
SubstanceProperty - Class in ambit2.base.data.substance
 
SubstanceProperty(String, String, String, String) - Constructor for class ambit2.base.data.substance.SubstanceProperty
 
SubstanceProperty(String, String, String, String, ILiteratureEntry) - Constructor for class ambit2.base.data.substance.SubstanceProperty
 
SubstancePropertyCategory - Class in ambit2.base.data.substance
 
SubstancePropertyCategory(String, String, String, String) - Constructor for class ambit2.base.data.substance.SubstancePropertyCategory
 
SubstancePropertyCategory(String, String, String, String, ILiteratureEntry) - Constructor for class ambit2.base.data.substance.SubstancePropertyCategory
 
SubstancePublicName - Class in ambit2.base.data.substance
 
SubstancePublicName() - Constructor for class ambit2.base.data.substance.SubstancePublicName
 
SubstanceRDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> - Class in ambit2.rest.substance
 
SubstanceRDFReporter(Request, MediaType) - Constructor for class ambit2.rest.substance.SubstanceRDFReporter
 
SubstanceRecord - Class in ambit2.base.data
Same as the parent class, but with related structures
SubstanceRecord() - Constructor for class ambit2.base.data.SubstanceRecord
 
SubstanceRecord(String) - Constructor for class ambit2.base.data.SubstanceRecord
 
SubstanceRecord(int) - Constructor for class ambit2.base.data.SubstanceRecord
 
SubstanceRecord.jsonSubstance - Enum in ambit2.base.data
 
SubstanceRecordAnnotationProcessor - Class in ambit2.base.ro
 
SubstanceRecordAnnotationProcessor(File, boolean) - Constructor for class ambit2.base.ro.SubstanceRecordAnnotationProcessor
 
SubstanceRecordStaxWriter - Class in ambit2.rest.substance
RDF output for substances and studies designed after BAO
SubstanceRecordStaxWriter(QueryURIReporter<SubstanceRecord, IQueryRetrieval<SubstanceRecord>>) - Constructor for class ambit2.rest.substance.SubstanceRecordStaxWriter
 
SubstanceRecordXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> - Class in ambit2.db.reporters.xlsx
 
SubstanceRecordXLSXReporter(String, boolean, SubstanceEndpointsBundle[], String) - Constructor for class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
SubstanceRecordXLSXReporter(String, boolean, Template, Profile, SubstanceEndpointsBundle[], String) - Constructor for class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
SubstanceRoleByBundle - Class in ambit2.db.facets.bundle
 
SubstanceRoleByBundle(String) - Constructor for class ambit2.db.facets.bundle.SubstanceRoleByBundle
 
substancesCount - Variable in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
SubstanceStudyDetailsProcessor - Class in ambit2.db.substance.study
 
SubstanceStudyDetailsProcessor(IQueryRetrieval<List<ProtocolApplication>>) - Constructor for class ambit2.db.substance.study.SubstanceStudyDetailsProcessor
 
SubstanceStudyDetailsProcessor() - Constructor for class ambit2.db.substance.study.SubstanceStudyDetailsProcessor
 
SubstanceStudyFacet - Class in ambit2.base.facet
 
SubstanceStudyFacet(String) - Constructor for class ambit2.base.facet.SubstanceStudyFacet
 
SubstanceStudyFacetQuery - Class in ambit2.db.substance.study.facet
 
SubstanceStudyFacetQuery(String) - Constructor for class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
SubstanceStudyFlatQuery - Class in ambit2.db.substance.study
 
SubstanceStudyFlatQuery(SubstanceRecord) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(Protocol) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(Protocol, String[]) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(SubstanceStudyFlatQuery._QUERY_TYPE, Protocol, String[]) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(Protocol, int[]) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(ProtocolApplication) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(ProtocolApplication, SubstanceStudyFlatQuery._QUERY_TYPE) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery() - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(SubstanceStudyFlatQuery._QUERY_TYPE, String...) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(SubstanceStudyFlatQuery._QUERY_TYPE) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(String, String) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery(String, ObjectNode) - Constructor for class ambit2.db.substance.study.SubstanceStudyFlatQuery
 
SubstanceStudyFlatQuery._QUERY_TYPE - Enum in ambit2.db.substance.study
 
SubstanceStudyParser - Class in ambit2.core.io.json
 
SubstanceStudyParser(InputStreamReader) - Constructor for class ambit2.core.io.json.SubstanceStudyParser
 
substancetype - Variable in class ambit2.base.data.SubstanceRecord
 
SUBSTANCETYPE - Static variable in class ambit2.core.config.AmbitCONSTANTS
Substance type
substanceType - Static variable in class ambit2.core.data.MoleculeTools
 
SubstanceURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> - Class in ambit2.rest.substance
 
SubstanceURIReporter(Request) - Constructor for class ambit2.rest.substance.SubstanceURIReporter
 
SubstanceURIReporter(Reference) - Constructor for class ambit2.rest.substance.SubstanceURIReporter
 
substanceUUID - Variable in class ambit2.base.data.study.ProtocolApplication
 
SubstanceUUID - Class in ambit2.base.data.substance
 
SubstanceUUID() - Constructor for class ambit2.base.data.substance.SubstanceUUID
 
substanceUUID - Variable in class ambit2.db.substance.study.UpdateEffectRecords
 
Substituent - Class in ambit2.groupcontribution.nmr
 
Substituent() - Constructor for class ambit2.groupcontribution.nmr.Substituent
 
substituent - Variable in class ambit2.groupcontribution.nmr.SubstituentInstance
 
SubstituentInstance - Class in ambit2.groupcontribution.nmr
 
SubstituentInstance() - Constructor for class ambit2.groupcontribution.nmr.SubstituentInstance
 
substituentInstances - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironmentInstance
 
substituentPosAtomIndices - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
substituents - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
substituentSufix - Variable in class ambit2.structure2name.rules.IUPACRuleDataBase
 
substractVector(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
substractVectorEqual(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
SubstructureFingerprinterWrapper - Class in ambit2.descriptors.fingerprints
Wrapper for SubstructureFingerprinter , implementing IMolecularDescriptor
SubstructureFingerprinterWrapper() - Constructor for class ambit2.descriptors.fingerprints.SubstructureFingerprinterWrapper
 
substTypeInorganic - Static variable in class ambit2.core.data.MoleculeTools
 
substTypeMetallic - Static variable in class ambit2.core.data.MoleculeTools
 
substTypeMixture - Static variable in class ambit2.core.data.MoleculeTools
 
substTypeOrganic - Static variable in class ambit2.core.data.MoleculeTools
 
subtasksStatus - Variable in exception ambit2.rest.exception.TaskException
 
subType - Variable in class ambit2.db.reporters.AbstractImageReporter
 
successNodes - Variable in class ambit2.reactions.reactor.ReactorResult
 
SulfGroup - Class in ambit2.tautomers.zwitterion
 
SulfGroup() - Constructor for class ambit2.tautomers.zwitterion.SulfGroup
 
SulfinicGroup - Class in ambit2.tautomers.zwitterion
 
SulfinicGroup() - Constructor for class ambit2.tautomers.zwitterion.SulfinicGroup
 
SulfonicGroup - Class in ambit2.tautomers.zwitterion
 
SulfonicGroup() - Constructor for class ambit2.tautomers.zwitterion.SulfonicGroup
 
summary - Variable in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
sumOfColumnElements(int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
sumOfElements() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
sumOfRowElements(int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
SuperAtom - Class in ambit2.core.groups
 
SuperAtom(String, int) - Constructor for class ambit2.core.groups.SuperAtom
 
superModel - Variable in class ambit2.rest.task.CallablePOST
 
SuppleAtomContainer - Class in ambit2.core.groups
 
SuppleAtomContainer() - Constructor for class ambit2.core.groups.SuppleAtomContainer
 
support - Variable in class ambit2.pubchem.PUGProcessor
 
support - Variable in class ambit2.rest.task.CallableDatasetCreator
 
supportDoubleBondAromaticityNotSpecified(boolean) - Method in class ambit2.smarts.SmartsManager
 
supported_extensions - Static variable in class ambit2.base.io.MolFileFilter
 
supported_exts_description - Static variable in class ambit2.base.io.MolFileFilter
 
supportedExtensions - Variable in class ambit2.core.io.FileState
 
supportMOEExtension(boolean) - Method in class ambit2.smarts.SmartsManager
 
supportOpenBabelExtension(boolean) - Method in class ambit2.smarts.SmartsManager
 
supportOpenEyeExtension(boolean) - Method in class ambit2.smarts.SmartsManager
 
supportsDistribution(Classifier) - Method in class ambit2.rest.task.weka.FilteredWekaModelBuilder
TODO - verify via reflection, not fixed check
supportsDistribution(Classifier) - Method in class ambit2.rest.task.weka.WekaModelBuilder
TODO - verify via reflection, not fixed check
supportsInput() - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
supportsOutput() - Method in enum ambit2.core.io.FileState._FILE_TYPE
 
supportsPaging() - Method in class ambit2.db.search.AbstractQuery
 
supportsPaging() - Method in class ambit2.db.search.property.FilteredCount
 
supportsPaging() - Method in class ambit2.db.search.QueryCombined
 
supportsPaging() - Method in class ambit2.db.search.StoredQuery
 
supportsPaging() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
supportsPaging() - Method in class ambit2.db.search.structure.QuerySMARTS
 
supportsPaging() - Method in class ambit2.db.substance.study.ReadSubstanceStudyFlat
 
supportsPredictedVarURI - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
swapRows(int, int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
switchPos(int, int, int[]) - Static method in class ambit2.smarts.ChiralPermutations
 
switchToCombinatorial() - Method in class ambit2.tautomers.RuleSelector
 
Sxx(Vector, double[]) - Static method in class ambit2.domain.stats.Tools
 
SymbolQueryAtomAromaticityNotSpecified - Class in ambit2.smarts
 
SymbolQueryAtomAromaticityNotSpecified(IChemObjectBuilder) - Constructor for class ambit2.smarts.SymbolQueryAtomAromaticityNotSpecified
 
synchronizeRankingRules() - Method in class ambit2.tautomers.KnowledgeBase
 
synonyms - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
synonyms - Variable in class ambit2.core.io.I5ReaderSimple
 
synthesis - Variable in class ambit2.export.isa.v1_0.objects.Constituent
 
synthesis - Variable in class ambit2.export.isa.v1_0.objects.McmMaterial
 
SyntheticAccessibilityCli - Class in ambit2.reactions.cli
 
SyntheticAccessibilityCli() - Constructor for class ambit2.reactions.cli.SyntheticAccessibilityCli
 
SyntheticAccessibilityManager - Class in ambit2.reactions.syntheticaccessibility
 
SyntheticAccessibilityManager() - Constructor for class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager
 
SyntheticAccessibilityManager.DescrData - Class in ambit2.reactions.syntheticaccessibility
 
SyntheticAccessibilityStrategy - Class in ambit2.reactions.syntheticaccessibility
 
SyntheticAccessibilityStrategy() - Constructor for class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityStrategy
 
SyntheticStrategy - Class in ambit2.reactions.retrosynth
 
SyntheticStrategy() - Constructor for class ambit2.reactions.retrosynth.SyntheticStrategy
 
SyntheticStrategy(File) - Constructor for class ambit2.reactions.retrosynth.SyntheticStrategy
 
SyntheticStrategy.ReactionCenterComplexityMethod - Enum in ambit2.reactions.retrosynth
 
SyntheticStrategyDescriptorSolver - Class in ambit2.reactions.rules
 
SyntheticStrategyDescriptorSolver() - Constructor for class ambit2.reactions.rules.SyntheticStrategyDescriptorSolver
 
System - Static variable in class ambit2.base.ro.I5CONSTANTS
 
systemDesignator - Variable in class ambit2.base.data.substance.ExternalIdentifier
 
systemIdentifier - Variable in class ambit2.base.data.substance.ExternalIdentifier
 
Syy(double[], double) - Static method in class ambit2.domain.stats.Tools
 
SzegedMatrixE(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
SzegedMatrixP(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
SzegedMatrixU(IAtomContainer) - Static method in class ambit2.descriptors.utils.GraphMatrices
 

T

t_example - Static variable in class ambit2.descriptors.FunctionalGroup
 
t_family - Static variable in class ambit2.dbui.QuerySmartsEditor
 
t_family - Static variable in class ambit2.descriptors.FunctionalGroup
 
t_group - Static variable in class ambit2.dbui.QuerySmartsEditor
 
t_group - Static variable in class ambit2.descriptors.FunctionalGroup
 
t_hint - Static variable in class ambit2.dbui.QuerySmartsEditor
 
t_hint - Static variable in class ambit2.descriptors.FunctionalGroup
 
t_name - Static variable in class ambit2.dbui.QuerySmartsEditor
 
t_name - Static variable in class ambit2.descriptors.FunctionalGroup
 
t_smarts - Static variable in class ambit2.dbui.QuerySmartsEditor
 
t_smarts - Static variable in class ambit2.descriptors.FunctionalGroup
 
TabFileUtils - Class in ambit2.export.isa.tab
 
TabFileUtils() - Constructor for class ambit2.export.isa.tab.TabFileUtils
 
table - Variable in class ambit2.core.io.PDFWriter
 
table - Variable in class ambit2.db.reporters.PDFReporter
 
table - Variable in class ambit2.dbui.QueryFunctionalGroupsEditor
 
table - Variable in class ambit2.mopac.AbstractMopacShell
 
table - Variable in class ambit2.ui.HeaderComboBoxModel
 
tableChanged(TableModelEvent) - Method in class ambit2.ui.table.BrowsableTableModel
 
tables - Variable in class ambit2.ui.editors.SelectFieldsPanel
 
tablesExists(Connection, String) - Static method in class ambit2.db.processors.DbCreateDatabase
 
tableStyle - Variable in class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter
 
tag - Variable in class ambit2.base.facet.BundleRoleFacet
 
tag - Variable in class ambit2.db.processors.ProcessorCreateProfileQuery
 
tag - Variable in class ambit2.domain.stats.datastructures.SubcategoryBin
 
tag_ENTREZ_ErrorList - Static variable in class ambit2.pubchem.EntrezESearchParser
 
tag_ENTREZ_esearch - Static variable in class ambit2.pubchem.EntrezESearchParser
 
tag_ENTREZ_Id - Static variable in class ambit2.pubchem.EntrezESearchParser
 
tag_ENTREZ_IdList - Static variable in class ambit2.pubchem.EntrezESearchParser
 
tag_ENTREZ_PhraseNotFound - Static variable in class ambit2.pubchem.EntrezESearchParser
 
tag_PCT_Data - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Data_input - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Data_output - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_download_3D - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download_compression - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download_format - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download_uids - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download_URL - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Download_URL_url - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_ID_List - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_ID_List_db - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_ID_List_uids - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_ID_List_uids_E - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_InputData - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_InputData_download - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_OutputData - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_OutputData_output - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_OutputData_output_download_url - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_OutputData_output_waiting - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_OutputData_status - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_QueryUids - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_QueryUids_ids - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Waiting - Static variable in class ambit2.pubchem.PUGProcessor
 
tag_PCT_Waiting_reqid - Static variable in class ambit2.pubchem.PUGProcessor
 
tagCount - Variable in class ambit2.core.io.ToXMLReaderSimple
 
tags - Variable in class ambit2.core.io.fp.MultiFingerprintsWriter
 
tags - Variable in class ambit2.core.io.ToXMLReaderSimple
 
tags - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
tags_to_keep - Variable in class ambit2.core.io.fp.MultiFingerprintsWriter
 
Tanimoto - Static variable in class ambit2.core.config.AmbitCONSTANTS
Ttanimoto coefficient
tanimoto(Histogram) - Method in class ambit2.domain.stats.datastructures.Histogram
 
tanimoto(BitSet, BitSet) - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
Returns (1-Tanimoto distance) where Tanimoto = ( bc / (b1.cardinality() + b2.cardinality() - bc) bc = bs1.and(bs2).cardinality (the number of common bits set to 1) (1- Tanimoto) is used to make it compatible with distances approach (the larger the distance value, the more dissimilar the compounds
tanimoto(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingerprintsTanimoto
 
tanimoto(Histogram) - Method in class ambit2.similarity.stats.Histogram
 
target - Variable in class ambit2.reactions.GenericReactionInstance
 
target - Variable in class ambit2.reactions.rules.scores.MolecularComplexity
 
target - Variable in class ambit2.rest.task.CallableQueryProcessor
 
target - Variable in class ambit2.smarts.EquivalenceTester
 
target - Variable in class ambit2.smarts.IsomorphismTester
 
target - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
targetAt - Variable in class ambit2.smarts.IsomorphismTester
 
targetAt - Variable in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
targetLocalProperty - Variable in class ambit2.groupcontribution.dataset.DataSetObject
 
targetProperty - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
targetSmiles - Variable in class ambit2.reactions.cli.SyntheticAccessibilityCli
 
targetURI - Variable in class ambit2.model.builder.AbstractModelBuilder
 
targetURI - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
task - Variable in class ambit2.rest.task.ExecutableTask
 
task - Variable in class ambit2.rest.task.SingleTaskIterator
 
Task<REFERENCE,USERID> - Class in ambit2.rest.task
 
Task(USERID) - Constructor for class ambit2.rest.task.Task
 
task - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
Task.TaskProperty - Enum in ambit2.rest.task
 
task_id - Variable in class ambit2.rest.task.FilteredTasksIterator
 
TaskApplication<USERID> - Class in ambit2.rest
 
TaskApplication() - Constructor for class ambit2.rest.TaskApplication
 
taskCleanupRate - Variable in class ambit2.rest.task.TaskStorage
 
taskCleanupUnit - Variable in class ambit2.rest.task.TaskStorage
 
TaskException - Exception in ambit2.rest.exception
 
TaskException(Status, String, Throwable) - Constructor for exception ambit2.rest.exception.TaskException
 
TaskJSONReporter<USERID> - Class in ambit2.rest.task
 
TaskJSONReporter(ITaskStorage<USERID>) - Constructor for class ambit2.rest.task.TaskJSONReporter
 
TaskJSONReporter(ITaskStorage<USERID>, Request) - Constructor for class ambit2.rest.task.TaskJSONReporter
 
TaskJSONReporter(ITaskStorage<USERID>, Reference) - Constructor for class ambit2.rest.task.TaskJSONReporter
 
TaskRDFReporter<USERID> - Class in ambit2.rest.reporters
RDF generation for Task
TaskRDFReporter(ITaskStorage<USERID>, Request, MediaType) - Constructor for class ambit2.rest.reporters.TaskRDFReporter
 
TaskResult - Class in ambit2.rest.task
 
TaskResult(String) - Constructor for class ambit2.rest.task.TaskResult
 
TaskResult(String, boolean) - Constructor for class ambit2.rest.task.TaskResult
 
taskResults(OTRemoteTaskPool, OTDatasets) - Method in class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
tasks - Variable in class ambit2.rest.task.TaskStorage
 
tasksCompleted(OTRemoteTaskPool) - Method in class ambit2.rest.legacy.OTProcessingResource
Deprecated.
 
TaskStorage<USERID> - Class in ambit2.rest.task
 
TaskStorage(String, Logger) - Constructor for class ambit2.rest.task.TaskStorage
 
taskStorage - Variable in class ambit2.rest.TaskApplication
 
TaskURIReporter<USERID> - Class in ambit2.rest.reporters
URI of the task
TaskURIReporter(ITaskStorage<USERID>) - Constructor for class ambit2.rest.reporters.TaskURIReporter
 
TaskURIReporter(ITaskStorage<USERID>, Request) - Constructor for class ambit2.rest.reporters.TaskURIReporter
 
TaskURIReporter(ITaskStorage<USERID>, Reference) - Constructor for class ambit2.rest.reporters.TaskURIReporter
 
tautomer1 - Variable in class ambit2.tautomers.TautomerRelation
 
tautomer1Index - Variable in class ambit2.tautomers.TautomerRelation
 
tautomer1RuleStates - Variable in class ambit2.tautomers.TautomerRelation
 
tautomer2 - Variable in class ambit2.tautomers.TautomerRelation
 
Tautomer2DescriptorUtils - Class in ambit2.tautomers
 
Tautomer2DescriptorUtils() - Constructor for class ambit2.tautomers.Tautomer2DescriptorUtils
 
tautomer2Index - Variable in class ambit2.tautomers.TautomerRelation
 
tautomer2RuleStates - Variable in class ambit2.tautomers.TautomerRelation
 
TAUTOMER_RANK - Static variable in class ambit2.tautomers.TautomerConst
 
TautomerAnalysis - Class in ambit2.tautomers.tools
 
TautomerAnalysis() - Constructor for class ambit2.tautomers.tools.TautomerAnalysis
 
TautomerAnalysis.Task - Enum in ambit2.tautomers.tools
 
TautomerConst - Class in ambit2.tautomers
 
TautomerConst() - Constructor for class ambit2.tautomers.TautomerConst
 
TautomerConst.CanonicTautomerMethod - Enum in ambit2.tautomers
 
TautomerConst.GAT - Enum in ambit2.tautomers
 
TautomerConst.RSM - Enum in ambit2.tautomers
 
TautomerDistribution - Class in ambit2.tautomers
 
TautomerDistribution() - Constructor for class ambit2.tautomers.TautomerDistribution
 
tautomerFilter - Variable in class ambit2.tautomers.TautomerManager
 
tautomerFullInfo(int, String) - Method in class ambit2.tautomers.Tautomer2DescriptorUtils
 
TautomerIncrementStep - Class in ambit2.tautomers
 
TautomerIncrementStep() - Constructor for class ambit2.tautomers.TautomerIncrementStep
 
tautomerManager - Variable in class ambit2.tautomers.processor.TautomerProcessor
 
TautomerManager - Class in ambit2.tautomers
 
TautomerManager() - Constructor for class ambit2.tautomers.TautomerManager
 
TautomerPair() - Constructor for class ambit2.tautomers.TautomerUtils.TautomerPair
 
TautomerProcessor - Class in ambit2.tautomers.processor
 
TautomerProcessor(Logger) - Constructor for class ambit2.tautomers.processor.TautomerProcessor
 
TautomerRanking - Class in ambit2.tautomers
 
TautomerRanking() - Constructor for class ambit2.tautomers.TautomerRanking
 
TautomerRanking(double) - Constructor for class ambit2.tautomers.TautomerRanking
 
TautomerRegion - Class in ambit2.tautomers.rules
 
TautomerRegion() - Constructor for class ambit2.tautomers.rules.TautomerRegion
 
tautomerRegion - Variable in class ambit2.tautomers.TautomerManager
 
TautomerRelation - Class in ambit2.base.relation
 
TautomerRelation(IStructureRecord, IStructureRecord) - Constructor for class ambit2.base.relation.TautomerRelation
 
TautomerRelation(IStructureRecord, IStructureRecord, Double) - Constructor for class ambit2.base.relation.TautomerRelation
 
TautomerRelation - Class in ambit2.tautomers
 
TautomerRelation() - Constructor for class ambit2.tautomers.TautomerRelation
 
TautomerRelationGraph - Class in ambit2.tautomers
 
TautomerRelationGraph() - Constructor for class ambit2.tautomers.TautomerRelationGraph
 
TautomerRelationGraph.StructureFormat - Enum in ambit2.tautomers
 
tautomers - Variable in class ambit2.tautomers.processor.StructureStandardizer
 
tautomers - Variable in class ambit2.tautomers.TautomerRelationGraph
 
TautomerStringCode - Class in ambit2.tautomers.ranking
 
TautomerStringCode() - Constructor for class ambit2.tautomers.ranking.TautomerStringCode
 
TautomerUtils - Class in ambit2.tautomers
 
TautomerUtils() - Constructor for class ambit2.tautomers.TautomerUtils
 
TautomerUtils.TautomerPair - Class in ambit2.tautomers
 
technologyPlatform - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
technologyType - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
TechnologyType - Class in ambit2.export.isa.v1_0.objects
 
TechnologyType() - Constructor for class ambit2.export.isa.v1_0.objects.TechnologyType
 
tempFile - Variable in class ambit2.db.reporters.ARFFReporter
 
template - Variable in class ambit2.base.data.PropertyTemplateStats
 
Template - Class in ambit2.base.data
Templates are just a (meaningful) set of properties
Template() - Constructor for class ambit2.base.data.Template
 
Template(String) - Constructor for class ambit2.base.data.Template
 
template - Variable in class ambit2.db.processors.ProcessorOntology
 
template - Variable in class ambit2.db.reporters.AbstractStructureRecordReporter
 
template - Variable in class ambit2.db.reporters.QueryHeaderReporter
 
template - Variable in class ambit2.db.reporters.QueryPacketReporter
 
template - Variable in class ambit2.db.reporters.SDFReporter
 
template - Variable in class ambit2.db.reporters.SmilesReporter
 
template - Variable in class ambit2.db.search.StoredQuery
 
template - Variable in class ambit2.rest.dataset.DatasetRDFWriter
 
template - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
template2Header(Template, boolean) - Method in class ambit2.db.reporters.CSVReporter
 
template2Header(Template, boolean) - Method in class ambit2.db.reporters.QueryHeaderReporter
 
template2Header(Template, boolean) - Method in class ambit2.rest.dataset.DatasetRDFWriter
 
TemplateAddProperty - Class in ambit2.db.update.dictionary
 
TemplateAddProperty(Dictionary, Property) - Constructor for class ambit2.db.update.dictionary.TemplateAddProperty
 
TemplateAddProperty() - Constructor for class ambit2.db.update.dictionary.TemplateAddProperty
 
templateDefWriter - Variable in class ambit2.db.processors.AbstractPropertyWriter
 
TemplateDeleteProperty - Class in ambit2.db.update.dictionary
 
TemplateDeleteProperty(Dictionary, Property) - Constructor for class ambit2.db.update.dictionary.TemplateDeleteProperty
 
TemplateDeleteProperty() - Constructor for class ambit2.db.update.dictionary.TemplateDeleteProperty
 
templateDependent - Variable in class ambit2.db.update.model.CreateModel
 
TemplateEditor - Class in ambit2.ui.editors
 
TemplateEditor() - Constructor for class ambit2.ui.editors.TemplateEditor
 
templateName - Variable in class ambit2.rest.freemarker.FreeMarkerSupport
 
templatePredicted - Variable in class ambit2.db.update.model.CreateModel
 
templatePredictors - Variable in class ambit2.db.update.model.CreateModel
 
templateProperties - Static variable in class ambit2.base.config.AMBITConfigProperties
 
TemplatePropertyPanel - Class in ambit2.dbui.dictionary
 
TemplatePropertyPanel() - Constructor for class ambit2.dbui.dictionary.TemplatePropertyPanel
 
TemplateQuery - Class in ambit2.db.search.property
 
TemplateQuery() - Constructor for class ambit2.db.search.property.TemplateQuery
 
term - Variable in class ambit2.pubchem.EntrezSearchOptions
 
termAccession - Variable in class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
terminal - Variable in class ambit2.descriptors.PKANode
 
terminal1 - Variable in class ambit2.smarts.ExtendedChiralityInfo
 
terminal2 - Variable in class ambit2.smarts.ExtendedChiralityInfo
 
termSource - Variable in class ambit2.export.isa.v1_0.objects.OntologyAnnotation
 
test - Variable in class ambit2.core.io.ToXMLReaderSimple
 
test(T) - Method in class ambit2.db.search.AbstractQuery
 
test(Double) - Method in class ambit2.db.search.structure.QueryDistance
 
test4CAS(String) - Static method in class ambit2.base.data.Property
 
testCombinations() - Method in class ambit2.smarts.SmartsManager
 
TestCondition - Static variable in class ambit2.base.ro.I5CONSTANTS
 
testFor2CharElement() - Method in class ambit2.smarts.SmartsParser
 
testForDefaultAND() - Method in class ambit2.smarts.SmartsParser
 
testInstances - Variable in class ambit2.core.data.model.ModelWrapper
 
testSubQueries() - Method in class ambit2.smarts.SmartsManager
 
testTopLayers() - Method in class ambit2.smarts.SmartsManager
 
tetrahedralChirality2String(TetrahedralChirality, IAtomContainer) - Static method in class ambit2.smarts.StereoChemUtils
 
text - Variable in class ambit2.base.data.AbstractLabel
 
text - Variable in class ambit2.db.search.structure.QueryStructureByID
 
textDelimiter - Variable in class ambit2.core.io.DelimitedFileFormat
 
textValue - Variable in class ambit2.base.data.study.EffectRecord
 
textValue - Variable in class ambit2.base.data.study.ValueAnnotated
 
tf_formula - Variable in class ambit2.dbui.QueryInfoEditor
 
tf_identifier1 - Variable in class ambit2.dbui.QueryInfoEditor
 
tf_identifier2 - Variable in class ambit2.dbui.QueryInfoEditor
 
tf_identifier3 - Variable in class ambit2.dbui.QueryInfoEditor
 
tf_inchi - Variable in class ambit2.dbui.QueryInfoEditor
 
tf_smiles - Variable in class ambit2.dbui.QueryInfoEditor
 
threshold - Variable in class ambit2.db.search.property.QueryPairwiseTanimoto
 
threshold - Variable in class ambit2.db.search.QueryInfo
 
threshold - Variable in class ambit2.db.search.structure.QuerySimilarity
 
threshold - Variable in class ambit2.dbui.QueryInfoEditor
 
threshold - Variable in class ambit2.featureselection.RRelieFFAttributeSelection
 
threshold - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
threshold - Variable in class ambit2.model.numeric.DataCoverage
 
threshold_dactivity - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
threshold_options - Static variable in class ambit2.db.search.QueryInfo
 
threshold_similarity - Variable in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
thumbnail - Variable in class ambit2.db.chart.ChartGenerator
 
time_elapsed - Variable in class ambit2.descriptors.AtomEnvironment
 
TIMEOUT - Static variable in class ambit2.base.config.Preferences
 
timeout - Variable in class ambit2.base.processors.batch.BatchProcessor
 
timeout - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader
 
timeout - Variable in class ambit2.pubchem.HTTPRequest
 
timeout - Variable in class ambit2.pubchem.SearchApplication
 
timesVector(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
timesVectorEqual(Matrix, double[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
title - Variable in class ambit2.base.data.AmbitUser
 
title - Variable in class ambit2.base.data.ClassHolder
 
title - Variable in class ambit2.base.data.LiteratureEntry
 
title - Variable in class ambit2.base.data.SelectionBean
 
title - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
title - Variable in class ambit2.base.io.SimpleErrorHandler
 
title - Static variable in class ambit2.descriptors.PKASmartsDescriptor
 
title - Variable in class ambit2.descriptors.processors.AtomEnvironmentList
 
title - Variable in class ambit2.export.isa.v1_0.objects.Investigation
 
title - Variable in class ambit2.export.isa.v1_0.objects.Publication
 
title - Variable in class ambit2.export.isa.v1_0.objects.Study
 
title - Variable in class ambit2.similarity.stats.ModelValuesHistogram
 
title - Variable in class ambit2.ui.editors.AmbitUserEditor
 
TLProp - Static variable in class ambit2.smarts.TopLayer
 
tman - Variable in class ambit2.tautomers.FilterTautomers
 
tman - Variable in class ambit2.tautomers.ranking.CanonicTautomer
 
tman - Variable in class ambit2.tautomers.tools.TautomerAnalysis
 
tmpFileName - Variable in class ambit2.rest.model.task.CallableModelPredictor
 
tmpValue - Variable in class ambit2.core.io.ECHAPreregistrationListReader
 
tmpValue - Variable in class ambit2.core.io.I5ReaderSimple
 
tmpValue - Variable in class ambit2.core.io.ToXMLReaderSimple
 
tmpWriter - Variable in class ambit2.db.reporters.ARFFReporter
 
to1DGrid(int[], double[], double[], double[], int) - Method in interface ambit2.domain.stats.transforms.densityestimation.DrawableDensity
 
to1DGrid(int[], double[], double[], double[], int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
to1dGrid DrawableDensity interface this is general solution, write more efficient one in the subclass
to1DGridUnfiltered(int[], double[], double[], double[], int) - Method in interface ambit2.domain.stats.transforms.densityestimation.DrawableDensity
 
to1DGridUnfiltered(int[], double[], double[], double[], int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
Deprecated.
to1DGridUnfiltered Density Drawable interface
to2DGrid(int[], double[], double[], double[], int) - Method in interface ambit2.domain.stats.transforms.densityestimation.DrawableDensity
 
to2DGrid(int[], double[], double[], double[], int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
to2DGrid Density Drawable interface
to2DGridUnfiltered(int[], double[], double[], double[], int) - Method in interface ambit2.domain.stats.transforms.densityestimation.DrawableDensity
 
to2DGridUnfiltered(int[], double[], double[], double[], int) - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
to2DGridUnfiltered Density Drawable interface
toArray() - Method in class ambit2.core.groups.FilteredList
 
toArray(T[]) - Method in class ambit2.core.groups.FilteredList
 
toAtom(IAtom) - Method in class ambit2.smarts.SmartsToChemObject
This function tries to convert this object to a classic CDK Atom If it is impossible to determine the atom type null is returned
toBond(IBond) - Method in class ambit2.smarts.SmartsToChemObject
 
toCollection() - Method in class ambit2.db.results.AmbitRows
 
toCollection(int) - Method in class ambit2.db.results.AmbitRows
 
toCollection(String) - Method in class ambit2.db.results.AmbitRows
 
toHumanReadable() - Method in interface ambit2.base.data.study.IValue
 
toHumanReadable() - Method in class ambit2.base.data.study.MultiValue
 
toHumanReadable() - Method in class ambit2.base.data.study.Value
 
toHumanReadable() - Method in class ambit2.base.data.study.ValueAnnotated
 
toHumanReadable() - Method in enum ambit2.base.relation.STRUCTURE_RELATION
 
toIndex - Variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ClientAnchorDetail
 
toJSON() - Method in enum ambit2.base.data.Bookmark._fields
 
toJSON() - Method in class ambit2.base.data.Bookmark
 
toJSON() - Method in class ambit2.base.data.PropertyAnnotation
 
toJSON(StringBuilder) - Method in class ambit2.base.data.PropertyAnnotation
 
toJSON() - Method in class ambit2.base.data.PropertyAnnotations
 
toJSON() - Method in enum ambit2.base.data.study.EffectRecord._fields
 
toJSON(StringBuilder) - Method in class ambit2.base.data.study.Value
 
toJSON(StringBuilder) - Method in class ambit2.base.data.study.ValueAnnotated
 
toJSON(String) - Method in class ambit2.base.data.SubstanceRecord
 
toJSON(String, String) - Method in class ambit2.base.facet.AbstractFacet
 
toJSON(String, String) - Method in class ambit2.base.facet.BundleRoleFacet
 
toJSON(String, String) - Method in class ambit2.base.facet.SubstanceStudyFacet
 
toJSON(String, String) - Method in class ambit2.base.relation.composition.CompositionRelation
 
toJSON() - Method in class ambit2.base.relation.composition.Proportion
 
toJSON(String, String) - Method in class ambit2.db.facets.bundle.BundleSummaryFacet
 
toJSON(String, String) - Method in class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet
 
toJSON(String, String) - Method in class ambit2.db.substance.study.facet.ResultsCountFacet
 
toJSON(String, String) - Method in class ambit2.db.substance.study.facet.SubstanceByCategoryFacet
 
toJSON(String, String) - Method in class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet
 
toJSON() - Method in class ambit2.rest.task.Task
 
toJSONField() - Method in enum ambit2.base.data.study.ValueAnnotated._fields
 
toJsonField(double[]) - Static method in class ambit2.rules.json.JSONParsingUtils
 
toJSONKeyWord(String) - Method in class ambit2.sln.io.SLN2SubstanceConfig
 
toJsonString() - Method in class ambit2.groupcontribution.GroupContributionModel
 
toJSONString(String) - Method in class ambit2.reactions.reactor.ReactorStrategy
 
toJSONString(EnergyRule) - Static method in class ambit2.tautomers.rules.JsonRuleParser
 
toJSONString(EnergyRule, String) - Static method in class ambit2.tautomers.rules.JsonRuleParser
 
toJSONString(EnergyCorrection, String) - Static method in class ambit2.tautomers.rules.JsonRuleParser
 
tokens - Variable in class ambit2.rules.conditions.DescriptorExpression
 
tokens - Variable in class ambit2.sln.SLNAtomExpression
 
tokens - Variable in class ambit2.sln.SLNBondExpression
 
tokens - Variable in class ambit2.smarts.SmartsAtomExpression
 
tokens - Variable in class ambit2.smarts.SmartsBondExpression
 
Tools - Class in ambit2.domain.stats
Title: Various statistical routines
Tools() - Constructor for class ambit2.domain.stats.Tools
 
tools - Variable in class ambit2.ui.Panel2D
 
topCategory - Variable in class ambit2.base.data.study.Protocol
 
topcategory - Variable in class ambit2.base.data.substance.SubstanceProperty
 
topcategory - Variable in class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery
 
TopLayer - Class in ambit2.smarts
 
TopLayer() - Constructor for class ambit2.smarts.TopLayer
 
topObject - Variable in class ambit2.rest.rdf.RDFObjectIterator
 
TopologicalLayers - Class in ambit2.descriptors.utils
 
TopologicalLayers() - Constructor for class ambit2.descriptors.utils.TopologicalLayers
 
TopologicalUtilities - Class in ambit2.descriptors.utils
 
TopologicalUtilities() - Constructor for class ambit2.descriptors.utils.TopologicalUtilities
 
toRepresentation(Map<String, Object>, String, MediaType) - Method in class ambit2.rest.freemarker.FreeMarkerResource
 
toRepresentation(Map<String, Object>, String, MediaType) - Method in class ambit2.rest.freemarker.FreeMarkerStatusService
 
toSLN(SLNContainer) - Method in class ambit2.sln.SLNHelper
 
toSmarts(IQueryAtomContainer) - Method in class ambit2.smarts.SmartsHelper
 
toStatus(boolean) - Method in interface ambit2.model.IModelStatistics
 
toStatus(boolean) - Method in class ambit2.similarity.stats.ClassificationModelStatistics
 
toStatus(boolean) - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
toStatus(boolean) - Method in class ambit2.similarity.stats.PredictionModelStatistics
 
toString() - Method in class ambit2.balloon.ShellBalloon
 
toString() - Method in class ambit2.base.data.AbstractLabel
 
toString() - Method in class ambit2.base.data.AmbitUser
 
toString() - Method in class ambit2.base.data.Bookmark
 
toString() - Method in class ambit2.base.data.ClassHolder
 
toString() - Method in class ambit2.base.data.Dictionary
 
toString() - Method in enum ambit2.base.data.ILiteratureEntry._type
 
toString() - Method in enum ambit2.base.data.ISourceDataset.license
 
toString() - Method in class ambit2.base.data.LiteratureEntry
 
toString() - Method in class ambit2.base.data.Property
 
toString() - Method in class ambit2.base.data.PropertyAnnotation
 
toString() - Method in class ambit2.base.data.PropertyStats
 
toString() - Method in class ambit2.base.data.PropertyTemplateStats
 
toString() - Method in class ambit2.base.data.Range
 
toString() - Method in class ambit2.base.data.SelectionBean
 
toString() - Method in class ambit2.base.data.SourceDataset
 
toString() - Method in class ambit2.base.data.StringBean
 
toString() - Method in class ambit2.base.data.StructureRecord
 
toString() - Method in class ambit2.base.data.study.EffectRecord
 
toString() - Method in class ambit2.base.data.study.Params
 
toString() - Method in enum ambit2.base.data.study.Protocol._categories
 
toString() - Method in class ambit2.base.data.study.Protocol
 
toString() - Method in class ambit2.base.data.study.ProtocolApplication
 
toString() - Method in class ambit2.base.data.study.Value
 
toString() - Method in class ambit2.base.data.substance.ExternalIdentifier
 
toString() - Method in enum ambit2.base.data.substance.ParticleTypes
 
toString() - Method in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
toString() - Method in class ambit2.base.data.SubstanceRecord
 
toString() - Method in class ambit2.base.data.Template
 
toString() - Method in exception ambit2.base.exceptions.HttpException
 
toString() - Method in class ambit2.base.external.Command
 
toString() - Method in class ambit2.base.facet.AbstractFacet
 
toString() - Method in class ambit2.core.data.AbstractDescriptorResultType
 
toString() - Method in class ambit2.core.data.ArrayResult
 
toString() - Method in class ambit2.core.data.HashDescriptorResult
 
toString() - Method in class ambit2.core.data.HashIntDescriptorResult
 
toString() - Method in class ambit2.core.data.model.Algorithm
 
toString() - Method in enum ambit2.core.data.model.AlgorithmType
 
toString() - Method in class ambit2.core.data.model.ModelQueryResults
 
toString() - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
toString() - Method in class ambit2.core.filter.MoleculeFilter
 
toString() - Method in class ambit2.core.filter.RecordIntervalCondition
 
toString() - Method in class ambit2.core.io.DelimitedFileReader
 
toString() - Method in class ambit2.core.io.DelimitedFileWriter
 
toString() - Method in class ambit2.core.io.FileState
 
toString() - Method in class ambit2.core.io.InteractiveIteratingMDLReader
 
toString() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper
 
toString() - Method in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
toString() - Method in class ambit2.core.io.IteratingFileReader
 
toString() - Method in class ambit2.core.io.IteratingFolderReader
 
toString() - Method in class ambit2.core.io.IteratingXLSReader
 
toString() - Method in class ambit2.core.io.MolPropertiesIOSetting
 
toString() - Method in class ambit2.core.io.StringArrayHeader
 
toString() - Method in class ambit2.core.io.XLSFileWriter
 
toString() - Method in class ambit2.core.processors.structure.FingerprintGenerator
 
toString() - Method in class ambit2.core.processors.structure.key.PropertyKey
 
toString() - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
toString() - Method in class ambit2.db.cache.QueryCachedResults
 
toString() - Method in class ambit2.db.chemrelation.ReadDatasetRelation
 
toString() - Method in class ambit2.db.chemrelation.ReadStructureRelation
 
toString() - Method in class ambit2.db.facets.bundle.BundleSummaryQuery
 
toString() - Method in class ambit2.db.facets.datasets.EndpointCompoundFacetQuery
 
toString() - Method in class ambit2.db.facets.datasets.PrefixFacetQuery
 
toString() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacet
 
toString() - Method in class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery
 
toString() - Method in class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats
 
toString() - Method in class ambit2.db.facets.qlabel.DatasetStructureQualityStats
 
toString() - Method in class ambit2.db.facets.qlabel.DatasetStrucTypeStats
 
toString() - Method in class ambit2.db.LoginInfo
 
toString() - Method in class ambit2.db.processors.DescriptorsCalculator
 
toString() - Method in class ambit2.db.readers.PropertyValue
 
toString() - Method in class ambit2.db.readers.RetrieveDatasets
 
toString() - Method in class ambit2.db.readers.RetrieveField
 
toString() - Method in class ambit2.db.search.AbstractQuery
 
toString() - Method in class ambit2.db.search.DictionaryQuery
 
toString() - Method in class ambit2.db.search.property.FreeTextPropertyQuery
 
toString() - Method in class ambit2.db.search.property.QueryOntology
 
toString() - Method in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
toString() - Method in class ambit2.db.search.qlabel.QueryConsensus
 
toString() - Method in class ambit2.db.search.qlabel.QueryQLabel
 
toString() - Method in class ambit2.db.search.QueryCombined
 
toString() - Method in class ambit2.db.search.QueryUser
 
toString() - Method in class ambit2.db.search.StoredQuery
 
toString() - Method in class ambit2.db.search.structure.byproperty.QueryStructureByProperty
 
toString() - Method in class ambit2.db.search.structure.FingerprintsByStatus
 
toString() - Method in class ambit2.db.search.structure.FreeTextQuery
 
toString() - Method in class ambit2.db.search.structure.MissingFingerprintsQuery
 
toString() - Method in class ambit2.db.search.structure.MissingInChIsQuery
 
toString() - Method in class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery
 
toString() - Method in enum ambit2.db.search.structure.QueryAtomEnvironment.q_modifier
 
toString() - Method in class ambit2.db.search.structure.QueryAtomEnvironment
 
toString() - Method in class ambit2.db.search.structure.QueryDataset
 
toString() - Method in class ambit2.db.search.structure.QueryDatasetByID
 
toString() - Method in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
toString() - Method in class ambit2.db.search.structure.QueryField
 
toString() - Method in class ambit2.db.search.structure.QueryFieldMultiple
 
toString() - Method in class ambit2.db.search.structure.QueryFieldNumeric
 
toString() - Method in class ambit2.db.search.structure.QueryLookupStructure
 
toString() - Method in class ambit2.db.search.structure.QueryMissingDescriptor
 
toString() - Method in class ambit2.db.search.structure.QueryMissingDistances
 
toString() - Method in class ambit2.db.search.structure.QueryMissingProperty
 
toString() - Method in class ambit2.db.search.structure.QueryPrescreenBitSet
 
toString() - Method in class ambit2.db.search.structure.QuerySimilarity
 
toString() - Method in class ambit2.db.search.structure.QuerySimilarityStructure
 
toString() - Method in class ambit2.db.search.structure.QuerySMARTS
 
toString() - Method in class ambit2.db.search.structure.QueryStoredResults
 
toString() - Method in class ambit2.db.search.structure.QueryStoredResultsByName
 
toString() - Method in class ambit2.db.search.structure.QueryStructure
 
toString() - Method in class ambit2.db.search.structure.QueryStructureByID
 
toString() - Method in class ambit2.db.search.structure.QueryStructureByQuality
 
toString() - Method in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
toString() - Method in class ambit2.db.search.structure.QueryStructureByValueQuality
 
toString() - Method in class ambit2.db.search.structure.QueryStructureType
 
toString() - Method in class ambit2.db.search.structure.QueryStrucType
 
toString() - Method in class ambit2.db.search.structure.ScopeQuery
 
toString() - Method in class ambit2.db.SessionID
 
toString() - Method in class ambit2.db.simiparity.space.QueryQMapStructures
 
toString() - Method in class ambit2.db.substance.ReadByReliabilityFlags
 
toString() - Method in class ambit2.db.substance.ReadSubstanceByExternalIDentifier
 
toString() - Method in class ambit2.db.substance.ReadSubstanceByName
 
toString() - Method in class ambit2.db.substance.ReadSubstanceByOwner
 
toString() - Method in class ambit2.db.substance.ReadSubstanceByStudy
 
toString() - Method in class ambit2.db.substance.ReadSubstanceByType
 
toString() - Method in class ambit2.db.substance.relation.ChemicalBySubstanceRelation
 
toString() - Method in class ambit2.db.substance.relation.ReadSubstanceRelation
 
toString() - Method in class ambit2.db.update.bookmark.ReadAnnotation
 
toString() - Method in class ambit2.db.update.bookmark.ReadBookmark
 
toString() - Method in class ambit2.db.update.bundle.ReadBundle
 
toString() - Method in class ambit2.db.update.dataset.QueryDatasetByFeatures
 
toString() - Method in class ambit2.db.update.dataset.ReadDataset
 
toString() - Method in class ambit2.db.update.dataset.ReadDatasetLicense
 
toString() - Method in class ambit2.db.update.fp.Fingerprint
 
toString() - Method in class ambit2.db.update.model.AbstractModelQuery
 
toString() - Method in class ambit2.db.update.model.ReadModel
 
toString() - Method in class ambit2.db.update.property.ReadProperty
 
toString() - Method in class ambit2.db.update.queryfolder.ReadQueryFolder
 
toString() - Method in class ambit2.db.update.reference.ReadReference
 
toString() - Method in class ambit2.db.update.structure.ChemicalByDataset
 
toString() - Method in class ambit2.dbui.LoginInfoBean
 
toString() - Method in enum ambit2.descriptors.AbstractKekulizationVerifier.names_index
 
toString() - Method in class ambit2.descriptors.AtomEnvironment
 
toString() - Method in class ambit2.descriptors.CrossSectionalDiameterDescriptor
 
toString() - Method in class ambit2.descriptors.FunctionalGroup
 
toString() - Method in class ambit2.descriptors.FunctionalGroupDescriptor
 
toString() - Method in class ambit2.descriptors.MaximumDiameterDescriptor
 
toString() - Method in class ambit2.descriptors.PKANode
 
toString() - Method in class ambit2.descriptors.PlanarityDescriptor
 
toString() - Method in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
toString() - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
toString() - Method in class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator
 
toString() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixBitset
 
toString() - Method in class ambit2.descriptors.simmatrix.SimilarityMatrixDouble
 
toString() - Method in class ambit2.descriptors.SizeDescriptor
 
toString() - Method in class ambit2.descriptors.SpherosityDescriptor
 
toString(int[][]) - Static method in class ambit2.descriptors.utils.GraphMatrices
 
toString() - Method in class ambit2.descriptors.VerboseDescriptorResult
 
toString() - Method in class ambit2.domain.stats.datastructures.Histogram
 
toString() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMD
 
toString() - Method in class ambit2.domain.stats.transforms.densityestimation.KDensityMDProduct
 
toString() - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
toString() - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
toString() - Method in class ambit2.dragon.DescriptorDragonShell
 
toString() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
toString() - Method in class ambit2.dragon.DragonShell
 
toString() - Method in enum ambit2.export.isa.base.ISAConst.ISAFormat
 
toString() - Method in class ambit2.export.isa.base.ISALocation
 
toString() - Method in enum ambit2.export.isa.v1_0.objects.Data.Type
 
toString() - Method in enum ambit2.export.isa.v1_0.objects.Material.Type
 
toString(IAtomContainer) - Method in class ambit2.groupcontribution.dataset.LocalProperties
 
toString() - Method in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
toString() - Method in class ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment
 
toString() - Method in class ambit2.groupcontribution.nmr.nmr_1h.HNMRKnowledgeBase
 
toString() - Method in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
toString() - Method in class ambit2.groupcontribution.nmr.Substituent
 
toString(int, int) - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
toString() - Method in class ambit2.model.evaluation.EvaluationStats
 
toString() - Method in enum ambit2.model.numeric.ADomainMethodType
 
toString() - Method in class ambit2.model.numeric.DataCoverage
 
toString() - Method in class ambit2.model.numeric.DataCoverageDescriptors
 
toString() - Method in enum ambit2.model.structure.AtomEnvironmentDistanceType
 
toString() - Method in class ambit2.mopac.AbstractMopacShell
 
toString() - Method in class ambit2.mopac.DescriptorMopacShell
 
toString() - Method in class ambit2.mopac.Mopac7Reader
 
toString() - Method in class ambit2.mopac.Mopac7Writer
 
toString() - Method in class ambit2.pubchem.EntrezSearchOptions
 
toString() - Method in class ambit2.pubchem.rest.PUGRestRequest
 
toString() - Method in class ambit2.reactions.GenericReaction
 
toString() - Method in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
toString() - Method in class ambit2.reactions.ReactionDataBase
 
toString(Reactor) - Method in class ambit2.reactions.reactor.ReactorNode
 
toString() - Method in class ambit2.reactions.reactor.ReactorStrategy
 
toString() - Method in class ambit2.reactions.retrosynth.ReactionKnowledgeBase
 
toString() - Method in class ambit2.reactions.retrosynth.ReactionSequence
 
toString() - Method in class ambit2.reactions.retrosynth.ReactionSequenceLevel
 
toString() - Method in class ambit2.reactions.retrosynth.RetroSynthesisResult
 
toString() - Method in class ambit2.reactions.retrosynth.RetroSynthPath
 
toString() - Method in class ambit2.reactions.rules.RetroSynthRule
 
toString() - Method in class ambit2.reactions.rules.scores.ReactionScore
 
toString() - Method in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
toString() - Method in class ambit2.reactions.sets.ReactionData
 
toString() - Method in enum ambit2.rest.legacy.OTCompound._titles
Deprecated.
 
toString() - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
toString() - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
toString() - Method in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
toString() - Method in class ambit2.rest.model.predictor.CoveragePredictor
 
toString() - Method in class ambit2.rest.model.predictor.DescriptorPredictor
 
toString() - Method in class ambit2.rest.model.predictor.ModelPredictor
 
toString() - Method in class ambit2.rest.model.predictor.Structure2DProcessor
 
toString() - Method in class ambit2.rest.model.predictor.StructureProcessor
 
toString() - Method in class ambit2.rest.task.ExecutableTask
 
toString() - Method in class ambit2.rest.task.Task
 
toString() - Method in class ambit2.rest.task.TaskResult
 
toString() - Method in class ambit2.rest.task.weka.FilteredWekaPredictor
 
toString() - Method in class ambit2.rest.task.weka.WekaPredictor
 
toString() - Method in class ambit2.rules.conditions.DescriptorValueCondition
 
toString() - Method in class ambit2.search.chemidplus.ChemIdPlusRequest
 
toString() - Method in class ambit2.search.csls.CSLSRequest
 
toString() - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
toString() - Method in class ambit2.similarity.measure.AtomEnvironmentsDistance
 
toString() - Method in class ambit2.similarity.measure.BinaryKernelDistance
 
toString() - Method in class ambit2.similarity.measure.DistanceComparable
 
toString() - Method in class ambit2.similarity.measure.EuclideanDistance
 
toString() - Method in class ambit2.similarity.measure.FingerprintDistance
 
toString() - Method in class ambit2.similarity.measure.MCSSDistance
 
toString() - Method in class ambit2.similarity.stats.Bin
 
toString() - Method in class ambit2.similarity.stats.ConfusionMatrix
 
toString() - Method in class ambit2.similarity.stats.Histogram
 
toString() - Method in class ambit2.similarity.stats.ModelValuesHistogram
 
toString() - Method in class ambit2.similarity.stats.MutableInt
 
toString() - Method in class ambit2.similarity.stats.SelfBin
 
toString() - Method in class ambit2.similarity.stats.ValuePair
 
toString() - Method in class ambit2.sln.SLNAtom
 
toString() - Method in class ambit2.sln.SLNAtomExpression
 
toString() - Method in class ambit2.sln.SLNBond
 
toString() - Method in class ambit2.sln.SLNBondExpression
 
toString() - Method in class ambit2.sln.SLNContainerAttributes
 
toString(boolean) - Method in class ambit2.sln.SLNExpressionToken
 
toString() - Method in class ambit2.sln.SLNParserError
 
toString() - Method in class ambit2.smarts.AliphaticSymbolQueryAtom
 
toString() - Method in class ambit2.smarts.AromaticSymbolQueryAtom
 
toString() - Method in class ambit2.smarts.AtomEquivalenceInfo
 
toString(IAtomContainer) - Method in class ambit2.smarts.Node
 
toString() - Method in class ambit2.smarts.processors.SMIRKSTransformation
 
toString() - Method in class ambit2.smarts.query.AbstractSmartsPattern
 
toString() - Method in class ambit2.smarts.QuerySequenceElement
 
toString(IQueryAtomContainer) - Method in class ambit2.smarts.QuerySequenceElement
 
toString() - Method in class ambit2.smarts.SequenceElement
 
toString() - Method in class ambit2.smarts.SmartsAtomExpression
 
toString() - Method in class ambit2.smarts.SmartsBondExpression
 
toString() - Method in class ambit2.smarts.SmartsFlags
 
toString(int[]) - Static method in class ambit2.smarts.SmartsHelper
 
toString() - Method in class ambit2.smarts.SmartsParserError
 
toString(IAtomContainer) - Method in class ambit2.smarts.StereoChange
 
toString() - Method in class ambit2.smarts.StereoDBTransformation
 
toString() - Method in class ambit2.smarts.SymbolQueryAtomAromaticityNotSpecified
 
toString() - Method in class ambit2.smarts.TopLayer
 
toString() - Method in class ambit2.smi23d.ShellMengine
 
toString() - Method in class ambit2.smi23d.ShellSmi2SDF
 
toString() - Method in class ambit2.some.DescriptorSOMEShell
 
toString() - Method in class ambit2.some.SOMEShell
 
toString() - Method in class ambit2.structure2name.rules.CarbonData
 
toString() - Method in class ambit2.structure2name.rules.FunctionalGroupData
 
toString() - Method in class ambit2.tautomers.RankingRule
 
toString() - Method in class ambit2.tautomers.Rule
 
toString() - Method in class ambit2.tautomers.RuleStateBondDistribution
 
toString() - Method in class ambit2.tautomers.TautomerRelation
 
toString() - Method in class ambit2.vega.VegaShell
 
toStringExhaustive(SuppleAtomContainer) - Static method in class ambit2.markush.MarkushHelpers
 
toStringLine() - Method in class ambit2.reactions.rules.scores.ReactionScore
 
TOTAL_COLUMN_COORDINATE_POSITIONS - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
TOTAL_ROW_COORDINATE_POSITIONS - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
totalGroupNum(Map<String, Integer>) - Static method in class ambit2.reactions.rules.scores.ChemComplexityUtils
 
totalScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
ToxCast_signature - Static variable in class ambit2.core.io.ToxcastAssayReader
 
ToxcastAssayReader - Class in ambit2.core.io
ToxCast assay data are TXT tab delimited files.
Lines starting with # are comments.
The column SOURCE_NAME_SID contains DSSTOX_RID (DSSTOX record ID) , prependend with "DSSTOX_" string, e.g.
ToxcastAssayReader(InputStream) - Constructor for class ambit2.core.io.ToxcastAssayReader
 
ToxcastAssayReader(Reader) - Constructor for class ambit2.core.io.ToxcastAssayReader
 
ToxcastFileFormat - Class in ambit2.core.io
Toxcast Assay files are tab delimited files
ToxcastFileFormat() - Constructor for class ambit2.core.io.ToxcastFileFormat
 
toxForest_ext - Static variable in class ambit2.base.io.MolFileFilter
 
toxForest_ext_descr - Static variable in class ambit2.base.io.MolFileFilter
 
toXML(Document) - Method in class ambit2.descriptors.FunctionalGroup
 
toXML() - Method in class ambit2.dragon.DragonDescriptorDictionary
 
ToXMLReaderSimple - Class in ambit2.core.io
 
ToXMLReaderSimple(InputStream) - Constructor for class ambit2.core.io.ToXMLReaderSimple
 
ToXMLReaderSimple.toxml_attributes - Enum in ambit2.core.io
 
ToXMLReaderSimple.toxml_names - Enum in ambit2.core.io
 
ToXMLReaderSimple.toxml_quantity_types - Enum in ambit2.core.io
 
ToXMLReaderSimple.toxml_tags - Enum in ambit2.core.io
 
ToXMLReaderSimple.toxml_tags_level1 - Enum in ambit2.core.io
toxml.xsd 3.0.8
toxTree_ext - Static variable in class ambit2.base.io.MolFileFilter
 
toxTree_ext_descr - Static variable in class ambit2.base.io.MolFileFilter
 
toxTree_ext_descr_save - Static variable in class ambit2.base.io.MolFileFilter
 
toxTree_ext_save - Static variable in class ambit2.base.io.MolFileFilter
 
trace - Variable in class ambit2.descriptors.VerboseDescriptorResult
 
Trade_name - Static variable in class ambit2.base.data.LiteratureEntry
 
train() - Method in class ambit2.groupcontribution.Learner
 
trainingData - Variable in class ambit2.model.builder.AbstractModelBuilder
 
trainingData - Variable in class ambit2.rest.legacy.OTModel
Deprecated.
 
trainingSetFile - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
trainSetFile - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
transaction(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
transferSequenceToOwner() - Method in class ambit2.smarts.IsomorphismTester
 
transferSequenceToOwner() - Method in class ambit2.smarts.smirks.SmartsIsomorphismTester
 
transform(IAtomContainer) - Method in class ambit2.balloon.ShellBalloon
 
transform(Process, INPUT) - Method in class ambit2.base.external.CommandShell
 
transform(INPUT) - Method in class ambit2.base.external.CommandShell
 
transform(IStructureRecord, RESULT) - Method in class ambit2.base.processors.search.AbstractFinder
 
transform(CSVRecord) - Method in class ambit2.core.io.RawIteratingCSVReader
 
transform(Object) - Method in class ambit2.core.io.RawIteratingWrapper
 
transform(X) - Method in class ambit2.core.smiles.OpenBabelAbstractShell
 
transform(Target) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
transform(DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorValuesWriter
 
transform(DescriptorValue) - Method in class ambit2.db.processors.DbDescriptorWriter
 
transform(IStructureRecord) - Method in class ambit2.db.processors.PropertyValuesWriter
 
transform - Variable in class ambit2.db.readers.RetrieveAtomContainer
 
transform(IAtomContainer) - Method in class ambit2.dragon.AbstractDescriptorShell
 
transform(double) - Method in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
transform(double) - Method in interface ambit2.groupcontribution.transformations.IValueTransformation
 
transform(double) - Method in class ambit2.groupcontribution.transformations.TransformationComposition
 
transform(double) - Method in class ambit2.groupcontribution.transformations.TransformationExp
 
transform(double) - Method in class ambit2.groupcontribution.transformations.TransformationLin
 
transform(double) - Method in class ambit2.groupcontribution.transformations.TransformationLn
 
transform(double) - Method in class ambit2.groupcontribution.transformations.TransformationPow
 
transform(CSVRecord, int) - Method in interface ambit2.ml.io.IMLOutput
 
transform(CSVRecord, int) - Method in class ambit2.ml.io.OutputARFF
 
transform(CSVRecord, int) - Method in class ambit2.ml.io.OutputVW
 
transform(CSVRecord, int) - Method in class ambit2.ml.io.OutputVW_LDA
 
transform(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
 
transform(IStructureRecord[]) - Method in class ambit2.rest.model.builder.AbstractStructuresModelBuilder
 
transform(IStructureRecord[]) - Method in class ambit2.rest.model.builder.SMSDModelBuilder
 
transform(Input) - Method in class ambit2.rest.model.predictor.CoveragePredictor
 
transform(IStructureRecord) - Method in class ambit2.rest.model.predictor.FingerprintsPredictor
 
transform(IStructureRecord) - Method in class ambit2.rest.model.predictor.NumericADPredictor
 
transform(IAtomContainer) - Method in class ambit2.smi23d.ShellMengine
 
transform(IAtomContainer) - Method in class ambit2.smi23d.ShellSmi2SDF
 
transform(IAtomContainer) - Method in class ambit2.some.SOMEShell
 
transform - Variable in class ambit2.ui.table.StructureRecordsTableModel
 
transform2Kekule(IAtomContainer) - Method in class ambit2.descriptors.AbstractKekulizationVerifier
 
transform2Kekule(IAtomContainer) - Method in class ambit2.descriptors.SaturationCheckerVerifier
 
transform_input(INPUT) - Method in class ambit2.base.external.CommandShell
 
transform_input(IAtomContainer) - Method in class ambit2.dragon.DragonShell
 
transform_input(IAtomContainer) - Method in class ambit2.mopac.AbstractMopacShell
This is not thread safe!
transform_input(IAtomContainer) - Method in class ambit2.some.SOMEShell
 
transform_input(IAtomContainer) - Method in class ambit2.vega.VegaShell
 
transformationasproperties - Variable in class ambit2.smarts.processors.SMIRKSProcessor
 
TransformationComposition - Class in ambit2.groupcontribution.transformations
 
TransformationComposition(IValueTransformation[]) - Constructor for class ambit2.groupcontribution.transformations.TransformationComposition
 
transformationDataToString() - Method in class ambit2.smarts.SMIRKSReaction
 
TransformationExp - Class in ambit2.groupcontribution.transformations
 
TransformationExp() - Constructor for class ambit2.groupcontribution.transformations.TransformationExp
 
TransformationLin - Class in ambit2.groupcontribution.transformations
 
TransformationLin() - Constructor for class ambit2.groupcontribution.transformations.TransformationLin
 
TransformationLin(double, double) - Constructor for class ambit2.groupcontribution.transformations.TransformationLin
 
TransformationLn - Class in ambit2.groupcontribution.transformations
 
TransformationLn() - Constructor for class ambit2.groupcontribution.transformations.TransformationLn
 
TransformationLn(double) - Constructor for class ambit2.groupcontribution.transformations.TransformationLn
 
TransformationPow - Class in ambit2.groupcontribution.transformations
 
TransformationPow(double) - Constructor for class ambit2.groupcontribution.transformations.TransformationPow
 
transformations - Variable in class ambit2.smarts.processors.SMIRKSProcessor
 
Transformations - Class in ambit2.smarts.smirks
 
Transformations() - Constructor for class ambit2.smarts.smirks.Transformations
 
TransformationUtils - Class in ambit2.groupcontribution.transformations
 
TransformationUtils() - Constructor for class ambit2.groupcontribution.transformations.TransformationUtils
 
transformAttributes(NearestNeighborsSearch<T>) - Method in class ambit2.featureselection.AbstractAttributeSelection
Transforms attributes stored in NearestNeighborsSearch, leaving only selected ones.
transformAttributes(NearestNeighborsSearch<T>) - Method in interface ambit2.featureselection.IAttributeSelection
 
transformAttributes(Features) - Method in class ambit2.similarity.knn.NearestNeighborsSimilarity
 
TransformedStartMaterialData() - Constructor for class ambit2.reactions.SimilarityManager.TransformedStartMaterialData
 
transformedValue - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager.DescrData
 
transformer - Variable in class ambit2.core.processors.structure.key.CASKey
 
TransformError - Variable in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
TransformFilter - Class in ambit2.domain.stats.transforms.transformfilters
Abstract class for data transformation
TransformFilter() - Constructor for class ambit2.domain.stats.transforms.transformfilters.TransformFilter
 
TransformPoints(Matrix) - Method in class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform
 
TransformPoints(Matrix) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
Transforms points from original to transformed space
TransformPoints(Matrix, int[]) - Method in class ambit2.domain.stats.transforms.transformfilters.TransformFilter
Transforms points from original to transformed space only nPoints with indices stored in pointsToProcess are evaluated
transformRawValues(List<String>, List<Object>) - Method in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
transformResult(IStructureRecord, IStructureRecord) - Method in class ambit2.base.processors.search.AbstractFinder
 
transformResult(IStructureRecord, String) - Method in class ambit2.base.processors.search.AbstractFinder
 
transformScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
transformScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
transformToSelected(T) - Method in interface ambit2.featureselection.IAttributeSelection
 
transformType - Variable in class ambit2.reactions.GenericReaction
 
transfUtils - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorManager
 
transposed() - Method in class ambit2.groupcontribution.utils.math.MatrixDouble
 
trasformTypeScores - Variable in class ambit2.reactions.retrosynth.SyntheticStrategy
 
traverse(IAtomContainer, PKANode, ArrayList<String>) - Method in class ambit2.descriptors.PKASmartsDescriptor
 
TreatmentRelated - Static variable in class ambit2.base.ro.I5CONSTANTS
 
tree - Variable in class ambit2.descriptors.PKASmartsDescriptor
 
TripleBondAromaticityNotSpecified - Class in ambit2.smarts
 
TripleBondAromaticityNotSpecified(IChemObjectBuilder) - Constructor for class ambit2.smarts.TripleBondAromaticityNotSpecified
 
tuples_batchExecutor - Variable in class ambit2.db.processors.ValueWriterNew
Tuples
type - Variable in class ambit2.base.data.AmbitUser
 
type - Variable in class ambit2.base.data.Bookmark
 
type - Variable in class ambit2.base.data.LiteratureEntry
 
type - Variable in class ambit2.base.data.PropertyAnnotation
 
type - Variable in class ambit2.base.data.StructureRecord
 
type - Variable in class ambit2.core.data.model.Algorithm
 
type - Variable in class ambit2.core.groups.ContainerGroup
 
type - Variable in class ambit2.export.isa.v1_0.objects.Data
 
type - Variable in class ambit2.export.isa.v1_0.objects.DataFile
 
type - Variable in class ambit2.export.isa.v1_0.objects.Material
 
type - Variable in class ambit2.groupcontribution.dataset.LocalProperties
 
type - Variable in class ambit2.reactions.io.ReactionReadUtils.ReactionDataObject
 
type - Variable in class ambit2.reactions.retrosynth.IReactionSequenceHandler.RSEvent
 
type - Variable in class ambit2.rules.functions.ValueTransformation
 
type - Variable in class ambit2.sln.SLNContainerAttributes
 
type - Variable in class ambit2.sln.SLNExpressionToken
 
type - Variable in class ambit2.smarts.SmartsExpressionToken
 
type - Variable in class ambit2.structure2name.components.ComponentConnection
 
type - Variable in class ambit2.tautomers.Filter
 
type - Variable in class ambit2.tautomers.Rule
 
type_SLNAttr - Variable in class ambit2.sln.io.SLN2SubstanceConfig
 
TypedListModel<P> - Interface in ambit2.base.data
 
typer - Variable in class ambit2.descriptors.AtomTypeVerifierDescriptor
 
typer - Variable in class ambit2.descriptors.SaturationCheckerVerifier
 
typical - Variable in class ambit2.base.relation.composition.Proportion
 
typical_unit - Variable in class ambit2.base.relation.composition.Proportion
 
typical_value - Variable in class ambit2.base.relation.composition.Proportion
 

U

uc - Variable in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
uit - Variable in class ambit2.db.search.structure.QueryExactStructure
Deprecated.
 
uit - Variable in class ambit2.db.search.structure.QuerySimilarityStructure
 
uit - Variable in class ambit2.smarts.SmartsManager
 
undoDelete() - Method in class ambit2.db.results.AmbitRows
 
undoInsert() - Method in class ambit2.db.results.AmbitRows
 
undoUpdate() - Method in class ambit2.db.results.AmbitRows
 
union - Static variable in class ambit2.db.search.QueryCombined
 
UNIQUE_SMILES - Static variable in class ambit2.core.config.AmbitCONSTANTS
Unique SMILES
UNIQUE_SMILES_TIME - Static variable in class ambit2.core.config.AmbitCONSTANTS
Time to generate an unique smiles
unit - Variable in class ambit2.base.data.study.EffectRecord
 
unit - Variable in class ambit2.export.isa.v1_0.objects.FactorValue
 
unit - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttributeValue
 
unit - Variable in class ambit2.export.isa.v1_0.objects.ProcessParameterValue
 
UNIT_OFFSET_LENGTH - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
UNIT_OFFSET_MAP - Static variable in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
 
unitCategories - Variable in class ambit2.export.isa.v1_0.objects.Assay
 
unitCategories - Variable in class ambit2.export.isa.v1_0.objects.Study
 
units - Variable in class ambit2.base.data.Property
 
units - Variable in class ambit2.base.data.study.Value
 
units - Static variable in class ambit2.mopac.Mopac7Reader
 
units - Variable in class ambit2.rest.legacy.OTFeature
Deprecated.
 
unresolved - Variable in class ambit2.reactions.retrosynth.RetroSynthNode
 
unsetMatchColumn(int) - Method in class ambit2.db.results.AmbitRows
 
unsetMatchColumn(int[]) - Method in class ambit2.db.results.AmbitRows
 
unsetMatchColumn(String) - Method in class ambit2.db.results.AmbitRows
 
unsetMatchColumn(String[]) - Method in class ambit2.db.results.AmbitRows
 
UnsupportedGroupOperation - Exception in ambit2.core.groups
 
UnsupportedGroupOperation(String) - Constructor for exception ambit2.core.groups.UnsupportedGroupOperation
 
UnsupportedGroupOperation(String, Exception) - Constructor for exception ambit2.core.groups.UnsupportedGroupOperation
 
unUsedRuleInstances - Variable in class ambit2.tautomers.TautomerIncrementStep
 
unzip(File, File, OPTIONS) - Method in class ambit2.core.io.ZipReader
 
unzip(InputStream, File, OPTIONS) - Method in class ambit2.core.io.ZipReader
 
unzipEntry(ZipEntry, InputStream, File) - Method in class ambit2.core.io.ZipReader
 
update(Object) - Method in interface ambit2.base.processors.IAmbitResult
 
update(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
update(Group) - Method in class ambit2.db.processors.AbstractUpdateProcessor
 
update(IStructureRecord) - Method in class ambit2.db.processors.DbStructureWriter
 
update(IStructureRecord) - Method in class ambit2.db.processors.RepositoryWriter
 
update(int, IStructureRecord) - Method in class ambit2.db.results.StoredQueryTableModel
 
update(StoredQuery, ResultSet) - Method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
 
update(Object) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
update(Task, Object) - Method in enum ambit2.rest.task.Task.TaskProperty
 
update() - Method in class ambit2.rest.task.Task
does nothing, should be autoupdated by ExecutableTask
update_sql - Static variable in class ambit2.db.substance.UpdateSubstance
 
update_sql - Static variable in class ambit2.db.update.bookmark.UpdateBookmark
 
update_sql - Static variable in class ambit2.db.update.chemical.UpdateChemical
 
update_sql - Static variable in class ambit2.db.update.model.UpdateModel
 
update_sql - Static variable in class ambit2.db.update.property.UpdateProperty
 
update_sql - Static variable in class ambit2.db.update.reference.UpdateReference
 
update_sql - Static variable in class ambit2.db.update.storedquery.UpdateSelectedRecords
 
update_sql - Static variable in class ambit2.db.update.storedquery.UpdateStoredQuery
 
update_sql_id - Static variable in class ambit2.db.update.storedquery.QueryAddTemplate
 
update_sql_id - Static variable in class ambit2.db.update.storedquery.QueryDeleteTemplate
 
update_sql_name - Static variable in class ambit2.db.update.storedquery.QueryAddTemplate
 
updateArray(int, Array) - Method in class ambit2.db.results.AmbitRows
 
updateArray(String, Array) - Method in class ambit2.db.results.AmbitRows
 
updateAsciiStream(int, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
updateAsciiStream(String, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
updateBigDecimal(int, BigDecimal) - Method in class ambit2.db.results.AmbitRows
 
updateBigDecimal(String, BigDecimal) - Method in class ambit2.db.results.AmbitRows
 
updateBinaryStream(int, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
updateBinaryStream(String, InputStream, int) - Method in class ambit2.db.results.AmbitRows
 
updateBlob(int, Blob) - Method in class ambit2.db.results.AmbitRows
 
updateBlob(String, Blob) - Method in class ambit2.db.results.AmbitRows
 
UpdateBookmark - Class in ambit2.db.update.bookmark
Updates content of the model
UpdateBookmark(Bookmark) - Constructor for class ambit2.db.update.bookmark.UpdateBookmark
 
UpdateBookmark() - Constructor for class ambit2.db.update.bookmark.UpdateBookmark
 
updateBoolean(int, boolean) - Method in class ambit2.db.results.AmbitRows
 
updateBoolean(String, boolean) - Method in class ambit2.db.results.AmbitRows
 
UpdateBundle - Class in ambit2.db.update.bundle
 
UpdateBundle(SubstanceEndpointsBundle) - Constructor for class ambit2.db.update.bundle.UpdateBundle
 
UpdateBundle() - Constructor for class ambit2.db.update.bundle.UpdateBundle
 
UpdateBundle._published_status - Enum in ambit2.db.update.bundle
 
updateByte(int, byte) - Method in class ambit2.db.results.AmbitRows
 
updateByte(String, byte) - Method in class ambit2.db.results.AmbitRows
 
updateBytes(int, byte[]) - Method in class ambit2.db.results.AmbitRows
 
updateBytes(String, byte[]) - Method in class ambit2.db.results.AmbitRows
 
updateCharacterStream(int, Reader, int) - Method in class ambit2.db.results.AmbitRows
 
updateCharacterStream(String, Reader, int) - Method in class ambit2.db.results.AmbitRows
 
UpdateChemical<C extends IChemical> - Class in ambit2.db.update.chemical
 
UpdateChemical(C) - Constructor for class ambit2.db.update.chemical.UpdateChemical
 
UpdateChemical() - Constructor for class ambit2.db.update.chemical.UpdateChemical
 
updateClob(int, Clob) - Method in class ambit2.db.results.AmbitRows
 
updateClob(String, Clob) - Method in class ambit2.db.results.AmbitRows
 
UpdateCompoundPropertyValueNumber - Class in ambit2.db.update.value
 
UpdateCompoundPropertyValueNumber() - Constructor for class ambit2.db.update.value.UpdateCompoundPropertyValueNumber
 
UpdateCompoundPropertyValueString - Class in ambit2.db.update.value
 
UpdateCompoundPropertyValueString() - Constructor for class ambit2.db.update.value.UpdateCompoundPropertyValueString
 
updateConnectionData(String, String, String) - Method in class ambit2.base.data.AmbitUser
 
updated - Variable in class ambit2.base.data.study.ProtocolApplication
 
updated - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
UpdateDataset - Class in ambit2.db.update.dataset
 
UpdateDataset(SourceDataset) - Constructor for class ambit2.db.update.dataset.UpdateDataset
 
UpdateDataset() - Constructor for class ambit2.db.update.dataset.UpdateDataset
 
updateDate(int, Date) - Method in class ambit2.db.results.AmbitRows
 
updateDate(String, Date) - Method in class ambit2.db.results.AmbitRows
 
UpdateDictionary - Class in ambit2.db.update.dictionary
 
UpdateDictionary(Dictionary) - Constructor for class ambit2.db.update.dictionary.UpdateDictionary
 
UpdateDictionary() - Constructor for class ambit2.db.update.dictionary.UpdateDictionary
 
updateDouble(int, double) - Method in class ambit2.db.results.AmbitRows
 
updateDouble(String, double) - Method in class ambit2.db.results.AmbitRows
 
UpdateEffectRecords - Class in ambit2.db.substance.study
 
UpdateEffectRecords(String, ProtocolApplication<Protocol, Params, String, Params, String>, EffectRecord) - Constructor for class ambit2.db.substance.study.UpdateEffectRecords
 
UpdateEffectRecordsBundle - Class in ambit2.db.substance.study
 
UpdateEffectRecordsBundle(SubstanceEndpointsBundle, String, ProtocolApplication<Protocol, Params, String, Params, String>, EffectRecord) - Constructor for class ambit2.db.substance.study.UpdateEffectRecordsBundle
 
updateExecutor - Variable in class ambit2.db.results.StoredQueryTableModel
 
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> - Class in ambit2.db
 
UpdateExecutor() - Constructor for class ambit2.db.UpdateExecutor
 
updateFloat(int, float) - Method in class ambit2.db.results.AmbitRows
 
updateFloat(String, float) - Method in class ambit2.db.results.AmbitRows
 
updateHeaderColumn(int, COLUMN) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader
 
updateInt(int, int) - Method in class ambit2.db.results.AmbitRows
 
updateInt(String, int) - Method in class ambit2.db.results.AmbitRows
 
updateLong(int, long) - Method in class ambit2.db.results.AmbitRows
 
updateLong(String, long) - Method in class ambit2.db.results.AmbitRows
 
UpdateModel - Class in ambit2.db.update.model
Updates content of the model
UpdateModel(ModelQueryResults) - Constructor for class ambit2.db.update.model.UpdateModel
 
UpdateModel() - Constructor for class ambit2.db.update.model.UpdateModel
 
updateMolecule(IAtomContainer) - Method in class ambit2.jchempaint.editor.MoleculeEditAction
 
updateNull(int) - Method in class ambit2.db.results.AmbitRows
 
updateNull(String) - Method in class ambit2.db.results.AmbitRows
 
updateObject(int, Object) - Method in class ambit2.db.results.AmbitRows
 
updateObject(String, Object) - Method in class ambit2.db.results.AmbitRows
 
updateObject(int, Object, int) - Method in class ambit2.db.results.AmbitRows
 
updateObject(String, Object, int) - Method in class ambit2.db.results.AmbitRows
 
updateProfile(Profile) - Method in class ambit2.db.results.MemoryRowsModel
 
UpdateProperty - Class in ambit2.db.update.property
 
UpdateProperty(Property) - Constructor for class ambit2.db.update.property.UpdateProperty
 
UpdateProperty() - Constructor for class ambit2.db.update.property.UpdateProperty
 
UpdatePropertyAnnotation - Class in ambit2.db.update.propertyannotations
 
UpdatePropertyAnnotation() - Constructor for class ambit2.db.update.propertyannotations.UpdatePropertyAnnotation
 
UpdateQueryFolder - Class in ambit2.db.update.queryfolder
 
UpdateQueryFolder(AmbitUser, SessionID) - Constructor for class ambit2.db.update.queryfolder.UpdateQueryFolder
 
UpdateQueryFolder() - Constructor for class ambit2.db.update.queryfolder.UpdateQueryFolder
 
updateRef(int, Ref) - Method in class ambit2.db.results.AmbitRows
 
updateRef(String, Ref) - Method in class ambit2.db.results.AmbitRows
 
UpdateReference - Class in ambit2.db.update.reference
 
UpdateReference(ILiteratureEntry) - Constructor for class ambit2.db.update.reference.UpdateReference
 
UpdateReference() - Constructor for class ambit2.db.update.reference.UpdateReference
 
updateRow() - Method in class ambit2.db.results.AmbitRows
 
UpdateSelectedRecords - Class in ambit2.db.update.storedquery
 
UpdateSelectedRecords() - Constructor for class ambit2.db.update.storedquery.UpdateSelectedRecords
 
updateSGroups(String, SuppleAtomContainer, Hashtable<Integer, ISGroup>) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
 
updateShort(int, short) - Method in class ambit2.db.results.AmbitRows
 
updateShort(String, short) - Method in class ambit2.db.results.AmbitRows
 
UpdateStoredQuery - Class in ambit2.db.update.storedquery
 
UpdateStoredQuery(IStoredQuery) - Constructor for class ambit2.db.update.storedquery.UpdateStoredQuery
 
UpdateStoredQuery() - Constructor for class ambit2.db.update.storedquery.UpdateStoredQuery
 
updateString(int, String) - Method in class ambit2.db.results.AmbitRows
 
updateString(String, String) - Method in class ambit2.db.results.AmbitRows
 
updateStructure - Variable in class ambit2.db.processors.DbStructureWriter
 
UpdateStructure - Class in ambit2.db.update.structure
 
UpdateStructure(IStructureRecord) - Constructor for class ambit2.db.update.structure.UpdateStructure
 
UpdateStructure() - Constructor for class ambit2.db.update.structure.UpdateStructure
 
updateStructure - Variable in class ambit2.rest.model.predictor.AbstractStructureProcessor
 
UpdateStructurePropertyIDNumber - Class in ambit2.db.update.value
Updates property value of a structure
UpdateStructurePropertyIDNumber() - Constructor for class ambit2.db.update.value.UpdateStructurePropertyIDNumber
 
UpdateStructurePropertyIDString - Class in ambit2.db.update.value
Changes property value for a given structure
UpdateStructurePropertyIDString() - Constructor for class ambit2.db.update.value.UpdateStructurePropertyIDString
 
UpdateStructureRelation - Class in ambit2.db.chemrelation
 
UpdateStructureRelation() - Constructor for class ambit2.db.chemrelation.UpdateStructureRelation
 
UpdateStructureRelation(IStructureRecord, IStructureRecord, String) - Constructor for class ambit2.db.chemrelation.UpdateStructureRelation
 
UpdateStructureRelation(IStructureRecord, IStructureRecord, String, Double) - Constructor for class ambit2.db.chemrelation.UpdateStructureRelation
 
UpdateSubstance<C extends SubstanceRecord> - Class in ambit2.db.substance
 
UpdateSubstance(C) - Constructor for class ambit2.db.substance.UpdateSubstance
 
UpdateSubstance() - Constructor for class ambit2.db.substance.UpdateSubstance
 
UpdateSubstanceIdentifiers<C extends SubstanceRecord> - Class in ambit2.db.substance.ids
 
UpdateSubstanceIdentifiers(C) - Constructor for class ambit2.db.substance.ids.UpdateSubstanceIdentifiers
 
UpdateSubstanceIdentifiers() - Constructor for class ambit2.db.substance.ids.UpdateSubstanceIdentifiers
 
UpdateSubstanceRelation - Class in ambit2.db.substance.relation
 
UpdateSubstanceRelation(CompositionRelation) - Constructor for class ambit2.db.substance.relation.UpdateSubstanceRelation
 
UpdateSubstanceRelation() - Constructor for class ambit2.db.substance.relation.UpdateSubstanceRelation
 
UpdateSubstanceStudy - Class in ambit2.db.substance.study
 
UpdateSubstanceStudy(String, ProtocolApplication<Protocol, IParams, String, IParams, String>) - Constructor for class ambit2.db.substance.study.UpdateSubstanceStudy
 
UpdateSubstanceStudyBundle - Class in ambit2.db.substance.study
Write studies into bundle_substance_protocolapplication
UpdateSubstanceStudyBundle(SubstanceEndpointsBundle, String, ProtocolApplication<Protocol, IParams, String, IParams, String>) - Constructor for class ambit2.db.substance.study.UpdateSubstanceStudyBundle
 
updateTime(int, Time) - Method in class ambit2.db.results.AmbitRows
 
updateTime(String, Time) - Method in class ambit2.db.results.AmbitRows
 
updateTimestamp(int, Timestamp) - Method in class ambit2.db.results.AmbitRows
 
updateTimestamp(String, Timestamp) - Method in class ambit2.db.results.AmbitRows
 
updateUI() - Method in class ambit2.ui.EditableHeader
 
upQualifier - Variable in class ambit2.base.data.study.EffectRecord
 
upQualifier - Variable in class ambit2.base.data.study.Value
 
upValue - Variable in class ambit2.base.data.study.EffectRecord
 
upValue - Variable in class ambit2.base.data.study.Value
 
URI - Variable in class ambit2.core.io.ToXMLReaderSimple
 
uri - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
uri - Variable in class ambit2.rest.legacy.OTObject
Deprecated.
 
uri - Variable in class ambit2.rest.task.TaskResult
 
uri - Variable in class ambit2.rest.wrapper.WrappedService
 
URI_to_handle() - Method in class ambit2.rest.AbstractResource
 
urilookup - Variable in class ambit2.rest.rdf.RDFInstancesIterator
 
uriReporter - Variable in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
uriReporter - Variable in class ambit2.rest.QueryStaXReporter
 
urireporter - Variable in class ambit2.rest.reporters.TaskRDFReporter
 
URL - Variable in class ambit2.base.data.LiteratureEntry
 
url - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
url - Variable in exception ambit2.base.exceptions.HttpException
 
url - Variable in class ambit2.base.facet.AbstractFacet
 
url - Variable in class ambit2.pubchem.HTTPRequest
 
URL - Variable in exception ambit2.rest.exception.TaskException
 
url - Variable in class ambit2.rest.legacy.OTRemoteTask
Deprecated.
 
urlPrefix - Variable in class ambit2.db.reporters.ARFFReporter
 
urlPrefix - Variable in class ambit2.db.reporters.CSVReporter
 
use13ShiftRulesOnly(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
use15ShiftRules(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
use17ShiftRules(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
use19ShiftRules(boolean) - Method in class ambit2.tautomers.KnowledgeBase
 
useCache - Variable in class ambit2.db.StatementExecutor
 
useCache - Variable in class ambit2.descriptors.processors.PropertyCalculationProcessor
 
useCDKIsomorphism - Variable in class ambit2.smarts.query.SmartsPatternAmbit
 
usedRuleInstances - Variable in class ambit2.tautomers.TautomerIncrementStep
 
useExactStructureID() - Method in class ambit2.core.processors.structure.key.EmptyKey
 
useExactStructureID() - Method in class ambit2.core.processors.structure.key.InchiKey
 
useExactStructureID() - Method in interface ambit2.core.processors.structure.key.IStructureKey
 
useExactStructureID() - Method in class ambit2.core.processors.structure.key.PropertyKey
 
useExactStructureID() - Method in class ambit2.core.processors.structure.key.PubchemSID
 
useExactStructureID() - Method in class ambit2.core.processors.structure.key.SmilesKey
 
useExistingStructure - Variable in class ambit2.db.processors.RepositoryWriter
 
useHydrogens - Variable in class ambit2.descriptors.processors.AtomEnvironmentGenerator
 
useMOEvPrimitive(boolean) - Method in class ambit2.smarts.query.FastSmartsMatcher
 
useMOEvPrimitive(boolean) - Method in interface ambit2.smarts.query.ISmartsPattern
 
useMOEvPrimitive(boolean) - Method in class ambit2.smarts.query.SmartsPatternAmbit
 
useMOEvPrimitive(boolean) - Method in class ambit2.smarts.query.SmartsPatternCDK
 
useMOEvPrimitive(boolean) - Method in class ambit2.smarts.SmartsManager
 
useMolecule(IAtomContainer, int) - Method in interface ambit2.core.filter.IMoleculeFilterCondition
 
useMolecule(IAtomContainer, int) - Method in class ambit2.core.filter.IntPropertyIntervalCondition
 
useMolecule(IAtomContainer, int) - Method in class ambit2.core.filter.MoleculeFilter
 
useMolecule(IAtomContainer, int) - Method in class ambit2.core.filter.RecordIntervalCondition
 
useOriginalStructure - Variable in class ambit2.mopac.AbstractMopacShell
 
useOriginalStructure - Variable in class ambit2.some.SOMEShell
 
usePrecalculatedAtomProperties - Variable in class ambit2.db.search.structure.QuerySMARTS
 
usePreferedStructure() - Method in class ambit2.base.data.StructureRecord
 
usePreferedStructure() - Method in interface ambit2.base.interfaces.IChemical
 
usePreferedStructure() - Method in interface ambit2.base.interfaces.IStructureRecord
 
usePreferedStructure() - Method in class ambit2.base.relation.composition.CompositionRelation
 
USER - Static variable in class ambit2.base.config.Preferences
 
user - Variable in class ambit2.base.data.AbstractLabel
 
user - Variable in class ambit2.db.LoginInfo
 
userDefiendAttr - Variable in class ambit2.sln.SLNContainerAttributes
 
useRegion() - Method in class ambit2.tautomers.rules.TautomerRegion
 
userid - Variable in class ambit2.rest.task.Task
 
userName - Variable in class ambit2.base.data.SourceDataset
 
userName - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
userName - Variable in class ambit2.rest.model.builder.ExpertModelBuilder
 
userPass - Variable in class ambit2.db.processors.DbCreateDatabase
 
useSecureCookie(Request) - Method in class ambit2.rest.ProtectedResource
 
util - Variable in class ambit2.smarts.processors.SMARTSPropertiesReader
 
utils - Variable in class ambit2.smarts.processors.SMARTSPropertiesGenerator
 
Utils - Class in ambit2.ui
Useful functions.
Utils() - Constructor for class ambit2.ui.Utils
 
uuid - Variable in class ambit2.base.data.Bookmark
 
uuid - Variable in class ambit2.rest.task.CallableMockup
 
uuid - Variable in class ambit2.rest.task.CallableProtectedTask
 
uuid - Variable in class ambit2.rest.task.Task
 

V

validate(SubstanceRecord) - Method in class ambit2.base.data.study.StructureRecordValidator
 
validate(SubstanceRecord, ProtocolApplication<Protocol, IParams, String, IParams, String>) - Method in class ambit2.base.data.study.StructureRecordValidator
 
validate(SubstanceRecord, CompositionRelation) - Method in class ambit2.base.data.study.StructureRecordValidator
 
validate() - Method in class ambit2.groupcontribution.Learner
 
validation - Variable in class ambit2.groupcontribution.cli.GroupContributionCli
 
ValidationConfig - Class in ambit2.groupcontribution.utils.math
 
ValidationConfig() - Constructor for class ambit2.groupcontribution.utils.math.ValidationConfig
 
validationString - Variable in class ambit2.groupcontribution.GroupContributionModel.GCMConfigInfo
 
Value<VALUE> - Class in ambit2.base.data.study
TODO extend with a field to store the location of where the value came from make it an interface here IDataLocation and implementation in the export package
Value() - Constructor for class ambit2.base.data.study.Value
 
Value(VALUE) - Constructor for class ambit2.base.data.study.Value
 
Value(VALUE, String) - Constructor for class ambit2.base.data.study.Value
 
value - Variable in class ambit2.base.facet.AbstractFacet
 
value - Variable in class ambit2.core.data.AbstractDescriptorResultType
 
value - Variable in class ambit2.core.data.model.Parameter
 
value - Variable in class ambit2.db.search.AbstractQuery
 
value - Variable in class ambit2.db.search.property.FilteredCount
 
value - Variable in class ambit2.db.update.storedquery.FilteredSelectStoredQuery
 
value - Variable in class ambit2.export.isa.v1_0.objects.Comment
 
value - Variable in class ambit2.export.isa.v1_0.objects.FactorValue
 
value - Variable in class ambit2.export.isa.v1_0.objects.MaterialAttributeValue
 
value - Variable in class ambit2.export.isa.v1_0.objects.ProcessParameterValue
 
value - Variable in class ambit2.groupcontribution.nmr.nmr_1h.HShift
 
value - Variable in class ambit2.reactions.syntheticaccessibility.SyntheticAccessibilityManager.DescrData
 
value - Variable in class ambit2.rest.model.predictor.ExpertModelpredictor
 
Value - Class in ambit2.rules.conditions.value
 
Value() - Constructor for class ambit2.rules.conditions.value.Value
 
Value(double, IValue.Relation) - Constructor for class ambit2.rules.conditions.value.Value
 
Value(double, String) - Constructor for class ambit2.rules.conditions.value.Value
 
value - Variable in class ambit2.similarity.stats.MutableInt
 
value_dataset - Variable in class ambit2.db.update.dataset.QueryCountDatasetIntersection
 
ValueAnnotated<VALUE,IDRESULT> - Class in ambit2.base.data.study
 
ValueAnnotated() - Constructor for class ambit2.base.data.study.ValueAnnotated
 
ValueAnnotated._fields - Enum in ambit2.base.data.study
 
ValueCondition - Class in ambit2.rules.conditions
 
ValueCondition(IValue) - Constructor for class ambit2.rules.conditions.ValueCondition
 
ValueInterval - Class in ambit2.rules.conditions.value
 
ValueInterval() - Constructor for class ambit2.rules.conditions.value.ValueInterval
 
ValueInterval(double, double) - Constructor for class ambit2.rules.conditions.value.ValueInterval
 
ValueInterval(double, double, IValue.Relation, IValue.Relation) - Constructor for class ambit2.rules.conditions.value.ValueInterval
 
valueOf(String) - Static method in enum ambit2.base.config.AMBITConfig
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.config.Preferences.VINDEX
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.config.Preferences.VTAGS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.AbstractDataset._props
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.AmbitUser.USER_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.Bookmark._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.Bookmark.ResourceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Class
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ConsensusLabel.CONSENSUS_LABELS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ILiteratureEntry._type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ISelectableRecords.SELECTION_MODE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ISourceDataset.fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.ISourceDataset.license
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.Property.IO_QUESTION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.QLabel.QUALITY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study._FIELDS_RANGE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study._FIELDS_RELIABILITY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.EffectRecord._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.Protocol._categories
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.Protocol._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.ProtocolApplication._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.ReliabilityParams._r_flags
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.study.ValueAnnotated._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.substance.ParticleTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.data.SubstanceRecord.jsonSubstance
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.interfaces.ICategory.CategoryType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.interfaces.IStructureRecord.MOL_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.interfaces.IStructureRecord.STRUC_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.processors.search.AbstractFinder.MODE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.processors.search.AbstractFinder.SITE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.relation.composition.CompositionRelation.jsonFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.relation.STRUCTURE_RELATION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.base.ro.AbstractAnnotator._dictionaries
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.Algorithm.AlgorithmFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.Algorithm.requires
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.AlgorithmType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.IEvaluation.EVStatsType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.IEvaluation.EVType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.data.model.Parameter.ParameterScope
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.filter.IntPropertyIntervalCondition.PropertyType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.groups.ContainerGroup.SGROUP_MIXTURE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.groups.DataGroup.DGROUP_DISPLAY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.groups.DataGroup.SGROUP_FIELD
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ECHAPreregistrationListReader.echa_tags
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.FileState._FILE_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.I5ReaderSimple.i5_refs_attr
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.I5ReaderSimple.i5_tags
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.RawIteratingFolderReader.FileNameMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_CONNECTIVITY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_POLYMER_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_attributes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_names
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_quantity_types
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_tags
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_tags_level1
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.processors.structure.key.ExactStructureSearchMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.processors.structure.key.IStructureKey.Matcher
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.DbReader.cached_results
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.AbstractPropertyWriter.mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.AbstractRepositoryWriter.OP
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.FP1024Writer.FP1024_status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.ICommand.COMMAND
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.ProcessorOntology.OP
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.processors.ProcessorOntology.SIDE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.readers.AbstractStructureRetrieval._sqlids
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.readers.RetrieveProfileValues.SearchMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.reporters.SmilesReporter.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.results.StoredQueryTableModel.FIELDS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval._PROPERTY_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.ANNOTATIONS_TABLE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.PROPERTY_TABLE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.REFERENCE_TABLE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.SearchMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.ModelTemplates._ModelTemplates
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.PropertiesByDataset.QField
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.PropertiesByQuery.QField
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.PropertyCount.PropertyCriteria
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.property.RetrieveProfile.QueryMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.QueryCombined.COMBINE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.SQLFileQueryParams._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.structure.AbstractStructureQuery.FIELD_NAMES
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.structure.pairwise.ChemicalSpaceQuery.ChemSpaceMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.structure.pairwise.RetrieveStructurePair.rs_index
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.structure.QueryAtomEnvironment.q_modifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.search.structure.SCOPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.AbstractReadSubstance._sqlids
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.QueryCountProtocolApplications._mode_related
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.ReadSubstanceByName._namecondition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.ReadSubstanceByOwner._ownersearchmode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.ReadSubstanceByStudy._studysearchmode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix._matrix
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.bundle.UpdateBundle._published_status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.dataset.AbstractReadDataset._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.fp.QueryFingerprints._order
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.propertyannotations.ReadPropertyAnnotations._fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.AbstractKekulizationVerifier.names_index
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.AtomEnvironentMatrix._param
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.AtomEnvironmentDescriptor._param
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.processors.DescriptorValue2Property.answer
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.processors.FPTable
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.descriptors.utils.GraphMatrices.DMAtomState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.dragon.DragonShell._options
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.base.ExternalDataFileManager.StorageMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.base.ISAConst.DataFileFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.base.ISAConst.ISAFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.base.ISAConst.ISAVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.base.ISALocation.Layer
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.v1_0.objects.Data.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.export.isa.v1_0.objects.Material.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.correctionfactors.ICorrectionFactor.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.dataset.LocalProperties.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.descriptors.ILocalDescriptor.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.GroupContributionModel.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.groups.IGroup.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment.ShiftAssociation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.rules.ILocalDescriptorRule.RuleType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.groupcontribution.utils.math.CrossValidation.ObjectSelection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ml.io.app.AmbitML.out_formats
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.model.IModelStatistics.ModelStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.model.numeric.ADomainMethodType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.model.numeric.DatasetCenterPoint
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.model.structure.AtomEnvironmentDistanceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.NCISearchProcessor.METHODS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.rest.PUGRestImageRequest.IMAGE_SIZE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.rest.PUGRestImageRequest.RECORD_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_INPUT
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OPERATION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OUTPUT
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.GenericReaction.ReactionConfigStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.GenericReaction.ReactionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.GenericReaction.TransformType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.reactor.ReactorNode.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.retrosynth.IReactionSequenceHandler.EventType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.retrosynth.ReactionSequence.MoleculeStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.retrosynth.ReactionSequence.SortingMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.retrosynth.StartingMaterialsDataBase.AccessType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.retrosynth.SyntheticStrategy.ReactionCenterComplexityMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.rules.conditions.ReactionGroupCondition.RGConditionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.rules.IRetroSynthRule.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.rules.IStrategyRule.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.reactions.SimilarityManager.SimilarityTransformation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rendering.CompoundImageTools.Mode2D
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rendering.StructureEditorProcessor._commands
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.DisplayMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.freemarker.FreeMarkerStatusService.REPORT_LEVEL
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.legacy.IOTDataset.dataset_size
Deprecated.
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.legacy.OTCompound._titles
Deprecated.
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.legacy.OTDataset.dataset_size
Deprecated.
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.OpenTox.params
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.OpenTox.URI
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.Annotea.AnnoteaProperty
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.Annotea.Bookmark
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.Annotea.BookmarkProperty
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.BibTex.BTClass
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.OTA.OTAClass
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.OTA.OTAProperty
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.OTEE.OTAProperty
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.rdf.OTEE.OTEEClass
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.substance.RDFTermsSubstance
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rest.task.Task.TaskProperty
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rules.conditions.DescriptorExpression.LogicalOperation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rules.conditions.ICondition.CondType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rules.conditions.value.IValue.Relation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rules.functions.ValueTransformation.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.rules.json.JSONParsingUtils.STRUCTURE_RECORD_INPUT_INFO
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.sln.dictionary.ISLNDictionaryObject.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.sln.io.LinearNotationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.sln.SLNContainer.SLNObjectType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.DoubleBondStereoInfo.DBStereo
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.query.SmartsPatternFactory.SmartsParser
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.SmartsConst.HandleHAtoms
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.SmartsConst.SSM_MODE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.smirks.SmartsMatch.AttributeComparison
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.smirks.SmartsMatch.MatchMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.smirks.SmirksTransformationFlag
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.smarts.StereoChange.StereoElementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.some.SOMERawReader.someindex
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.structure2name.components.ComponentConnection.ConType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.structure2name.components.ComponentUtils.Comparison
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.structure2name.components.IIUPACComponent.CompState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.structure2name.components.IIUPACComponent.CompType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.TautomerConst.CanonicTautomerMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.TautomerConst.GAT
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.TautomerConst.RSM
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.TautomerRelationGraph.StructureFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.tools.TautomerAnalysis.Task
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.zwitterion.IAcidicCenter.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.tautomers.zwitterion.IBasicCenter.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ui.Panel2D._atomrendermode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ui.Panel2D.property_name
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ui.table.IBrowserMode.BrowserMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ambit2.ui.WizardPanel.ANSWER_MODE
Returns the enum constant of this type with the specified name.
ValuePair - Class in ambit2.similarity.stats
 
ValuePair(Comparable, Comparable) - Constructor for class ambit2.similarity.stats.ValuePair
 
values() - Static method in enum ambit2.base.config.AMBITConfig
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.config.Preferences.VINDEX
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.config.Preferences.VTAGS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.AbstractDataset._props
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.AmbitUser.USER_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.Bookmark._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.Bookmark.ResourceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Class
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ChEMBLProperties.ChEMBL_Property
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ConsensusLabel.CONSENSUS_LABELS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ILiteratureEntry._type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ISelectableRecords.SELECTION_MODE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ISourceDataset.fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.ISourceDataset.license
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ambit2.base.data.Profile
 
values() - Static method in enum ambit2.base.data.Property.IO_QUESTION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.QLabel.QUALITY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study._FIELDS_RANGE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study._FIELDS_RELIABILITY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study.EffectRecord._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ambit2.base.data.study.Params
 
values() - Static method in enum ambit2.base.data.study.Protocol._categories
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study.Protocol._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study.ProtocolApplication._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study.ReliabilityParams._r_flags
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.study.ValueAnnotated._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.substance.ParticleTypes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.data.SubstanceRecord.jsonSubstance
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.interfaces.ICategory.CategoryType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.interfaces.IStructureRecord.MOL_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.interfaces.IStructureRecord.STRUC_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.processors.search.AbstractFinder.MODE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.processors.search.AbstractFinder.SITE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.relation.composition.CompositionRelation.jsonFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.relation.STRUCTURE_RELATION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.base.ro.AbstractAnnotator._dictionaries
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.Algorithm.AlgorithmFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.Algorithm.requires
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.AlgorithmType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.IEvaluation.EVStatsType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.IEvaluation.EVType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.data.model.Parameter.ParameterScope
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.filter.IntPropertyIntervalCondition.PropertyType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.groups.ContainerGroup.SGROUP_MIXTURE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.groups.DataGroup.DGROUP_DISPLAY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.groups.DataGroup.SGROUP_FIELD
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ECHAPreregistrationListReader.echa_tags
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.FileState._FILE_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.I5ReaderSimple.i5_refs_attr
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.I5ReaderSimple.i5_tags
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader
 
values() - Static method in enum ambit2.core.io.RawIteratingFolderReader.FileNameMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_CONNECTIVITY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_POLYMER_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_attributes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_names
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_quantity_types
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_tags
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.io.ToXMLReaderSimple.toxml_tags_level1
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.processors.structure.key.ExactStructureSearchMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.processors.structure.key.IStructureKey.Matcher
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.DbReader.cached_results
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.AbstractPropertyWriter.mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.AbstractRepositoryWriter.OP
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.FP1024Writer.FP1024_status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.ICommand.COMMAND
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.ProcessorOntology.OP
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.processors.ProcessorOntology.SIDE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.readers.AbstractStructureRetrieval._sqlids
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.readers.RetrieveProfileValues.SearchMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.reporters.SmilesReporter.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.results.StoredQueryTableModel.FIELDS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval._PROPERTY_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.ANNOTATIONS_TABLE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.PROPERTY_TABLE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.REFERENCE_TABLE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.AbstractPropertyRetrieval.SearchMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.ModelTemplates._ModelTemplates
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.PropertiesByDataset.QField
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.PropertiesByQuery.QField
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.PropertyCount.PropertyCriteria
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.property.RetrieveProfile.QueryMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.QueryCombined.COMBINE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.SQLFileQueryParams._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.structure.AbstractStructureQuery.FIELD_NAMES
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.structure.pairwise.ChemicalSpaceQuery.ChemSpaceMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.structure.pairwise.RetrieveStructurePair.rs_index
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.structure.QueryAtomEnvironment.q_modifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.search.structure.SCOPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.AbstractReadSubstance._sqlids
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.QueryCountProtocolApplications._mode_related
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.ReadSubstanceByName._namecondition
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.ReadSubstanceByOwner._ownersearchmode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.ReadSubstanceByStudy._studysearchmode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.substance.study.SubstanceStudyFlatQuery._QUERY_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix._matrix
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.bundle.UpdateBundle._published_status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.dataset.AbstractReadDataset._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.dataset.QueryDatasetByFeatures.c_feature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.fp.QueryFingerprints._order
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.model.AbstractModelQuery._models_criteria
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.propertyannotations.ReadPropertyAnnotations._fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.db.update.storedquery.ReadStoredQuery._query
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.AbstractKekulizationVerifier.names_index
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.AtomEnvironentMatrix._param
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.AtomEnvironmentDescriptor._param
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.processors.DescriptorValue2Property.answer
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.processors.FPTable
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.descriptors.utils.GraphMatrices.DMAtomState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.dragon.DragonShell._options
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.base.ExternalDataFileManager.StorageMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.base.ISAConst.DataFileFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.base.ISAConst.ISAFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.base.ISAConst.ISAVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.base.ISALocation.Layer
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.v1_0.objects.Data.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.export.isa.v1_0.objects.Material.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.correctionfactors.ICorrectionFactor.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.dataset.LocalProperties.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.descriptors.ILocalDescriptor.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.GroupContributionModel.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.groups.IGroup.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.nmr.nmr_1h.HAtomEnvironment.ShiftAssociation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.rules.ILocalDescriptorRule.RuleType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.groupcontribution.utils.math.CrossValidation.ObjectSelection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.ml.io.app.AmbitML.out_formats
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ambit2.model.dataset.DoubleArrayDataset
 
values() - Static method in enum ambit2.model.IModelStatistics.ModelStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.model.numeric.ADomainMethodType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.model.numeric.DatasetCenterPoint
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.model.structure.AtomEnvironmentDistanceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.NCISearchProcessor.METHODS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.rest.PUGRestImageRequest.IMAGE_SIZE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.rest.PUGRestImageRequest.RECORD_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_INPUT
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OPERATION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.pubchem.rest.PUGRestRequest.COMPOUND_DOMAIN_OUTPUT
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.GenericReaction.ReactionConfigStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.GenericReaction.ReactionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.GenericReaction.TransformType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.reactor.ReactorNode.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.retrosynth.IReactionSequenceHandler.EventType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.retrosynth.ReactionSequence.MoleculeStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.retrosynth.ReactionSequence.SortingMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.retrosynth.StartingMaterialsDataBase.AccessType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.retrosynth.SyntheticStrategy.ReactionCenterComplexityMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.rules.conditions.ReactionGroupCondition.RGConditionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.rules.IRetroSynthRule.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.rules.IStrategyRule.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.reactions.SimilarityManager.SimilarityTransformation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rendering.CompoundImageTools.Mode2D
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rendering.StructureEditorProcessor._commands
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.aa.opensso.OpenSSOServicesConfig.CONFIG
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.DisplayMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.freemarker.FreeMarkerStatusService.REPORT_LEVEL
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ambit2.rest.legacy.CSVFeatureValuesIterator
Deprecated.
 
values() - Static method in enum ambit2.rest.legacy.IOTDataset.dataset_size
Deprecated.
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.legacy.OTCompound._titles
Deprecated.
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.legacy.OTDataset.dataset_size
Deprecated.
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.OpenTox.params
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.OpenTox.URI
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.Annotea.AnnoteaProperty
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.Annotea.Bookmark
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.Annotea.BookmarkProperty
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.BibTex.BTClass
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.OTA.OTAClass
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.OTA.OTAProperty
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.OTEE.OTAProperty
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.rdf.OTEE.OTEEClass
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rest.substance.RDFTermsSubstance
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ambit2.rest.task.dsl.OTDatasetReport
 
values() - Static method in enum ambit2.rest.task.Task.TaskProperty
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rules.conditions.DescriptorExpression.LogicalOperation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rules.conditions.ICondition.CondType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rules.conditions.value.IValue.Relation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rules.functions.ValueTransformation.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.rules.json.JSONParsingUtils.STRUCTURE_RECORD_INPUT_INFO
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.sln.dictionary.ISLNDictionaryObject.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.sln.io.LinearNotationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.sln.SLNContainer.SLNObjectType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.DoubleBondStereoInfo.DBStereo
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.query.SmartsPatternFactory.SmartsParser
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.SmartsConst.HandleHAtoms
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.SmartsConst.SSM_MODE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.smirks.SmartsMatch.AttributeComparison
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.smirks.SmartsMatch.MatchMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.smirks.SmirksTransformationFlag
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.smarts.StereoChange.StereoElementType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.some.SOMERawReader.someindex
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.structure2name.components.ComponentConnection.ConType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.structure2name.components.ComponentUtils.Comparison
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.structure2name.components.IIUPACComponent.CompState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.structure2name.components.IIUPACComponent.CompType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.TautomerConst.CanonicTautomerMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.TautomerConst.GAT
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.TautomerConst.RSM
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.TautomerRelationGraph.StructureFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.tools.TautomerAnalysis.Task
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.zwitterion.IAcidicCenter.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.tautomers.zwitterion.IBasicCenter.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.ui.editors.SelectFieldsPanel.MOVE
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ambit2.ui.HeaderComboBoxModel
 
values() - Static method in enum ambit2.ui.Panel2D._atomrendermode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.ui.Panel2D.property_name
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.ui.table.IBrowserMode.BrowserMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ambit2.ui.WizardPanel.ANSWER_MODE
Returns an array containing the constants of this enum type, in the order they are declared.
ValuesByTemplateReader<Result> - Class in ambit2.db.readers
Reads set of fields and values given template name
ValuesByTemplateReader() - Constructor for class ambit2.db.readers.ValuesByTemplateReader
 
ValuesQualityCheck - Class in ambit2.db.update.qlabel
Identificators correspondence between different origins the user selects key field (e.g.
ValuesQualityCheck() - Constructor for class ambit2.db.update.qlabel.ValuesQualityCheck
 
ValuesReader - Class in ambit2.db.search.property
 
ValuesReader() - Constructor for class ambit2.db.search.property.ValuesReader
 
ValuesReader(ProcessorStructureRetrieval) - Constructor for class ambit2.db.search.property.ValuesReader
 
valuesRequired - Variable in class ambit2.rest.model.predictor.ModelPredictor
 
valueTranform - Variable in class ambit2.groupcontribution.correctionfactors.DescriptorInfo
 
valueTranform - Variable in class ambit2.groupcontribution.descriptors.CDKDescriptorInfo
 
ValueTransformation - Class in ambit2.rules.functions
 
ValueTransformation() - Constructor for class ambit2.rules.functions.ValueTransformation
 
ValueTransformation.Type - Enum in ambit2.rules.functions
 
ValueTransformedGroup - Class in ambit2.groupcontribution.groups
 
ValueTransformedGroup() - Constructor for class ambit2.groupcontribution.groups.ValueTransformedGroup
 
valueTrnasformation - Variable in class ambit2.rules.weight.DescriptorWeight
 
ValueWriter<Target,Result> - Class in ambit2.db.processors
Writes values into property tables
ValueWriter() - Constructor for class ambit2.db.processors.ValueWriter
 
ValueWriterNew - Class in ambit2.db.processors
 
ValueWriterNew() - Constructor for class ambit2.db.processors.ValueWriterNew
 
variant - Variable in exception ambit2.rest.exception.RResourceException
 
VEGA_HOME - Static variable in class ambit2.vega.VegaShell
 
VegaShell - Class in ambit2.vega
Launches VEGA as external executable
VegaShell() - Constructor for class ambit2.vega.VegaShell
 
VegaShell(String) - Constructor for class ambit2.vega.VegaShell
 
verbose - Variable in class ambit2.descriptors.FunctionalGroupDescriptor
 
VerboseDescriptorResult<T,Result extends org.openscience.cdk.qsar.result.IDescriptorResult> - Class in ambit2.descriptors
 
VerboseDescriptorResult(Result, T) - Constructor for class ambit2.descriptors.VerboseDescriptorResult
 
verboseMatch - Variable in class ambit2.descriptors.FunctionalGroup
 
verboseReport - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 
verifyDXProperty(Property, Object, ILiteratureEntry) - Method in class ambit2.core.io.dx.DXParser
 
verifyEntry(File) - Method in class ambit2.core.io.ZipReader
 
verifySuperEndpoints(IStructureRecord, Property) - Method in class ambit2.core.io.dx.DXParser
 
version - Variable in class ambit2.base.data.substance.SubstanceEndpointsBundle
 
version - Static variable in class ambit2.core.config.AmbitCONSTANTS
Version
version - Static variable in class ambit2.descriptors.AbstractKekulizationVerifier
 
version - Variable in class ambit2.export.isa.v1_0.objects.OntologySourceReference
 
version - Variable in class ambit2.export.isa.v1_0.objects.Protocol
 
version - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
version_build - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
version_timestamp - Static variable in class ambit2.rest.config.AMBITAppConfigProperties
 
versionLong - Variable in class ambit2.rest.freemarker.FreeMarkerApplication
 
versionShort - Variable in class ambit2.rest.freemarker.FreeMarkerApplication
 
visibility - Variable in class ambit2.base.data.ProfileListModel
 
visibility - Variable in class ambit2.base.data.PropertiesTableModel
 
visibleFields - Variable in class ambit2.base.data.PropertiesTableModel
 
visibleIndex - Variable in class ambit2.base.data.ProfileListModel
 
visit(IRenderingElement) - Method in class ambit2.rendering.AWTDrawVisitorWithImageMap
visualizer - Variable in class ambit2.some.DescriptorSOMEShell
 

W

w - Static variable in class ambit2.core.data.EINECS
 
wait(OTRemoteTask, long) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
wait_ms - Variable in class ambit2.pubchem.NCISearchProcessor
 
waittime - Variable in class ambit2.rest.task.TaskStorage
 
WARMUP_ENABLED - Static variable in class ambit2.rest.config.AMBITAppConfigInternal
 
warnFilters - Variable in class ambit2.tautomers.FilterTautomers
 
warnFiltersOriginalPos - Variable in class ambit2.tautomers.FilterTautomers
 
warning(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler
 
warningFilters - Variable in class ambit2.tautomers.KnowledgeBase
 
warningFragments - Static variable in class ambit2.tautomers.PredefinedKnowledgeBase
 
warnings - Variable in class ambit2.groupcontribution.io.GCM2Properties
 
wasNull() - Method in class ambit2.db.results.AmbitRows
 
weight - Variable in class ambit2.rules.weight.DescriptorWeight
 
weightedNumberOfStereoElements(IAtomContainer) - Static method in class ambit2.reactions.rules.scores.MolecularComplexity
 
weights - Variable in class ambit2.featureselection.RRelieFFAttributeSelection
 
WekaModelBuilder - Class in ambit2.rest.task.weka
Builds WEKA model from ModelQueryResults.
WekaModelBuilder(Reference, ModelURIReporter, AlgorithmURIReporter, String[], String[], String) - Constructor for class ambit2.rest.task.weka.WekaModelBuilder
 
WekaPredictor<T> - Class in ambit2.rest.task.weka
Wrapper for weka models
WekaPredictor(Reference, ModelQueryResults, ModelURIReporter) - Constructor for class ambit2.rest.task.weka.WekaPredictor
 
WekaPredictor(Reference, ModelQueryResults, ModelURIReporter, String[]) - Constructor for class ambit2.rest.task.weka.WekaPredictor
 
what - Variable in class ambit2.db.cache.QueryCachedResults
 
where - Variable in class ambit2.db.readers.RetrieveField
 
where - Variable in class ambit2.db.search.property.ModelTemplates
 
where - Static variable in class ambit2.db.search.property.PropertyCount
 
where - Static variable in class ambit2.db.search.property.RetrieveFieldNames
 
where - Static variable in class ambit2.db.search.property.RetrieveFieldNamesByAlias
 
WHERE - Static variable in class ambit2.db.search.QueryUser
 
where - Static variable in class ambit2.db.search.structure.QueryDataset
 
where - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
where - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
where - Static variable in class ambit2.db.search.structure.QueryStructureByValueQuality
 
where - Static variable in class ambit2.db.search.structure.QueryStructureType
 
where - Static variable in class ambit2.db.search.structure.QueryStrucType
 
where - Static variable in class ambit2.db.update.reference.ReadReference
 
where_all - Variable in class ambit2.db.search.structure.QueryFieldNumeric
 
where_and - Static variable in class ambit2.db.update.storedquery.DeleteStoredQuery
 
where_equal - Variable in class ambit2.db.search.structure.QueryFieldNumeric
 
where_group - Static variable in class ambit2.db.search.structure.AbstractStructureQuery
 
where_name - Static variable in class ambit2.db.facets.datasets.PrefixFacetQuery
 
where_name - Static variable in class ambit2.db.search.property.PropertyStatsString
 
where_name - Variable in class ambit2.db.search.structure.QueryFieldNumeric
 
WHERE_NAME - Static variable in class ambit2.db.search.structure.QueryMissingDescriptor
 
where_name - Static variable in class ambit2.db.search.structure.QueryStoredResults
 
where_null - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
where_null - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
where_null - Static variable in class ambit2.db.search.structure.QueryStructureByValueQuality
 
where_null - Static variable in class ambit2.db.search.structure.QueryStructureType
 
where_query - Static variable in class ambit2.db.search.structure.QueryStoredResults
 
where_query - Static variable in class ambit2.db.update.storedquery.DeleteStoredQuery
 
where_query - Static variable in class ambit2.db.update.storedquery.SearchStoredQueries
 
where_session - Static variable in class ambit2.db.update.storedquery.DeleteStoredQuery
 
where_session - Static variable in class ambit2.db.update.storedquery.SearchStoredQueries
 
where_struc_dataset - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
where_struc_dataset - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
where_struc_dataset - Static variable in class ambit2.db.search.structure.QueryStructureType
 
where_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureByQuality
 
where_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
where_struc_query - Static variable in class ambit2.db.search.structure.QueryStructureType
 
where_text - Static variable in class ambit2.db.search.structure.QueryStructureByQualityPairLabel
 
WHERE_TITLE - Static variable in class ambit2.db.search.structure.QueryMissingDescriptor
 
where_value - Static variable in class ambit2.db.search.property.PropertyStatsString
 
whereID - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
whereID - Static variable in class ambit2.db.update.queryfolder.ReadQueryFolder
 
whereLabel - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
whereLabel - Variable in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
whereLabel - Variable in class ambit2.db.update.qlabel.DeleteValueQLabel
 
whereName - Variable in class ambit2.db.search.property.ModelTemplates
 
whereName - Static variable in class ambit2.db.update.queryfolder.ReadQueryFolder
 
whereproperty - Static variable in class ambit2.db.search.property.PropertiesByQuery
 
wherepropertyName - Static variable in class ambit2.db.search.property.PropertiesByDataset
 
wherepropertyName - Static variable in class ambit2.db.search.property.PropertiesByQuery
 
whereRecalls - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
whereStructure - Variable in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
whereType - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
whereUser - Static variable in class ambit2.db.update.bookmark.ReadBookmark
 
whereUser - Variable in class ambit2.db.update.qlabel.DeleteStructureQLabel
 
whereUser - Variable in class ambit2.db.update.qlabel.DeleteValueQLabel
 
whereUser - Static variable in class ambit2.db.update.queryfolder.ReadQueryFolder
 
whereValue - Variable in class ambit2.db.update.qlabel.DeleteValueQLabel
 
whiteTransparent - Static variable in class ambit2.rendering.CompoundImageTools
 
width - Variable in class ambit2.db.chart.ChartGenerator
 
width - Variable in class ambit2.pubchem.rest.PUGRestImageRequest
 
width - Variable in class ambit2.search.csls.CSLSImageRequest
 
widthUnits2Millimetres(short) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
Convert Excels width units into millimetres.
widthUnits2Pixel(short) - Static method in class ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits
excel width units(units of 1/256th of a character width) to pixel units.
withAlgorithm(OTAlgorithm) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
withAlgorithm(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withCreator(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withDatasetService(Reference) - Method in interface ambit2.rest.legacy.IOTDataset
Deprecated.
 
withDatasetService(Reference) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Specify which dataset service to use for results
withDatasetService(String) - Method in interface ambit2.rest.legacy.IOTModel
Deprecated.
Specify which dataset service to use for results
withDatasetService(Reference) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
withDatasetService(String) - Method in class ambit2.rest.legacy.OTContainers
Deprecated.
 
withDatasetService(Reference) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
withDatasetService(String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
withDatasetService(Reference) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withDatasetService(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withFeatureService(Reference) - Method in interface ambit2.rest.legacy.IOTFeature
Deprecated.
 
withFeatureService(Reference) - Method in class ambit2.rest.legacy.OTFeature
Deprecated.
 
withName(String) - Method in interface ambit2.rest.legacy.IOTObject
Deprecated.
 
withName(String) - Method in class ambit2.rest.legacy.OTDataset
Deprecated.
 
withName(String) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
withOntologyService(String) - Method in class ambit2.rest.task.dsl.OTDatasetComparisonReport
 
withParams(Form) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
withParams(String, String) - Method in class ambit2.rest.legacy.OTAlgorithm
Deprecated.
 
withParams(Form) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withParams(String, String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
withParams(Form) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
withParams(String, String) - Method in class ambit2.rest.legacy.OTObject
Deprecated.
 
withTrainingData(String) - Method in class ambit2.rest.legacy.OTModel
Deprecated.
 
WizardPanel - Class in ambit2.ui
 
WizardPanel(String, Component, String) - Constructor for class ambit2.ui.WizardPanel
 
WizardPanel.ANSWER_MODE - Enum in ambit2.ui
 
workbook - Variable in class ambit2.core.io.IteratingXLSReader
 
workbook - Variable in class ambit2.core.io.XLSFileWriter
 
workbook - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
workFolder - Variable in class ambit2.base.external.CommandShell
 
workingRecord - Variable in class ambit2.db.results.StoredQueryTableModel
 
WrappedService<C extends org.apache.http.auth.Credentials> - Class in ambit2.rest.wrapper
 
WrappedService() - Constructor for class ambit2.rest.wrapper.WrappedService
 
wrapup() - Method in class ambit2.db.reporters.QueryPacketReporter
 
write(Writer) - Method in interface ambit2.base.processors.IAmbitResult
Writes the object
write(IChemObject) - Method in class ambit2.core.io.ArffWriter
 
write(IChemObject) - Method in class ambit2.core.io.DelimitedFileWriter
 
write(IChemObject) - Method in class ambit2.core.io.FileWithHeaderWriter
 
write(IChemObject) - Method in class ambit2.core.io.fp.MultiFingerprintsWriter
 
write(IChemObject) - Method in class ambit2.core.io.PDFWriter
 
write(Document, Content) - Method in class ambit2.core.processors.ProcessorFileExport
 
write(Target) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
write(Property) - Method in class ambit2.db.processors.AbstractPropertyWriter
 
write(Target) - Method in class ambit2.db.processors.AbstractRepositoryWriter
 
write(IStructureRecord) - Method in class ambit2.db.processors.DbStructureWriter
 
write(IStructureRecord) - Method in class ambit2.db.processors.FP1024Writer
 
write(IAtomContainer) - Method in class ambit2.db.processors.PropertyImporter
 
write(IStructureRecord) - Method in class ambit2.db.processors.PropertyValuesWriter
 
write(IStructureRecord) - Method in class ambit2.db.processors.RepositoryWriter
 
write(IStructureRecord) - Method in class ambit2.db.processors.ValueWriterNew
 
write(Writer) - Method in class ambit2.descriptors.processors.AtomEnvironmentList
 
write(IChemObject) - Method in class ambit2.mopac.Mopac7Writer
 
write(Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
write(Writer) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
writeAnnotationPropertyTriple(XMLStreamWriter, String) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
writeAnnotations(Template, UpdateExecutor) - Method in class ambit2.rest.model.task.CallableModelCreator
 
writeAtom(IAtom, double, double, double, int) - Method in class ambit2.mopac.Mopac7Writer
 
writeBitSetValue(int, BitSet, long, FP1024Writer.FP1024_status) - Method in class ambit2.db.processors.FP1024Writer
 
writeClassTriple(XMLStreamWriter, OT.OTClass) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
Writes OWL class triple.
writeCompoundURI - Variable in class ambit2.db.reporters.CSVReporter
 
writeData(int, String, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
writeData(int, List<String>, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
writeDataPropertyTriple(XMLStreamWriter, OT.DataProperty) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
 
writeDataset(IStructureRecord) - Method in class ambit2.db.processors.DbStructureWriter
 
writeDataset(IStructureRecord) - Method in class ambit2.db.processors.PropertyImporter
 
writeEndpoint(String, String, EffectRecord<String, IParams, String>) - Method in class ambit2.rest.substance.SubstanceRecordStaxWriter
33.4889 Potency
writeHasSource(Property) - Method in class ambit2.rest.dataset.DatasetRDFWriter
writeHeader() - Method in class ambit2.core.io.ArffWriter
 
writeHeader() - Method in class ambit2.core.io.DelimitedFileWriter
 
writeHeader() - Method in class ambit2.core.io.FilesWithHeaderWriter
 
writeHeader() - Method in class ambit2.core.io.FileWithHeaderWriter
 
writeHeader() - Method in class ambit2.core.io.PDFWriter
 
writeHeader() - Method in class ambit2.core.io.XLSFileWriter
 
writeHeader(Writer) - Method in class ambit2.db.reporters.ARFFReporter
 
writeHeader(Writer) - Method in class ambit2.db.reporters.CSVReporter
 
writeHeader(Document) - Method in class ambit2.db.reporters.PDFReporter
 
writeHeader(Writer) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
writeHeader(Writer) - Method in class ambit2.rest.task.dsl.OTDatasetTableReport
 
writeHTML(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport
 
writeIdentifiers(Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
writeInputSDF(String, IAtomContainer) - Method in class ambit2.balloon.ShellBalloon
 
writeInputSDF(String, IAtomContainer) - Method in class ambit2.core.external.ShellSDFoutput
 
writeMatrix(Matrix, ObjectOutputStream) - Method in class ambit2.model.numeric.DataCoverageLeverage
 
writeMatrix(Matrix, ObjectOutputStream) - Method in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
writeMeasurementgroups(String, List<ProtocolApplication>) - Method in class ambit2.rest.substance.SubstanceRecordStaxWriter
2015-06-13-05:00 ...
writeMessages(String[], int, int) - Method in class ambit2.descriptors.processors.DescriptorCalculationProcessor
 
writeMessages(String[], int, int) - Method in class ambit2.rest.model.predictor.ModelPredictor
 
writeModels(int, String, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetRDFReport
 
writeMolecule(IAtomContainer) - Method in class ambit2.core.io.DelimitedFileWriter
 
writeMolecule(IAtomContainer) - Method in class ambit2.core.io.FileWithHeaderWriter
 
writeMolecule(IAtomContainer) - Method in class ambit2.core.io.PDFWriter
 
writeMolecule(IAtomContainer) - Method in class ambit2.core.io.XLSFileWriter
 
writeMolecule(IAtomContainer) - Method in class ambit2.db.reporters.PDFReporter
 
writeObjectPropertyTriple(XMLStreamWriter, OT.OTProperty) - Method in class ambit2.rest.dataset.AbstractStaxRDFWriter
Writes OWL object property triple.
writePDF(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport
 
writeProperties(IStructureRecord) - Method in class ambit2.db.processors.DbStructureWriter
 
writeProperties - Variable in class ambit2.db.reporters.SmilesReporter
 
writer - Variable in class ambit2.core.io.ArffWriter
 
writer - Variable in class ambit2.core.io.DelimitedFileWriter
 
writer - Variable in class ambit2.core.io.RawIteratingWrapper
 
writer - Variable in class ambit2.db.processors.DescriptorsCalculator
 
writer - Variable in class ambit2.db.search.structure.pairwise.PairPropertiesWriter
 
writer - Variable in class ambit2.db.substance.processor.DBMatrixValueMarker
 
writeRow(int, List<String>, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetReport
 
writeRow(int, List<String>, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetScrollableReport
 
writeRow(int, List<String>, Writer) - Method in class ambit2.rest.task.dsl.OTDatasetTableReport
 
writeRTF(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport
 
writeSDF(Content, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport
 
writeSetOfMolecules(IAtomContainerSet) - Method in class ambit2.core.io.DelimitedFileWriter
 
writeSetOfMolecules(IAtomContainerSet) - Method in class ambit2.core.io.FileWithHeaderWriter
 
writeSetOfMolecules(IAtomContainerSet) - Method in class ambit2.core.io.PDFWriter
 
writeStructure(IStructureRecord, boolean) - Method in class ambit2.db.processors.DbStructureWriter
 
writeToCfg(GroupContributionModel, String) - Static method in class ambit2.groupcontribution.io.ModelWriter
 
writeToXML(GroupContributionModel, String) - Static method in class ambit2.groupcontribution.io.ModelWriter
 
writeXLS(Content, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport
 
writingStarted - Variable in class ambit2.core.io.FilesWithHeaderWriter
 
writingStarted - Variable in class ambit2.core.io.FileWithHeaderWriter
 
writingStarted - Variable in class ambit2.core.io.XLSFileWriter
 
writingStarted - Variable in class ambit2.db.reporters.xlsx.AbstractXLSXReporter
 
www - Variable in class ambit2.base.data.AmbitUser
 
www - Variable in class ambit2.ui.editors.AmbitUserEditor
 

X

X - Static variable in class ambit2.base.ro.I5CONSTANTS
 
X - Variable in class ambit2.model.numeric.DataCoverageLeverage
 
X - Variable in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 
XLSFileFormat - Class in ambit2.core.io
Microsoft Excel XLS file format.
XLSFileFormat() - Constructor for class ambit2.core.io.XLSFileFormat
 
XLSFileWriter - Class in ambit2.core.io
 
XLSFileWriter(OutputStream, Boolean) - Constructor for class ambit2.core.io.XLSFileWriter
 
XSDDouble - Static variable in class ambit2.db.search.property.AbstractPropertyRetrieval
 
XSDInt - Static variable in class ambit2.db.search.property.AbstractPropertyRetrieval
 
XSDString - Static variable in class ambit2.db.search.property.AbstractPropertyRetrieval
 
XTabChartGenerator - Class in ambit2.db.chart
select group_concat(distinct b),a-mod(a,10), count(*) from ( select a,b from ( select value_num as a,idchemical from query_results join property_values using(idstructure) join properties using(idproperty) where name = "LLNA EC3 %" and idquery=2 group by idchemical,value_num ) as X join ( select value as b,idchemical from query_results join property_values using(idstructure) join property_string using(idvalue_string) join properties using(idproperty) where name = "Michael Acceptors" and idquery=2 group by idchemical,value_num ) as Y using(idchemical) ) as p group by b,a-mod(a,10)
XTabChartGenerator() - Constructor for class ambit2.db.chart.XTabChartGenerator
 
XTX1 - Variable in class ambit2.model.numeric.DataCoverageLeverage
 
XTX1 - Variable in class ambit2.model.numeric.DataCoverageLeverageHatMatrix
 

Y

Y - Static variable in class ambit2.base.ro.I5CONSTANTS
 
yieldHi - Variable in class ambit2.reactions.GenericReaction
 
yieldLo - Variable in class ambit2.reactions.GenericReaction
 
yieldScore - Variable in class ambit2.reactions.rules.scores.ReactionScore
 
yieldScoreWeight - Variable in class ambit2.reactions.rules.scores.ReactionScoreSchema
 
yScrambling - Variable in class ambit2.groupcontribution.GCMTestConfig
 
yScramblingIterations - Variable in class ambit2.groupcontribution.utils.math.ValidationConfig
 

Z

Z - Static variable in class ambit2.base.ro.I5CONSTANTS
 
zero - Static variable in class ambit2.base.processors.CASProcessor
 
zeroBits(List<BitSet>) - Method in class ambit2.model.structure.DataCoverageFingeprintsMissingFragments
 
ZipReader<OPTIONS> - Class in ambit2.core.io
 
ZipReader(File) - Constructor for class ambit2.core.io.ZipReader
 
ZipReader(File, OPTIONS) - Constructor for class ambit2.core.io.ZipReader
 
ZipReader(InputStream) - Constructor for class ambit2.core.io.ZipReader
 
ZipReader(InputStream, OPTIONS) - Constructor for class ambit2.core.io.ZipReader
 
zoom(double, double) - Method in class ambit2.ui.table.BrowsableTableModel
 
zoom(double, double) - Method in enum ambit2.ui.table.IBrowserMode.BrowserMode
 
zoom(double, double) - Method in interface ambit2.ui.table.IBrowserMode
 
zoomFactor - Variable in class ambit2.ui.table.BrowsableTableModel
 
zoomIn - Variable in class ambit2.ui.table.BrowserModeNavigator
 
zoomOut - Variable in class ambit2.ui.table.BrowserModeNavigator
 
zwitterionCounts - Variable in class ambit2.tautomers.zwitterion.ZwitterionManager
 
ZwitterionManager - Class in ambit2.tautomers.zwitterion
 
ZwitterionManager() - Constructor for class ambit2.tautomers.zwitterion.ZwitterionManager
 

_

_FIELDS_RANGE - Enum in ambit2.base.data.study
 
_FIELDS_RELIABILITY - Enum in ambit2.base.data.study
 
_FPLength - Static variable in class ambit2.core.data.MoleculeTools
 
_idmode - Variable in class ambit2.db.update.bundle.ReadBundle
 
_MAX_COL - Static variable in class ambit2.core.io.study.StudyFormatter
 
_NS - Static variable in class ambit2.rest.rdf.BibTex
The namespace of the vocabulary as a string ("http://purl.org/net/nknouf/ns/bibtex#%s")
_NS - Static variable in class ambit2.rest.rdf.OTA
The namespace of the vocabalary as a string ("http://www.opentox.org/algorithmTypes.owl#%s")
_NS - Static variable in class ambit2.rest.rdf.OTEE
The namespace of the vocabalary as a string ("http://www.opentox.org/echaEndpoints.owl#%s")
_NS_ANNOTEA - Static variable in class ambit2.rest.rdf.Annotea
 
_NS_BOOKMARK - Static variable in class ambit2.rest.rdf.Annotea
 
_quote(JsonNode, String) - Static method in class ambit2.rest.study.BucketJson2CSVConvertor
 
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