Serialized Form (Ambit 2 4.0.1-SNAPSHOT API)

Package ambit2.balloon
- Class ambit2.balloon.ShellBalloon extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -872897475497724440L
  - Serialized Fields
    - hydrogens
```
boolean hydrogens
```
- Class ambit2.balloon.ShellBalloonWeb extends ShellBalloon implements Serializable
  
  serialVersionUID:
  
  -2707542734736846L
Package ambit2.base.data
- Class ambit2.base.data.AbstractDataset extends Object implements Serializable
  
  serialVersionUID:
  
  5988138848650016188L
  - Serialized Fields
    - ID
```
int ID
```
    - stars
```
int stars
```
    - properties
```
Hashtable<K,V> properties
```
- Class ambit2.base.data.AbstractLabel extends AmbitBean implements Serializable
  
  serialVersionUID:
  
  1373737719026207986L
  - Serialized Fields
    - label
```
Enum<E extends Enum<E>> label
```
    - user
```
AmbitUser user
```
    - text
```
String text
```
- Class ambit2.base.data.AmbitBean extends Object implements Serializable
  
  serialVersionUID:
  
  8003586225449465693L
- Class ambit2.base.data.Bookmark extends Object implements Serializable
  
  serialVersionUID:
  
  -7323544303939680815L
  - Serialized Fields
    - uuid
```
String uuid
```
    - relevance
```
double relevance
```
    - type
```
String type
```
    - id
```
int id
```
    - creator
```
String creator
```
    - recalls
```
String recalls
```
    - hasTopic
```
String hasTopic
```
    - title
```
String title
```
    - description
```
String description
```
    - created
```
long created
```
    - date
```
long date
```
- Class ambit2.base.data.ConsensusLabel extends AbstractLabel<ConsensusLabel.CONSENSUS_LABELS> implements Serializable
  
  serialVersionUID:
  
  1008781131664292956L
- Class ambit2.base.data.Dictionary extends Property implements Serializable
  
  serialVersionUID:
  
  -1091010081539426004L
  - Serialized Fields
    - relationship
```
String relationship
```
- Class ambit2.base.data.Endpoints extends Template implements Serializable
  
  serialVersionUID:
  
  -4825889208945754441L
- Class ambit2.base.data.LiteratureEntry extends AmbitBean implements Serializable
  
  serialVersionUID:
  
  -3089173811051934066L
  - Serialized Fields
    - title
```
String title
```
    - URL
```
String URL
```
    - id
```
int id
```
    - editable
```
boolean editable
```
    - type
```
ILiteratureEntry._type type
```
- Class ambit2.base.data.PredictedVarsTemplate extends Template implements Serializable
  
  serialVersionUID:
  
  1924945482444230735L
- Class ambit2.base.data.Profile extends Object implements Serializable
  
  serialVersionUID:
  
  5818041819278493531L
  - Serialized Fields
    - container
```
ArrayList<E> container
```
    - name
```
String name
```
- Class ambit2.base.data.ProfileListModel extends AbstractListModel implements Serializable
  
  serialVersionUID:
  
  -7758488965678782461L
  - Serialized Fields
    - fields
```
TypedListModel<P> fields
```
    - visibleIndex
```
List<E> visibleIndex
```
    - visibility
```
Boolean visibility
```
- Class ambit2.base.data.PropertiesTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  -4031712164231916058L
  - Serialized Fields
    - visibleFields
```
List<E> visibleFields
```
    - visibility
```
boolean visibility
```
    - columns
```
int columns
```
- Class ambit2.base.data.Property extends Object implements Serializable
  
  serialVersionUID:
  
  -6813235410505542235L
  - Serialized Fields
    - annotations
```
PropertyAnnotations annotations
```
    - isNominal
```
boolean isNominal
```
    - name
```
String name
```
    - label
```
String label
```
    - units
```
String units
```
    - id
```
int id
```
    - order
```
int order
```
    - clazz
```
Class<T> clazz
```
    - enabled
```
boolean enabled
```
    - reference
```
ILiteratureEntry reference
```
    - allowedValues
```
List<E> allowedValues
```
- Class ambit2.base.data.PropertyAnnotation extends Object implements Serializable
  
  serialVersionUID:
  
  6469337758176216737L
  - Serialized Fields
    - idproperty
```
int idproperty
```
    - type
```
String type
```
    - predicate
```
String predicate
```
    - object
```
Object object
```
- Class ambit2.base.data.PropertyAnnotations extends ArrayList<PropertyAnnotation> implements Serializable
  
  serialVersionUID:
  
  -1776802858368833193L
- Class ambit2.base.data.QLabel extends AbstractLabel<QLabel.QUALITY> implements Serializable
  
  serialVersionUID:
  
  6648276842177265920L
- Class ambit2.base.data.SelectionBean extends AmbitBean implements Serializable
  
  serialVersionUID:
  
  -4069289362667504269L
  - Serialized Fields
    - options
```
List<E> options
```
    - selected
```
int selected
```
    - title
```
String title
```
- Class ambit2.base.data.SourceDataset extends AmbitBean implements Serializable
  
  serialVersionUID:
  
  6881106188176017447L
  - Serialized Fields
    - reference
```
ILiteratureEntry reference
```
    - stars
```
int stars
```
    - licenseURI
```
String licenseURI
```
    - rightsHolder
```
String rightsHolder
```
    - maintainer
```
String maintainer
```
    - id
```
int id
```
    - name
```
String name
```
    - userName
```
String userName
```
- Class ambit2.base.data.StructureRecord extends Object implements Serializable
  
  serialVersionUID:
  
  -650816773926953033L
  - Serialized Fields
    - preferedStructure
```
boolean preferedStructure
```
    - dataEntryID
```
int dataEntryID
```
    - id_srcdataset
```
int id_srcdataset
```
    - inchiKey
```
String inchiKey
```
    - formula
```
String formula
```
    - smiles
```
String smiles
```
    - inchi
```
String inchi
```
    - idchemical
```
int idchemical
```
    - idstructure
```
int idstructure
```
    - content
```
String content
```
    - format
```
String format
```
    - reference
```
ILiteratureEntry reference
```
    - properties
```
Map<K,V> properties
```
    - type
```
IStructureRecord.STRUC_TYPE type
```
    - selected
```
boolean selected
```
    - facets
```
List<E> facets
```
- Class ambit2.base.data.SubstanceRecord extends StructureRecord implements Serializable
  
  serialVersionUID:
  
  -6844893699492741683L
  - Serialized Fields
    - externalids
```
List<E> externalids
```
    - ownerUUID
```
String ownerUUID
```
    - ownerName
```
String ownerName
```
    - idsubstance
```
int idsubstance
```
    - substancetype
```
String substancetype
```
    - internalName
```
String internalName
```
    - publicName
```
String publicName
```
    - internalUUID
```
String internalUUID
```
    - refsubstance_uuid
```
String refsubstance_uuid
```
    - measurements
```
List<E> measurements
```
    - relatedStructures
```
List<E> relatedStructures
```
- Class ambit2.base.data.Template extends Profile<Property> implements Serializable
  
  serialVersionUID:
  
  -9152728910421949089L
  - Serialized Fields
    - id
```
int id
```
Package ambit2.base.data.study
- Class ambit2.base.data.study.EffectRecord extends Object implements Serializable
  
  serialVersionUID:
  
  7520767344716433227L
  - Serialized Fields
    - sampleID
```
String sampleID
```
    - unit
```
Object unit
```
    - loQualifier
```
String loQualifier
```
    - loValue
```
Double loValue
```
    - upQualifier
```
String upQualifier
```
    - upValue
```
Double upValue
```
    - conditions
```
Object conditions
```
    - textValue
```
Object textValue
```
    - errQualifier
```
String errQualifier
```
    - errValue
```
Double errValue
```
    - idresult
```
int idresult
```
    - endpointGroup
```
Integer endpointGroup
```
    - endpointSynonyms
```
List<E> endpointSynonyms
```
    - endpoint
```
Object endpoint
```
    - endpointType
```
String endpointType
```
- Class ambit2.base.data.study.MultiValue extends ArrayList<V extends IValue> implements Serializable
  
  serialVersionUID:
  
  3939120449104897901L
- Class ambit2.base.data.study.ProtocolApplication extends Object implements Serializable
  
  serialVersionUID:
  
  747315722852709360L
  - Serialized Fields
    - reliability
```
ReliabilityParams<VALUE> reliability
```
    - interpretationResult
```
String interpretationResult
```
    - interpretationCriteria
```
String interpretationCriteria
```
    - parameters
```
Object parameters
```
    - reference
```
ambit2.base.data.study.Citation reference
```
    - effects
```
List<E> effects
```
    - companyName
```
String companyName
```
    - protocol
```
Object protocol
```
    - substanceUUID
```
String substanceUUID
```
    - companyUUID
```
String companyUUID
```
    - documentUUID
```
String documentUUID
```
    - investigationUUID
```
UUID investigationUUID
```
    - assayUUID
```
UUID assayUUID
```
    - updated
```
Date updated
```
    - referenceSubstanceUUID
```
String referenceSubstanceUUID
```
- Class ambit2.base.data.study.ProtocolApplicationAnnotated extends ProtocolApplication<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT> implements Serializable
  
  serialVersionUID:
  
  -8229267088974835650L
  - Serialized Fields
    - records_to_delete
```
List<E> records_to_delete
```
- Class ambit2.base.data.study.ProtocolEffectRecord extends EffectRecord<ENDPOINT,CONDITIONS,UNIT> implements Serializable
  
  serialVersionUID:
  
  7123248041424144730L
  - Serialized Fields
    - protocol
```
Protocol protocol
```
    - documentUUID
```
String documentUUID
```
    - studyResultType
```
String studyResultType
```
    - interpretationResult
```
String interpretationResult
```
- Class ambit2.base.data.study.ProtocolEffectRecordMatrix extends ProtocolEffectRecord<ENDPOINT,CONDITIONS,UNIT> implements Serializable
  
  serialVersionUID:
  
  7153942724319574909L
  - Serialized Fields
    - record_copied
```
boolean record_copied
```
    - record_deleted
```
boolean record_deleted
```
    - record_remarks
```
String record_remarks
```
    - protocolapp_copied
```
boolean protocolapp_copied
```
    - protocolapp_deleted
```
boolean protocolapp_deleted
```
    - protocolapp_remarks
```
String protocolapp_remarks
```
- Class ambit2.base.data.study.StructureRecordValidator extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  201323883830157691L
  - Serialized Fields
    - fixErrors
```
boolean fixErrors
```
    - prefix
```
String prefix
```
    - filename
```
String filename
```
- Class ambit2.base.data.study.ValueAnnotated extends Value<VALUE> implements Serializable
  
  serialVersionUID:
  
  5475187477998823176L
  - Serialized Fields
    - idresult
```
Object idresult
```
    - copied
```
boolean copied
```
    - deleted
```
boolean deleted
```
    - remark
```
String remark
```
    - textValue
```
String textValue
```
Package ambit2.base.data.substance
- Class ambit2.base.data.substance.SubstanceEndpointsBundle extends Object implements Serializable
  
  serialVersionUID:
  
  5712705809909948536L
  - Serialized Fields
    - title
```
String title
```
    - url
```
String url
```
    - stars
```
int stars
```
    - licenseURI
```
String licenseURI
```
    - rightsHolder
```
String rightsHolder
```
    - maintainer
```
String maintainer
```
    - name
```
String name
```
    - id
```
int id
```
    - userName
```
String userName
```
    - description
```
String description
```
    - bundle_number
```
UUID bundle_number
```
    - status
```
String status
```
    - referenceID
```
int referenceID
```
    - version
```
int version
```
    - created
```
long created
```
    - updated
```
long updated
```
- Class ambit2.base.data.substance.SubstanceName extends Property implements Serializable
  
  serialVersionUID:
  
  4436949404781828869L
- Class ambit2.base.data.substance.SubstanceOwner extends Property implements Serializable
  
  serialVersionUID:
  
  -7547507885884497869L
- Class ambit2.base.data.substance.SubstanceProperty extends Property implements Serializable
  
  serialVersionUID:
  
  4436949404781828869L
  - Serialized Fields
    - studyResultType
```
ReliabilityParams._r_flags studyResultType
```
    - extendedURI
```
boolean extendedURI
```
    - topcategory
```
String topcategory
```
    - endpointcategory
```
String endpointcategory
```
    - identifier
```
String identifier
```
- Class ambit2.base.data.substance.SubstancePropertyCategory extends SubstanceProperty implements Serializable
  
  serialVersionUID:
  
  -4004185521269367373L
- Class ambit2.base.data.substance.SubstancePublicName extends Property implements Serializable
  
  serialVersionUID:
  
  3780278515180239734L
- Class ambit2.base.data.substance.SubstanceUUID extends Property implements Serializable
  
  serialVersionUID:
  
  803512807002064994L
Package ambit2.base.exceptions
- Class ambit2.base.exceptions.AmbitIOException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  1758487706878089791L
- Class ambit2.base.exceptions.EmptyMoleculeException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  -7714390627755560814L
- Class ambit2.base.exceptions.HttpException extends ProcessorException implements Serializable
  
  serialVersionUID:
  
  6554884630280756615L
  - Serialized Fields
    - code
```
int code
```
    - url
```
String url
```
- Class ambit2.base.exceptions.NoDocumentUUIDException extends Exception implements Serializable
  
  serialVersionUID:
  
  -6250930399927583056L
  - Serialized Fields
    - papp
```
ProtocolApplication<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT> papp
```
- Class ambit2.base.exceptions.PropertyNotInTemplateException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  -5322902406955300615L
  - Serialized Fields
    - key
```
Object key
```
    - template
```
Template template
```
- Class ambit2.base.exceptions.QSARModelException extends Exception implements Serializable
  
  serialVersionUID:
  
  4931287199065879144L
Package ambit2.base.external
- Class ambit2.base.external.CommandShell extends Object implements Serializable
  
  serialVersionUID:
  
  -5771392099125415099L
  - Serialized Fields
    - prefix
```
String prefix
```
    - workFolder
```
String workFolder
```
    - logger
```
Logger logger
```
    - executables
```
Hashtable<K,V> executables
```
    - inputFile
```
String inputFile
```
    - outputFile
```
String outputFile
```
    - runAsync
```
boolean runAsync
```
    - enabled
```
boolean enabled
```
    - exitCode
```
int exitCode
```
- Class ambit2.base.external.ShellException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  992938262318013309L
  - Serialized Fields
    - shell
```
CommandShell<INPUT,OUTPUT> shell
```
Package ambit2.base.facet
- Class ambit2.base.facet.AbstractFacet extends Object implements Serializable
  
  serialVersionUID:
  
  1486718382701377463L
  - Serialized Fields
    - url
```
String url
```
    - count
```
int count
```
    - value
```
Object value
```
- Class ambit2.base.facet.BundleRoleFacet extends AbstractFacet<SubstanceEndpointsBundle> implements Serializable
  
  serialVersionUID:
  
  4897070929247809353L
  - Serialized Fields
    - tag
```
String tag
```
    - remarks
```
String remarks
```
- Class ambit2.base.facet.SubstanceStudyFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  9014078415852427522L
  - Serialized Fields
    - subcategory
```
String subcategory
```
    - sortingOrder
```
int sortingOrder
```
    - interpretation_result
```
String interpretation_result
```
Package ambit2.base.interfaces
Package ambit2.base.processors
- Class ambit2.base.processors.CASProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<String,String> implements Serializable
  
  serialVersionUID:
  
  144610103301504232L
- Class ambit2.base.processors.ProcessorException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  7644140308982655059L
  - Serialized Fields
    - processor
```
net.idea.modbcum.i.processors.IProcessor<Target,Result> processor
```
- Class ambit2.base.processors.StructureRecordsAppender extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  8988481466533697624L
  - Serialized Fields
    - records
```
List<E> records
```
Package ambit2.base.processors.batch
- Class ambit2.base.processors.batch.BatchProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<INPUT,net.idea.modbcum.i.batch.IBatchStatistics> implements Serializable
  
  serialVersionUID:
  
  -5659435501205598414L
  - Serialized Fields
    - processor
```
net.idea.modbcum.i.processors.ProcessorsChain<Target,Result,P extends net.idea.modbcum.i.processors.IProcessor> processor
```
    - cancelled
```
boolean cancelled
```
    - timeout
```
long timeout
```
- Class ambit2.base.processors.batch.BatchReporter extends net.idea.modbcum.p.DefaultAmbitProcessor<ItemList,Output> implements Serializable
  
  serialVersionUID:
  
  -3398613304724941241L
  - Serialized Fields
    - output
```
Object output
```
    - batch
```
BatchProcessor<INPUT,Target> batch
```
    - licenseURI
```
String licenseURI
```
    - processors
```
net.idea.modbcum.i.processors.ProcessorsChain<Target,Result,P extends net.idea.modbcum.i.processors.IProcessor> processors
```
- Class ambit2.base.processors.batch.ListReporter extends BatchReporter<Item,Iterator<Item>,Output> implements Serializable
  
  serialVersionUID:
  
  3018737752170422730L
Package ambit2.base.processors.search
- Class ambit2.base.processors.search.AbstractFinder extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  2897055153094159861L
  - Serialized Fields
    - request
```
Object request
```
    - profile
```
Template profile
```
    - mode
```
AbstractFinder.MODE mode
```
Package ambit2.base.relation
- Class ambit2.base.relation.AbstractRelation extends Object implements Serializable
  
  serialVersionUID:
  
  -6592354650015575251L
  - Serialized Fields
    - structure1
```
IStructureRecord structure1
```
    - structure2
```
IStructureRecord structure2
```
    - relation
```
Serializable relation
```
    - relationType
```
Object relationType
```
    - name
```
String name
```
- Class ambit2.base.relation.SimilarityRelation extends StructureRelation implements Serializable
  
  serialVersionUID:
  
  3387121122768795230L
- Class ambit2.base.relation.StructureRelation extends AbstractRelation<STRUCTURE_RELATION,Double,IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  6452365513215869937L
- Class ambit2.base.relation.TautomerRelation extends StructureRelation implements Serializable
  
  serialVersionUID:
  
  3387121122768795230L
Package ambit2.base.relation.composition
- Class ambit2.base.relation.composition.Additive extends CompositionRelation implements Serializable
  
  serialVersionUID:
  
  -6746334118446516264L
- Class ambit2.base.relation.composition.CompositionRelation extends AbstractRelation<STRUCTURE_RELATION,Proportion,SubstanceRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -1214326347782066597L
  - Serialized Fields
    - hidden
```
boolean hidden
```
    - compositionUUID
```
String compositionUUID
```
- Class ambit2.base.relation.composition.Constituent extends CompositionRelation implements Serializable
  
  serialVersionUID:
  
  -6746334118446516264L
- Class ambit2.base.relation.composition.Impurity extends CompositionRelation implements Serializable
  
  serialVersionUID:
  
  -6746334118446516264L
- Class ambit2.base.relation.composition.Proportion extends Object implements Serializable
  
  serialVersionUID:
  
  578781054130658046L
  - Serialized Fields
    - function
```
String function
```
    - typical
```
String typical
```
    - typical_value
```
Double typical_value
```
    - typical_unit
```
String typical_unit
```
    - real_lower
```
String real_lower
```
    - real_lowervalue
```
Double real_lowervalue
```
    - real_upper
```
String real_upper
```
    - real_uppervalue
```
Double real_uppervalue
```
    - real_unit
```
String real_unit
```
Package ambit2.base.ro
- Class ambit2.base.ro.AbstractAnnotator extends net.idea.modbcum.p.DefaultAmbitProcessor<U,V> implements Serializable
  
  serialVersionUID:
  
  -1938797533321541056L
  - Serialized Fields
    - lookup
```
Map<K,V> lookup
```
    - fulllinks
```
boolean fulllinks
```
- Class ambit2.base.ro.SubstanceRecordAnnotationProcessor extends AbstractAnnotator<SubstanceRecord,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  5447660472718234256L
Package ambit2.chebi
- Class ambit2.chebi.ChebiFinder extends AbstractFinder<ChEBIClient,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3706639378344745115L
Package ambit2.core.data
- Class ambit2.core.data.AbstractDescriptorResultType extends Object implements Serializable
  
  serialVersionUID:
  
  8385995485307723465L
  - Serialized Fields
    - value
```
Object value
```
- Class ambit2.core.data.ArrayResult extends Object implements Serializable
  
  serialVersionUID:
  
  8938268348726747293L
  - Serialized Fields
    - result
```
Object[] result
```
- Class ambit2.core.data.HashDescriptorResult extends Object implements Serializable
  
  serialVersionUID:
  
  4765713371505859931L
  - Serialized Fields
    - results
```
Map<K,V> results
```
- Class ambit2.core.data.HashIntDescriptorResult extends HashDescriptorResult<Integer> implements Serializable
  
  serialVersionUID:
  
  -8497822347752458361L
  - Serialized Fields
    - maxLevels
```
int maxLevels
```
    - factory
```
String factory
```
- Class ambit2.core.data.IntArrayResult extends ArrayResult<Integer> implements Serializable
  
  serialVersionUID:
  
  -8684782139337436394L
- Class ambit2.core.data.StringArrayResult extends ArrayResult<String> implements Serializable
  
  serialVersionUID:
  
  7274535049474222283L
- Class ambit2.core.data.StringDescriptorResultType extends AbstractDescriptorResultType<String> implements Serializable
  
  serialVersionUID:
  
  5993835059201650185L
Package ambit2.core.data.distances
- Class ambit2.core.data.distances.AtomDistanceProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,List<AtomDistance>> implements Serializable
  
  serialVersionUID:
  
  -2602737581794155267L
Package ambit2.core.data.model
- Class ambit2.core.data.model.Algorithm extends Object implements Serializable
  
  serialVersionUID:
  
  -6624262246346428281L
  - Serialized Fields
    - id
```
String id
```
    - name
```
String name
```
    - parameters
```
List<E> parameters
```
    - content
```
Serializable content
```
    - format
```
Algorithm.AlgorithmFormat format
```
    - type
```
String[] type
```
    - endpoint
```
String endpoint
```
    - requirement
```
Algorithm.requires requirement
```
    - implementationOf
```
String implementationOf
```
    - description
```
String description
```
    - input
```
Template input
```
- Class ambit2.core.data.model.ModelQueryResults extends ModelWrapper<String,String,String,String,String> implements Serializable
  
  serialVersionUID:
  
  6622500017764287129L
  - Serialized Fields
    - endpoint
```
String endpoint
```
    - hidden
```
boolean hidden
```
- Class ambit2.core.data.model.ModelWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  -9217727533985055359L
  - Serialized Fields
    - predictors
```
Template predictors
```
    - dependent
```
Template dependent
```
    - predicted
```
PredictedVarsTemplate predicted
```
    - parameters
```
String[] parameters
```
    - evaluations
```
List<E> evaluations
```
    - stars
```
int stars
```
    - instances
```
Object instances
```
    - testInstances
```
Object testInstances
```
    - algorithm
```
String algorithm
```
    - content
```
Object content
```
    - id
```
Integer id
```
    - name
```
String name
```
    - contentMediaType
```
String contentMediaType
```
    - creator
```
String creator
```
Package ambit2.core.external
- Class ambit2.core.external.ShellSDFoutput extends CommandShell<INPUT,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  8770974107691241294L
  - Serialized Fields
    - readOutput
```
boolean readOutput
```
Package ambit2.core.groups
- Class ambit2.core.groups.AbstractGroup extends org.openscience.cdk.PseudoAtom implements Serializable
  
  serialVersionUID:
  
  -151920308613450648L
  - Serialized Fields
    - atoms
```
List<E> atoms
```
    - bonds
```
List<E> bonds
```
    - number
```
int number
```
- Class ambit2.core.groups.ComponentGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -2031261520924881915L
  - Serialized Fields
    - order
```
Integer order
```
- Class ambit2.core.groups.ContainerGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -557546576995848521L
  - Serialized Fields
    - components
```
List<E> components
```
    - type
```
ContainerGroup.SGROUP_MIXTURE type
```
- Class ambit2.core.groups.DataGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  7303743162178189029L
  - Serialized Fields
    - multicenter
```
org.openscience.cdk.interfaces.IAtom multicenter
```
- Class ambit2.core.groups.GenericGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -5937379235403319622L
- Class ambit2.core.groups.GroupException extends Exception implements Serializable
  
  serialVersionUID:
  
  -153833446985294201L
- Class ambit2.core.groups.GroupNotFoundException extends GroupException implements Serializable
  
  serialVersionUID:
  
  6036398687823875010L
- Class ambit2.core.groups.MonomerGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -3150689169759708407L
- Class ambit2.core.groups.MultipleGroup extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -9110648470808236343L
  - Serialized Fields
    - multiplier
```
int multiplier
```
    - number
```
int number
```
    - parentAtoms
```
List<E> parentAtoms
```
    - parentBonds
```
List<E> parentBonds
```
    - expanded
```
boolean expanded
```
- Class ambit2.core.groups.StructureRepeatingUnit extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -3315050830717056405L
- Class ambit2.core.groups.SuperAtom extends AbstractGroup implements Serializable
  
  serialVersionUID:
  
  -3485052440705149342L
  - Serialized Fields
    - expanded
```
boolean expanded
```
    - contractedBonds
```
List<E> contractedBonds
```
- Class ambit2.core.groups.SuppleAtomContainer extends org.openscience.cdk.ChemObject implements Serializable
  
  serialVersionUID:
  
  -3228354237961385902L
  - Serialized Fields
    - atoms
```
FilteredList<T> atoms
```
    - bonds
```
FilteredList<T> bonds
```
    - lonePairs
```
List<E> lonePairs
```
    - singleElectrons
```
List<E> singleElectrons
```
      Internal array of single electrons.
    - stereoElements
```
Set<E> stereoElements
```
      Internal list of atom parities.
- Class ambit2.core.groups.UnsupportedGroupOperation extends GroupException implements Serializable
  
  serialVersionUID:
  
  8464902380972553534L
Package ambit2.core.io
- Class ambit2.core.io.FileInputState extends FileState implements Serializable
  
  serialVersionUID:
  
  4293026709920994430L
  - Serialized Fields
    - optionalSMILESHeader
```
String optionalSMILESHeader
```
    - optionalInChIKeyHeader
```
String optionalInChIKeyHeader
```
    - optionalInChIHeader
```
String optionalInChIHeader
```
- Class ambit2.core.io.FileOutputState extends FileState implements Serializable
- Class ambit2.core.io.FileState extends Object implements Serializable
  
  serialVersionUID:
  
  -9098389880881547516L
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException
```
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
```
private void writeObject(ObjectOutputStream out)
                  throws IOException
```
      Throws:
      
      IOException
  - Serialized Fields
    - responseType
```
String responseType
```
    - supportedExtensions
```
String[] supportedExtensions
```
    - extensionDescriptions
```
String[] extensionDescriptions
```
    - filename
```
String filename
```
    - length
```
long length
```
    - lastModified
```
long lastModified
```
    - hashCode
```
int hashCode
```
    - offset
```
long offset
```
    - currentRecord
```
long currentRecord
```
    - fileFormat
```
org.openscience.cdk.io.formats.IChemFormat fileFormat
```
Package ambit2.core.io.dx
- Class ambit2.core.io.dx.DXParser extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -1912095670898750150L
  - Serialized Fields
    - dx
```
com.fasterxml.jackson.databind.ObjectMapper dx
```
    - dxRoot
```
com.fasterxml.jackson.databind.JsonNode dxRoot
```
    - categories
```
PropertyAnnotations categories
```
Package ambit2.core.io.study
- Class ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty extends Object implements Serializable
  
  serialVersionUID:
  
  5597788664120240759L
Package ambit2.core.processors
- Class ambit2.core.processors.AbstractStructureProcessor extends Object implements Serializable
  
  serialVersionUID:
  
  -4672277305265874844L
  - Serialized Fields
    - sparseproperties
```
boolean sparseproperties
```
    - atomtypeasproperties
```
boolean atomtypeasproperties
```
    - enabled
```
boolean enabled
```
- Class ambit2.core.processors.FragmentProcessor extends AbstractStructureProcessor implements Serializable
  
  serialVersionUID:
  
  4826290923350893404L
- Class ambit2.core.processors.IsotopesProcessor extends AbstractStructureProcessor implements Serializable
  
  serialVersionUID:
  
  -4774343290932854421L
  - Serialized Fields
    - isotopesFactory
```
org.openscience.cdk.config.Isotopes isotopesFactory
```
- Class ambit2.core.processors.ProcessorFileExport extends net.idea.modbcum.p.DefaultAmbitProcessor<Content,FileOutputState> implements Serializable
  
  serialVersionUID:
  
  -5006607500469902058L
  - Serialized Fields
    - output
```
FileOutputState output
```
    - licenseURI
```
String licenseURI
```
- Class ambit2.core.processors.Structure2DBuilder extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -711201344724786569L
  - Serialized Fields
    - sdg
```
org.openscience.cdk.layout.StructureDiagramGenerator sdg
```
- Class ambit2.core.processors.StructureNormalizer extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -218665330663424435L
  - Serialized Fields
    - dxParser
```
DXParser dxParser
```
    - build2D
```
boolean build2D
```
Package ambit2.core.processors.batch
- Class ambit2.core.processors.batch.DefaultInputState extends DefaultIOState implements Serializable
  
  serialVersionUID:
  
  8642417087199310257L
  - Serialized Fields
    - fileFormat
```
org.openscience.cdk.io.formats.IChemFormat fileFormat
```
- Class ambit2.core.processors.batch.DefaultIOState extends Object implements Serializable
  - Serialized Fields
    - currentRecord
```
long currentRecord
```
    - responseType
```
String responseType
```
Package ambit2.core.processors.quality
- Class ambit2.core.processors.quality.ChemicalStructureQualityCheck extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,QLabel> implements Serializable
  
  serialVersionUID:
  
  -518931054923701570L
  - Serialized Fields
    - qualityVerifier
```
AmbitUser qualityVerifier
```
    - groundTruth
```
org.openscience.cdk.interfaces.IAtomContainer groundTruth
```
    - isoTester
```
org.openscience.cdk.isomorphism.IsomorphismTester isoTester
```
Package ambit2.core.processors.structure
- Class ambit2.core.processors.structure.AbstractPropertyGenerator extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  6923827535809255431L
  - Serialized Fields
    - reader
```
MoleculeReader reader
```
- Class ambit2.core.processors.structure.AtomConfigurator extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -1245226849382037921L
- Class ambit2.core.processors.structure.CloneProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -3628034858252983090L
- Class ambit2.core.processors.structure.FingerprintGenerator extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,BitSet> implements Serializable
  
  serialVersionUID:
  
  3905797414723139887L
  - Serialized Fields
    - FPLength
```
int FPLength
```
    - fingerprinter
```
org.openscience.cdk.fingerprint.IFingerprinter fingerprinter
```
    - hydrogens
```
boolean hydrogens
```
    - hAdder
```
org.openscience.cdk.tools.CDKHydrogenAdder hAdder
```
    - config
```
AtomConfigurator config
```
- Class ambit2.core.processors.structure.HydrogenAdderProcessor extends AtomConfigurator implements Serializable
  
  serialVersionUID:
  
  -6788800174158558265L
  - Serialized Fields
    - adder
```
org.openscience.cdk.tools.CDKHydrogenAdder adder
```
    - addEexplicitHydrogens
```
boolean addEexplicitHydrogens
```
- Class ambit2.core.processors.structure.InchiProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.inchi.InChIGenerator> implements Serializable
  
  serialVersionUID:
  
  -9052892261511104974L
  - Serialized Fields
    - factory
```
org.openscience.cdk.inchi.InChIGeneratorFactory factory
```
- Class ambit2.core.processors.structure.MoleculePairProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord[],IStructureRecord[]> implements Serializable
  
  serialVersionUID:
  
  -6601719866474797743L
  - Serialized Fields
    - reader
```
MoleculeReader reader
```
    - molecules
```
org.openscience.cdk.interfaces.IAtomContainer[] molecules
```
    - smartsProperty
```
Property smartsProperty
```
- Class ambit2.core.processors.structure.MoleculeReader extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  1811923574213153916L
  - Serialized Fields
    - inchiFactory
```
org.openscience.cdk.inchi.InChIGeneratorFactory inchiFactory
```
    - casTransformer
```
CASProcessor casTransformer
```
    - smiParser
```
org.openscience.cdk.smiles.SmilesParser smiParser
```
    - hadder
```
org.openscience.cdk.tools.CDKHydrogenAdder hadder
```
    - atomtypingonsmiles
```
boolean atomtypingonsmiles
```
    - removeCDKTitle
```
boolean removeCDKTitle
```
- Class ambit2.core.processors.structure.MoleculeWriter extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,String> implements Serializable
  
  serialVersionUID:
  
  7007704004927846803L
- Class ambit2.core.processors.structure.StructureTypeProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,IStructureRecord.STRUC_TYPE> implements Serializable
  
  serialVersionUID:
  
  470417245691484159L
Package ambit2.core.processors.structure.key
- Class ambit2.core.processors.structure.key.CASKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  3848970585289051369L
  - Serialized Fields
    - key
```
Property key
```
    - transformer
```
CASProcessor transformer
```
- Class ambit2.core.processors.structure.key.ChEMBLCompoundURI extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  -8549426639690399378L
- Class ambit2.core.processors.structure.key.DSSToxCID extends DSSToxID implements Serializable
  
  serialVersionUID:
  
  -5172763951258433726L
- Class ambit2.core.processors.structure.key.DSSToxGenericSID extends DSSToxID implements Serializable
  
  serialVersionUID:
  
  -5172763951258433726L
- Class ambit2.core.processors.structure.key.DSSToxID extends PropertyKey<Number> implements Serializable
  
  serialVersionUID:
  
  -3100634196576603225L
- Class ambit2.core.processors.structure.key.DSSToxRID extends DSSToxID implements Serializable
  
  serialVersionUID:
  
  2117618200041344844L
- Class ambit2.core.processors.structure.key.EINECSKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  -9098011521397491242L
- Class ambit2.core.processors.structure.key.EmptyKey extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,String> implements Serializable
  
  serialVersionUID:
  
  -2365056130992400384L
- Class ambit2.core.processors.structure.key.InchiKey extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,String> implements Serializable
  
  serialVersionUID:
  
  -4957862884677389524L
  - Serialized Fields
    - inchi
```
InchiProcessor inchi
```
    - key
```
Object key
```
- Class ambit2.core.processors.structure.key.InchiPropertyKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  1718062022783509128L
  - Serialized Fields
    - inchi
```
InchiProcessor inchi
```
- Class ambit2.core.processors.structure.key.NameKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  4988862647891373896L
- Class ambit2.core.processors.structure.key.NameOnlyProperty extends Property implements Serializable
  
  serialVersionUID:
  
  -4971559595379407362L
- Class ambit2.core.processors.structure.key.NoneKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  -5914214406075177640L
- Class ambit2.core.processors.structure.key.PropertyKey extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,Result> implements Serializable
  
  serialVersionUID:
  
  6393097111823664858L
  - Serialized Fields
    - key
```
Property key
```
- Class ambit2.core.processors.structure.key.PropertyNameKey extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  3707216961952814110L
- Class ambit2.core.processors.structure.key.PubchemCID extends PropertyKey<Number> implements Serializable
  
  serialVersionUID:
  
  -5172763951258433726L
- Class ambit2.core.processors.structure.key.PubchemSID extends PropertyKey<Number> implements Serializable
  
  serialVersionUID:
  
  -5172763951258433726L
- Class ambit2.core.processors.structure.key.ReferenceSubstanceUUID extends PropertyKey<String> implements Serializable
  
  serialVersionUID:
  
  2679648406249584207L
- Class ambit2.core.processors.structure.key.SampleKey extends PropertyNameKey implements Serializable
  
  serialVersionUID:
  
  6702546532075828636L
- Class ambit2.core.processors.structure.key.SmilesKey extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,String> implements Serializable
  
  serialVersionUID:
  
  8319267963784553472L
  - Serialized Fields
    - gen
```
org.openscience.cdk.smiles.SmilesGenerator gen
```
    - key
```
Object key
```
Package ambit2.core.smiles
- Class ambit2.core.smiles.OpenBabelAbstractShell extends ShellSDFoutput<X> implements Serializable
  
  serialVersionUID:
  
  -8439060274752318591L
  - Serialized Fields
    - hydrogens
```
boolean hydrogens
```
- Class ambit2.core.smiles.OpenBabelDepiction extends OpenBabelAbstractShell<String> implements Serializable
  
  serialVersionUID:
  
  1989646229616982430L
  - Serialized Fields
    - outputFileName
```
String outputFileName
```
    - size
```
int size
```
- Class ambit2.core.smiles.OpenBabelGen3D extends OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -9048435750478862463L
- Class ambit2.core.smiles.OpenBabelShell extends OpenBabelAbstractShell<String> implements Serializable
  
  serialVersionUID:
  
  -89551999366481056L
Package ambit2.db
- Class ambit2.db.DbReader extends net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<ResultType>,ResultType> implements Serializable
  
  serialVersionUID:
  
  -509334177829567145L
  - Serialized Fields
    - resultSet
```
ResultSet resultSet
```
    - executor
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> executor
```
    - handlePrescreen
```
boolean handlePrescreen
```
- Class ambit2.db.DbReaderStructure extends DbReader<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  7593295052807885237L
  - Serialized Fields
    - cache
```
CreateStoredQuery cache
```
    - cacheUpdater
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> cacheUpdater
```
    - strucQuery
```
ambit2.db.MyQuery strucQuery
```
    - hits
```
QueryCachedResultsBoolean hits
```
    - lookup
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> lookup
```
    - retriever
```
ProcessorStructureRetrieval retriever
```
- Class ambit2.db.PreparedStatementBatchExecutor extends StatementExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate,int[]> implements Serializable
  
  serialVersionUID:
  
  -6641899570004098671L
- Class ambit2.db.RepositoryReader extends net.idea.modbcum.p.AbstractDBProcessor<Target,StructureRecord> implements Serializable
  
  serialVersionUID:
  
  -7461302566335753091L
  - Serialized Fields
    - ps_structures
```
PreparedStatement ps_structures
```
    - ps_structurebyid
```
PreparedStatement ps_structurebyid
```
    - rs
```
ResultSet rs
```
- Class ambit2.db.SourceDatasetRows extends AmbitRows<M extends ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  -1029375286043564206L
- Class ambit2.db.StatementExecutor extends net.idea.modbcum.p.AbstractDBProcessor<Q extends net.idea.modbcum.i.IStatement,Results> implements Serializable
  
  serialVersionUID:
  
  -9188531629150175036L
  - Serialized Fields
    - cache
```
Hashtable<K,V> cache
```
    - useCache
```
boolean useCache
```
- Class ambit2.db.UpdateExecutor extends StatementExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate,Integer> implements Serializable
  
  serialVersionUID:
  
  -4621464032598050969L
Package ambit2.db.cache
- Class ambit2.db.cache.QueryCachedResults extends AbstractQuery<String,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,T> implements Serializable
  
  serialVersionUID:
  
  4381740451274951526L
  - Serialized Fields
    - category
```
String category
```
    - what
```
String what
```
- Class ambit2.db.cache.QueryCachedResultsBoolean extends QueryCachedResults<Boolean> implements Serializable
  
  serialVersionUID:
  
  5484965371846346063L
- Class ambit2.db.cache.RetrieveStructureImagePath extends RetrieveStructure implements Serializable
  
  serialVersionUID:
  
  -2535919053818523334L
  - Serialized Fields
    - queryName
```
String queryName
```
    - mimeType
```
String mimeType
```
Package ambit2.db.chart
- Class ambit2.db.chart.BarChartGenerator extends ChartGenerator<T extends ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  81990940570873057L
  - Serialized Fields
    - minX
```
Double minX
```
    - maxX
```
Double maxX
```
    - propertyX
```
Property propertyX
```
    - propertyY
```
Property propertyY
```
- Class ambit2.db.chart.BarChartGeneratorDataset extends BarChartGenerator<ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  5297256309410169743L
- Class ambit2.db.chart.ChartGenerator extends net.idea.modbcum.p.AbstractDBProcessor<T,BufferedImage> implements Serializable
  
  serialVersionUID:
  
  -5231855179501628510L
  - Serialized Fields
    - width
```
int width
```
    - height
```
int height
```
    - legend
```
boolean legend
```
    - param
```
String param
```
    - thumbnail
```
boolean thumbnail
```
    - logX
```
boolean logX
```
    - logY
```
boolean logY
```
- Class ambit2.db.chart.FingerprintHistogramDataset extends ChartGenerator<ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  8511066138461076352L
- Class ambit2.db.chart.FuncGroupsChartGenerator extends ChartGenerator<IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  -2988570985723641965L
- Class ambit2.db.chart.HistogramChartGenerator extends BarChartGeneratorDataset implements Serializable
  
  serialVersionUID:
  
  -8611312548411533271L
- Class ambit2.db.chart.Nominal2SimilarityChartGenerator extends ChartGenerator<IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  2946352054029479908L
  - Serialized Fields
    - property
```
Property property
```
- Class ambit2.db.chart.Numeric2SimilarityChartGenerator extends ChartGenerator<IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  -7655203169195131809L
  - Serialized Fields
    - property
```
Property property
```
- Class ambit2.db.chart.PieChartGenerator extends ChartGenerator<T extends ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  -4301713904733096802L
  - Serialized Fields
    - property
```
Property property
```
- Class ambit2.db.chart.PropertiesChartGenerator extends ChartGenerator<ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  81990940570873057L
  - Serialized Fields
    - propertyX
```
Property propertyX
```
    - propertyY
```
Property propertyY
```
- Class ambit2.db.chart.XTabChartGenerator extends ChartGenerator<ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  2946352054029479908L
  - Serialized Fields
    - propertyX
```
Property propertyX
```
    - propertyY
```
Property propertyY
```
    - binWidth
```
double binWidth
```
Package ambit2.db.chemrelation
- Class ambit2.db.chemrelation.ReadDatasetRelation extends AbstractQuery<String,ISourceDataset,net.idea.modbcum.q.conditions.BooleanCondition,StructureRelation> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
  - Serialized Fields
    - result
```
StructureRelation result
```
- Class ambit2.db.chemrelation.ReadStructureRelation extends AbstractStructureQuery<String,Integer,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
Package ambit2.db.facets.bookmarks
- Class ambit2.db.facets.bookmarks.BookmarksByTopicFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  -5838810808473432009L
  - Serialized Fields
    - creator
```
String creator
```
- Class ambit2.db.facets.bookmarks.BookmarksByTopicFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<Bookmark,String,net.idea.modbcum.q.conditions.StringCondition,BookmarksByTopicFacet> implements Serializable
  
  serialVersionUID:
  
  -4741289697057206809L
  - Serialized Fields
    - sql
```
String sql
```
    - record
```
BookmarksByTopicFacet record
```
Package ambit2.db.facets.bundle
- Class ambit2.db.facets.bundle.BundleSummaryFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  1282793950608440487L
- Class ambit2.db.facets.bundle.BundleSummaryQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<SubstanceEndpointsBundle,String,net.idea.modbcum.q.conditions.StringCondition,BundleSummaryFacet> implements Serializable
  
  serialVersionUID:
  
  -2156155776273258064L
  - Serialized Fields
    - record
```
BundleSummaryFacet record
```
- Class ambit2.db.facets.bundle.EndpointRoleByBundle extends net.idea.modbcum.q.facet.AbstractFacetQuery<SubstanceByCategoryFacet,SubstanceEndpointsBundle,net.idea.modbcum.q.conditions.StringCondition,BundleRoleFacet> implements Serializable
  
  serialVersionUID:
  
  2183619142564101671L
  - Serialized Fields
    - record
```
BundleRoleFacet record
```
- Class ambit2.db.facets.bundle.SubstanceRoleByBundle extends net.idea.modbcum.q.facet.AbstractFacetQuery<SubstanceRecord,SubstanceEndpointsBundle,net.idea.modbcum.q.conditions.StringCondition,BundleRoleFacet> implements Serializable
  
  serialVersionUID:
  
  -2880103630366030217L
  - Serialized Fields
    - record
```
BundleRoleFacet record
```
Package ambit2.db.facets.compounds
- Class ambit2.db.facets.compounds.ChemicalRoleByBundle extends net.idea.modbcum.q.facet.AbstractFacetQuery<IStructureRecord,SubstanceEndpointsBundle,net.idea.modbcum.q.conditions.StringCondition,BundleRoleFacet> implements Serializable
  
  serialVersionUID:
  
  -4741289697057206809L
  - Serialized Fields
    - record
```
BundleRoleFacet record
```
- Class ambit2.db.facets.compounds.CollectionsByChemical extends net.idea.modbcum.q.facet.AbstractFacetQuery<IStructureRecord,String[],net.idea.modbcum.q.conditions.StringCondition,net.idea.modbcum.i.facet.IFacet<String>> implements Serializable
  
  serialVersionUID:
  
  -4741289697057206809L
  - Serialized Fields
    - record
```
net.idea.modbcum.i.facet.IFacet<T> record
```
Package ambit2.db.facets.datasets
- Class ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery extends PrefixFacetQuery<IStructureRecord,DatasetPrefixFacet> implements Serializable
  
  serialVersionUID:
  
  -2156155776273258064L
- Class ambit2.db.facets.datasets.DatasetPrefixFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  3704763536776924159L
  - Serialized Fields
    - structure
```
IStructureRecord structure
```
- Class ambit2.db.facets.datasets.EndpointCompoundFacet extends PropertyDatasetFacet<Property,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3196764532235094256L
- Class ambit2.db.facets.datasets.EndpointCompoundFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<Property,IStructureRecord,net.idea.modbcum.q.conditions.StringCondition,EndpointCompoundFacet> implements Serializable
  
  serialVersionUID:
  
  -8340773122431657623L
  - Serialized Fields
    - record
```
EndpointCompoundFacet record
```
- Class ambit2.db.facets.datasets.PrefixFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<PARAM,String,net.idea.modbcum.q.conditions.StringCondition,FACET extends net.idea.modbcum.i.facet.IFacet<String>> implements Serializable
  
  serialVersionUID:
  
  -360487682677697165L
  - Serialized Fields
    - record
```
net.idea.modbcum.i.facet.IFacet<T> record
```
- Class ambit2.db.facets.datasets.StringQueryFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  6237749089413659830L
Package ambit2.db.facets.propertyvalue
- Class ambit2.db.facets.propertyvalue.PropertyDatasetFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  -2260081381044742166L
  - Serialized Fields
    - property
```
Object property
```
    - dataset
```
Object dataset
```
- Class ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<Property,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,PropertyDatasetFacet<Property,SourceDataset>> implements Serializable
  
  serialVersionUID:
  
  -2156155776273258064L
  - Serialized Fields
    - record
```
PropertyDatasetFacet<PROPERTY,DATASET> record
```
Package ambit2.db.facets.qlabel
- Class ambit2.db.facets.qlabel.DatasetChemicalsQualityStats extends net.idea.modbcum.q.facet.AbstractFacetQuery<ConsensusLabel.CONSENSUS_LABELS,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,DatasetConsensusLabelFacet> implements Serializable
  
  serialVersionUID:
  
  2657669483303463773L
  - Serialized Fields
    - record
```
DatasetConsensusLabelFacet record
```
    - summary
```
boolean summary
```
- Class ambit2.db.facets.qlabel.DatasetConsensusLabelFacet extends PropertyDatasetFacet<ConsensusLabel,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  4011962497826164064L
- Class ambit2.db.facets.qlabel.DatasetStructureQLabelFacet extends PropertyDatasetFacet<QLabel,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  4011962497826164064L
- Class ambit2.db.facets.qlabel.DatasetStructureQualityStats extends net.idea.modbcum.q.facet.AbstractFacetQuery<QLabel,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,DatasetStructureQLabelFacet> implements Serializable
  
  serialVersionUID:
  
  5183010855788077541L
  - Serialized Fields
    - record
```
DatasetStructureQLabelFacet record
```
- Class ambit2.db.facets.qlabel.DatasetStrucTypeFacet extends PropertyDatasetFacet<IStructureRecord.STRUC_TYPE,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  4011962497826164064L
- Class ambit2.db.facets.qlabel.DatasetStrucTypeStats extends net.idea.modbcum.q.facet.AbstractFacetQuery<IStructureRecord.STRUC_TYPE,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,DatasetStrucTypeFacet> implements Serializable
  
  serialVersionUID:
  
  5183010855788077541L
  - Serialized Fields
    - record
```
DatasetStrucTypeFacet record
```
Package ambit2.db.model
- Class ambit2.db.model.QueryCountModels extends QueryCount implements Serializable
  
  serialVersionUID:
  
  2826870937106055180L
Package ambit2.db.processors
- Class ambit2.db.processors.AbstractDescriptorCalculator extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3717059242431165100L
  - Serialized Fields
    - descriptors
```
Profile<P extends Property> descriptors
```
    - assignProperties
```
boolean assignProperties
```
- Class ambit2.db.processors.AbstractPropertyWriter extends AbstractRepositoryWriter<Target,Result> implements Serializable
  
  serialVersionUID:
  
  3962356158979832113L
  - Serialized Fields
    - annotationsWriter
```
CreatePropertyAnnotation annotationsWriter
```
    - propertyWriter
```
CreateProperty propertyWriter
```
    - templateDefWriter
```
DatasetTemplateAddProperty templateDefWriter
```
    - dataset
```
SourceDataset dataset
```
    - selectField
```
RetrieveFieldNames selectField
```
    - readProperty
```
ReadProperty readProperty
```
- Class ambit2.db.processors.AbstractRepositoryWriter extends net.idea.modbcum.p.AbstractDBProcessor<Target,Result> implements Serializable
  
  serialVersionUID:
  
  7620071794813020111L
  - Serialized Fields
    - operation
```
AbstractRepositoryWriter.OP operation
```
    - exec
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> exec
```
    - queryexec
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> queryexec
```
- Class ambit2.db.processors.AbstractUpdateProcessor extends AbstractRepositoryWriter<Group,Target> implements Serializable
  
  serialVersionUID:
  
  -3168837881397247324L
  - Serialized Fields
    - queryCreate
```
net.idea.modbcum.i.query.IQueryUpdate<Group,Target> queryCreate
```
    - queryDelete
```
net.idea.modbcum.i.query.IQueryUpdate<Group,Target> queryDelete
```
    - queryUpdate
```
net.idea.modbcum.i.query.IQueryUpdate<Group,Target> queryUpdate
```
- Class ambit2.db.processors.BatchDBProcessor extends net.idea.modbcum.p.batch.AbstractBatchProcessor<IInputState,ITEMTYPE> implements Serializable
  
  serialVersionUID:
  
  -5659435501205598414L
  - Serialized Fields
    - reference
```
ILiteratureEntry reference
```
- Class ambit2.db.processors.BatchStructuresListProcessor extends net.idea.modbcum.p.batch.AbstractBatchProcessor<List<IStructureRecord>,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  772067703553971396L
- Class ambit2.db.processors.ConnectionStatisticsProcessor extends ConnectionStatusProcessor<T> implements Serializable
  
  serialVersionUID:
  
  -2178161153920499747L
  - Serialized Fields
    - metadata
```
boolean metadata
```
    - sql
```
String[] sql
```
- Class ambit2.db.processors.ConnectionStatusProcessor extends net.idea.modbcum.p.AbstractDBProcessor<T,StringBuffer> implements Serializable
  
  serialVersionUID:
  
  3836666411270315603L
- Class ambit2.db.processors.DbCreateDatabase extends AbstractRepositoryWriter<StringBean,String> implements Serializable
  
  serialVersionUID:
  
  -335737998721944578L
  - Serialized Fields
    - useExistingDatabase
```
boolean useExistingDatabase
```
    - adminPass
```
String adminPass
```
    - userPass
```
String userPass
```
    - SQLFile
```
String SQLFile
```
- Class ambit2.db.processors.DbDescriptorValuesWriter extends ValueWriter<org.openscience.cdk.qsar.DescriptorValue,org.openscience.cdk.qsar.DescriptorValue> implements Serializable
  
  serialVersionUID:
  
  3453741433797677188L
  - Serialized Fields
    - helper
```
DescriptorValue2Property helper
```
- Class ambit2.db.processors.DbDescriptorWriter extends AbstractPropertyWriter<org.openscience.cdk.qsar.DescriptorValue,org.openscience.cdk.qsar.DescriptorValue> implements Serializable
  
  serialVersionUID:
  
  -358115974932302101L
- Class ambit2.db.processors.DBProcessorsChain extends net.idea.modbcum.i.processors.ProcessorsChain<Target,Result,P extends net.idea.modbcum.i.IDBProcessor<Target,Result>> implements Serializable
  
  serialVersionUID:
  
  -2269380236406696708L
  - Serialized Fields
    - connection
```
Connection connection
```
    - sessionID
```
SessionID sessionID
```
- Class ambit2.db.processors.DbStructureWriter extends AbstractRepositoryWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -5831358598266151159L
  - Serialized Fields
    - datasetAddStruc
```
DatasetAddStructure datasetAddStruc
```
    - createStructure
```
CreateStructure createStructure
```
    - updateStructure
```
UpdateStructure updateStructure
```
    - propertyWriter
```
PropertyValuesWriter propertyWriter
```
    - dataset
```
SourceDataset dataset
```
    - readDatasetQuery
```
ReadDataset readDatasetQuery
```
- Class ambit2.db.processors.DescriptorsCalculator extends AbstractDescriptorCalculator<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -2912324506031402660L
  - Serialized Fields
    - d
```
DescriptorsFactory d
```
    - writer
```
DbDescriptorValuesWriter writer
```
    - selfwriter
```
DescriptorValue2Property selfwriter
```
    - reader
```
MoleculeReader reader
```
    - ha
```
HydrogenAdderProcessor ha
```
    - cfg
```
AtomConfigurator cfg
```
    - calc
```
PropertyCalculationProcessor calc
```
- Class ambit2.db.processors.FP1024Writer extends AbstractRepositoryWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -2919255769379557423L
  - Serialized Fields
    - fpTable
```
FPTable fpTable
```
    - h16
```
BigInteger[] h16
```
    - ps_bitset
```
PreparedStatement ps_bitset
```
- Class ambit2.db.processors.ProcessorCloseReader extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.io.iterator.IIteratingChemObjectReader,IOException> implements Serializable
  
  serialVersionUID:
  
  6552870197903003218L
- Class ambit2.db.processors.processorCloseSession extends net.idea.modbcum.p.AbstractDBProcessor<SessionID,SessionID> implements Serializable
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.processors.ProcessorCreateProfileQuery extends net.idea.modbcum.p.AbstractDBProcessor<Profile<Property>,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  -3849627442305332766L
  - Serialized Fields
    - tag
```
Boolean tag
```
- Class ambit2.db.processors.ProcessorCreateQuery extends net.idea.modbcum.p.AbstractDBProcessor<net.idea.modbcum.i.IQueryObject<IStructureRecord>,IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  -6765755816334059911L
  - Serialized Fields
    - result
```
IStoredQuery result
```
    - copy
```
boolean copy
```
    - delete
```
boolean delete
```
    - profile
```
Template profile
```
    - exec
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> exec
```
    - qexec
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> qexec
```
    - queryName
```
String queryName
```
    - session
```
SessionID session
```
- Class ambit2.db.processors.ProcessorCreateSession extends net.idea.modbcum.p.AbstractDBProcessor<SessionID,SessionID> implements Serializable
  
  serialVersionUID:
  
  -4591852127943879992L
- Class ambit2.db.processors.ProcessorFile2FileReader extends net.idea.modbcum.p.DefaultAmbitProcessor<File,org.openscience.cdk.io.iterator.IIteratingChemObjectReader> implements Serializable
  
  serialVersionUID:
  
  -6446046376999783460L
- Class ambit2.db.processors.ProcessorOntology extends net.idea.modbcum.p.AbstractDBProcessor<Object,Dictionary> implements Serializable
  
  serialVersionUID:
  
  3423393486307151753L
  - Serialized Fields
    - template
```
Dictionary[] template
```
    - executor
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> executor
```
    - operation
```
ProcessorOntology.OP operation
```
    - currentSide
```
ProcessorOntology.SIDE currentSide
```
- Class ambit2.db.processors.ProcessorSetQueryScope extends net.idea.modbcum.p.AbstractDBProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  -6401864475830513693L
  - Serialized Fields
    - query
```
net.idea.modbcum.i.IQueryRetrieval<ResultType> query
```
- Class ambit2.db.processors.ProcessorStructureRetrieval extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  2086055435347535113L
  - Serialized Fields
    - query
```
net.idea.modbcum.i.IQueryRetrieval<ResultType> query
```
    - exec
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> exec
```
- Class ambit2.db.processors.PropertyImporter extends AbstractRepositoryWriter<org.openscience.cdk.interfaces.IAtomContainer,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  -723253191799638564L
  - Serialized Fields
    - propertyWriter
```
PropertyValuesWriter propertyWriter
```
    - queryKey
```
IStructureKey<Target,Result> queryKey
```
    - query_property
```
AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition> query_property
```
    - datasetAddStruc
```
DatasetAddStructure datasetAddStruc
```
- Class ambit2.db.processors.PropertyValuesWriter extends ValueWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3140079486695024274L
  - Serialized Fields
    - reference
```
LiteratureEntry reference
```
- Class ambit2.db.processors.QualityStatisticsProcessor extends ConnectionStatisticsProcessor<String> implements Serializable
  
  serialVersionUID:
  
  -9039738820989381748L
- Class ambit2.db.processors.QueryInfo2Query extends net.idea.modbcum.p.AbstractDBProcessor<QueryInfo,net.idea.modbcum.i.IQueryObject> implements Serializable
  
  serialVersionUID:
  
  2333531372300024401L
- Class ambit2.db.processors.QueryStatisticsProcessor extends ConnectionStatisticsProcessor<IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  1847691478569935696L
- Class ambit2.db.processors.QuickImportBatchProcessor extends BatchDBProcessor<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -4345359507645947184L
- Class ambit2.db.processors.RepositoryWriter extends AbstractRepositoryWriter<IStructureRecord,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  6530309499663693100L
  - Serialized Fields
    - structureWriter
```
DbStructureWriter structureWriter
```
    - query
```
QueryByIdentifierWithStructureFallback query
```
    - queryNum
```
QueryFieldNumeric queryNum
```
    - ps_seekdataset
```
PreparedStatement ps_seekdataset
```
    - normalizer
```
StructureNormalizer normalizer
```
    - useExistingStructure
```
boolean useExistingStructure
```
    - idchemical_tag
```
String idchemical_tag
```
- Class ambit2.db.processors.StructureStatisticsProcessor extends ConnectionStatisticsProcessor<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  4688263934254733569L
- Class ambit2.db.processors.ValueWriter extends AbstractPropertyWriter<Target,Result> implements Serializable
  
  serialVersionUID:
  
  8373222804070419878L
  - Serialized Fields
    - ps_descriptorvalue_string
```
PreparedStatement ps_descriptorvalue_string
```
    - ps_descriptorvalue_number
```
PreparedStatement ps_descriptorvalue_number
```
    - ps_insertstring
```
PreparedStatement ps_insertstring
```
    - structure
```
IStructureRecord structure
```
- Class ambit2.db.processors.ValueWriterNew extends AbstractRepositoryWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  8373222804070419878L
  - Serialized Fields
    - dataset
```
SourceDataset dataset
```
    - tuples_batchExecutor
```
PreparedStatementBatchExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> tuples_batchExecutor
```
      Tuples
    - property_batchExecutor
```
PreparedStatementBatchExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> property_batchExecutor
```
      Prepared statement for writing Property objects
    - qProperty
```
CreateProperty qProperty
```
    - pstring_batchExecutor
```
PreparedStatementBatchExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> pstring_batchExecutor
```
      Prepared statements for writing string and numeric values into property_values table
    - pnum_batchExecutor
```
PreparedStatementBatchExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> pnum_batchExecutor
```
    - qNumber
```
UpdateStructurePropertyIDNumber qNumber
```
      Prepared statements for writing string and numeric values into property_values table
    - qString
```
UpdateStructurePropertyIDString qString
```
    - features
```
RetieveFeatures features
```
      Looks for all Property, assigned to this structure and retrieves IDs from properties table.
Package ambit2.db.processors.quality
- Class ambit2.db.processors.quality.FPStructureWriter extends AbstractUpdateProcessor<IStructureRecord,BitSet> implements Serializable
  
  serialVersionUID:
  
  -5985642442961325777L
  - Serialized Fields
    - molReader
```
MoleculeReader molReader
```
    - g
```
FingerprintGenerator<FGenerator extends org.openscience.cdk.fingerprint.IFingerprinter> g
```
- Class ambit2.db.processors.quality.QualityLabelWriter extends AbstractRepositoryWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -7068666045941631192L
  - Serialized Fields
    - query
```
CreateQLabelFingerprints query
```
    - querySmiles
```
SmilesUniquenessCheck querySmiles
```
    - molReader
```
MoleculeReader molReader
```
    - g
```
FingerprintGenerator<FGenerator extends org.openscience.cdk.fingerprint.IFingerprinter> g
```
    - smilesKey
```
SmilesKey smilesKey
```
- Class ambit2.db.processors.quality.QualityValueWriter extends AbstractRepositoryWriter<IStructureRecord,Property> implements Serializable
  
  serialVersionUID:
  
  -3205301967748956995L
  - Serialized Fields
    - query
```
ValuesQualityCheck query
```
    - field
```
RetrieveField<ResultType> field
```
Package ambit2.db.readers
- Class ambit2.db.readers.AbstractStructureRetrieval extends AbstractQuery<Boolean,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,R> implements Serializable
  
  serialVersionUID:
  
  1L
- Class ambit2.db.readers.PropertyValue extends Object implements Serializable
  
  serialVersionUID:
  
  2035617875115805031L
  - Serialized Fields
    - id
```
int id
```
    - error
```
AbstractPropertyWriter.mode error
```
    - property
```
Property property
```
    - value
```
Object value
```
- Class ambit2.db.readers.ReadChemicalIds extends AbstractQuery<Object,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  2064999650126789112L
- Class ambit2.db.readers.RetrieveAtomContainer extends AbstractStructureRetrieval<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  6145574959713490136L
  - Serialized Fields
    - transform
```
MoleculeReader transform
```
    - reader
```
RetrieveStructure reader
```
- Class ambit2.db.readers.RetrieveDatasets extends AbstractQuery<IStructureRecord,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  -7226561858311078951L
  - Serialized Fields
    - readDataset
```
ReadDataset readDataset
```
- Class ambit2.db.readers.RetrieveDescriptor extends AbstractQuery<org.openscience.cdk.qsar.IMolecularDescriptor,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,org.openscience.cdk.qsar.DescriptorValue> implements Serializable
  
  serialVersionUID:
  
  -2275940362173809147L
- Class ambit2.db.readers.RetrieveField extends AbstractQuery<Property,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,ResultType> implements Serializable
  
  serialVersionUID:
  
  -7818288709974026824L
  - Serialized Fields
    - addNew
```
boolean addNew
```
    - searchMode
```
AbstractPropertyRetrieval.SearchMode searchMode
```
    - chemicalsOnly
```
boolean chemicalsOnly
```
    - sql_structure
```
String sql_structure
```
    - sql_structure_novalue
```
String sql_structure_novalue
```
    - sql_chemical
```
String sql_chemical
```
    - sql_chemical_novalue
```
String sql_chemical_novalue
```
    - where
```
String where
```
- Class ambit2.db.readers.RetrieveFieldPropertyValue extends RetrieveField<PropertyValue> implements Serializable
  
  serialVersionUID:
  
  -2730646908144430273L
- Class ambit2.db.readers.RetrieveFieldStructure extends RetrieveField<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8144364027565901933L
- Class ambit2.db.readers.RetrieveGroupedValuesByAlias extends AbstractQuery<Profile,IStructureRecord,net.idea.modbcum.q.conditions.SetCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8264868908094861525L
  - Serialized Fields
    - record
```
IStructureRecord record
```
    - sql_grouped
```
String sql_grouped
```
- Class ambit2.db.readers.RetrieveModelTemplates extends AbstractQuery<ModelQueryResults,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,ResultType> implements Serializable
  
  serialVersionUID:
  
  -7375755539942986234L
  - Serialized Fields
    - chemicalsOnly
```
boolean chemicalsOnly
```
    - sql_chemicals
```
String sql_chemicals
```
    - sql_structure
```
String sql_structure
```
    - sql_where
```
String sql_where
```
    - sql_templateall
```
String sql_templateall
```
- Class ambit2.db.readers.RetrieveModelTemplatesPropertyValue extends RetrieveModelTemplates<PropertyValue> implements Serializable
  
  serialVersionUID:
  
  8719815577496826171L
- Class ambit2.db.readers.RetrieveProfileValues extends AbstractQuery<Profile<Property>,IStructureRecord,net.idea.modbcum.q.conditions.SetCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  6445434992210833166L
  - Serialized Fields
    - record
```
IStructureRecord record
```
    - addNew
```
boolean addNew
```
    - searchMode
```
RetrieveProfileValues.SearchMode searchMode
```
    - chemicalsOnly
```
boolean chemicalsOnly
```
    - sql_structure
```
String sql_structure
```
    - sql_structure_novalue
```
String sql_structure_novalue
```
    - sql_chemical
```
String sql_chemical
```
    - sql_chemical_novalue
```
String sql_chemical_novalue
```
    - sql_propery
```
String sql_propery
```
    - sql_alias
```
String sql_alias
```
    - sql_name
```
String sql_name
```
- Class ambit2.db.readers.RetrieveProfileValuesAsRow extends AbstractQuery<Profile<Property>,int[],net.idea.modbcum.q.conditions.SetCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  6445434992210833166L
  - Serialized Fields
    - chemicalsOnly
```
Boolean chemicalsOnly
```
    - record
```
IStructureRecord record
```
    - addNew
```
boolean addNew
```
    - sql_property
```
String sql_property
```
    - sql_structure
```
String sql_structure
```
    - sql_chemical
```
String sql_chemical
```
- Class ambit2.db.readers.RetrieveStructure extends AbstractStructureRetrieval<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  7257863166977468657L
  - Serialized Fields
    - preferedStructure
```
boolean preferedStructure
```
    - sql_prefered
```
String sql_prefered
```
- Class ambit2.db.readers.RetrieveTemplate extends AbstractQuery<Template,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,ResultType> implements Serializable
  
  serialVersionUID:
  
  -7375755539942986234L
  - Serialized Fields
    - chemicalsOnly
```
boolean chemicalsOnly
```
    - sql_chemicals
```
String sql_chemicals
```
    - sql_structure
```
String sql_structure
```
    - sql_where
```
String sql_where
```
    - sql_where_name
```
String sql_where_name
```
    - sql_templateall
```
String sql_templateall
```
- Class ambit2.db.readers.RetrieveTemplatePropertyValue extends RetrieveTemplate<PropertyValue> implements Serializable
  
  serialVersionUID:
  
  -743370966710931692L
- Class ambit2.db.readers.RetrieveTemplateStructure extends RetrieveTemplate<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  5787823982680640645L
  - Serialized Fields
    - record
```
IStructureRecord record
```
    - addPropertiesToTemplate
```
boolean addPropertiesToTemplate
```
- Class ambit2.db.readers.ValuesByTemplateReader extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,Result> implements Serializable
  
  serialVersionUID:
  
  -8369720672395084533L
  - Serialized Fields
    - propertyQuery
```
net.idea.modbcum.i.IQueryRetrieval<ResultType> propertyQuery
```
    - names
```
RetrieveField<ResultType> names
```
    - executort
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> executort
```
    - executorn
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> executorn
```
Package ambit2.db.reporters
- Class ambit2.db.reporters.AbstractImageReporter extends net.idea.modbcum.r.QueryReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,OUTPUT> implements Serializable
  
  serialVersionUID:
  
  -8546489672452997303L
  - Serialized Fields
    - depict
```
CompoundImageTools depict
```
    - reader
```
MoleculeReader reader
```
    - cache
```
CreateStoredQuery cache
```
    - cacheUpdater
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> cacheUpdater
```
    - strucQuery
```
ambit2.db.reporters.MyQuery strucQuery
```
    - mainType
```
String mainType
```
    - subType
```
String subType
```
    - img
```
Property img
```
    - imageWrapper
```
CachedImage<MORE> imageWrapper
```
- Class ambit2.db.reporters.AbstractStructureRecordReporter extends QueryStructureReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Result> implements Serializable
  
  serialVersionUID:
  
  -7744663194192122818L
  - Serialized Fields
    - template
```
Template template
```
    - groupProperties
```
Profile<P extends Property> groupProperties
```
- Class ambit2.db.reporters.ARFF3ColReporter extends ARFFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
  - Serialized Fields
    - compounds
```
List<E> compounds
```
- Class ambit2.db.reporters.ARFFReporter extends QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
  - Serialized Fields
    - tempFile
```
File tempFile
```
    - tmpWriter
```
Writer tmpWriter
```
    - urlPrefix
```
String urlPrefix
```
    - delimiter
```
String delimiter
```
- Class ambit2.db.reporters.CMLReporter extends QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
  - Serialized Fields
    - reader
```
MoleculeReader reader
```
- Class ambit2.db.reporters.CSVReporter extends QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer> implements Serializable
  
  serialVersionUID:
  
  -4569410787926615089L
  - Serialized Fields
    - numberofHeaderLines
```
int numberofHeaderLines
```
    - writeCompoundURI
```
boolean writeCompoundURI
```
    - similarityColumn
```
Property similarityColumn
```
    - licenseColumn
```
String licenseColumn
```
    - folders
```
String[] folders
```
    - bundles
```
SubstanceEndpointsBundle[] bundles
```
    - urlPrefix
```
String urlPrefix
```
    - separator
```
String separator
```
    - lineseparator
```
String lineseparator
```
- Class ambit2.db.reporters.ImageAreaReporter extends AbstractImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,StringWriter> implements Serializable
  
  serialVersionUID:
  
  6323248045172976921L
  - Serialized Fields
    - jsonpcallback
```
String jsonpcallback
```
- Class ambit2.db.reporters.ImageReporter extends AbstractImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,BufferedImage> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
- Class ambit2.db.reporters.PDFReporter extends QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,com.lowagie.text.Document> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
  - Serialized Fields
    - reader
```
MoleculeReader reader
```
    - depict
```
CompoundImageTools depict
```
    - table
```
com.lowagie.text.pdf.PdfPTable table
```
    - font
```
com.lowagie.text.Font font
```
- Class ambit2.db.reporters.QueryHeaderReporter extends QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> implements Serializable
  
  serialVersionUID:
  
  4653171215072211975L
  - Serialized Fields
    - includeMol
```
boolean includeMol
```
    - groupProperties
```
Profile<P extends Property> groupProperties
```
    - template
```
Template template
```
    - header
```
List<E> header
```
- Class ambit2.db.reporters.QueryPacketReporter extends net.idea.modbcum.r.QueryAbstractReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> implements Serializable
  
  serialVersionUID:
  
  7517219316610459335L
  - Serialized Fields
    - exec
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> exec
```
    - chunkQuery
```
RetrieveProfileValuesAsRow chunkQuery
```
    - template
```
Profile<P extends Property> template
```
    - index
```
int index
```
    - idstructure
```
int[] idstructure
```
    - idcompound
```
int[] idcompound
```
- Class ambit2.db.reporters.QueryProperyReporter extends net.idea.modbcum.r.QueryReporter<Property,Q extends net.idea.modbcum.i.IQueryRetrieval<Property>,Output> implements Serializable
  
  serialVersionUID:
  
  -2662159144067243671L
- Class ambit2.db.reporters.QueryStructureReporter extends net.idea.modbcum.r.QueryReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> implements Serializable
  
  serialVersionUID:
  
  7383576401402360892L
- Class ambit2.db.reporters.QueryTemplateReporter extends QueryProperyReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<Property>,Template> implements Serializable
  
  serialVersionUID:
  
  -6474255197721950832L
- Class ambit2.db.reporters.RTFReporter extends QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,com.lowagie.text.Document> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
- Class ambit2.db.reporters.SDFReporter extends QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer> implements Serializable
  
  serialVersionUID:
  
  2931123688036795689L
  - Serialized Fields
    - template
```
Template template
```
    - MOLONLY
```
boolean MOLONLY
```
    - reader
```
MoleculeReader reader
```
    - first
```
boolean first
```
    - changeLineSeparators
```
boolean changeLineSeparators
```
    - groupProperties
```
Profile<P extends Property> groupProperties
```
- Class ambit2.db.reporters.SmilesReporter extends QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer> implements Serializable
  
  serialVersionUID:
  
  3648376868814044783L
  - Serialized Fields
    - template
```
Template template
```
    - writeProperties
```
boolean writeProperties
```
    - groupProperties
```
Profile<P extends Property> groupProperties
```
    - key
```
Property key
```
    - mode
```
SmilesReporter.Mode mode
```
- Class ambit2.db.reporters.StructureListReporter extends AbstractStructureRecordReporter<List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  4591388340477136425L
- Class ambit2.db.reporters.StructureRecordReporter extends AbstractStructureRecordReporter<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  4591388340477136425L

Package ambit2.db.reporters.xlsx

Class ambit2.db.reporters.xlsx.AbstractXLSXReporter extends QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,OutputStream> implements Serializable

serialVersionUID:

-6627313415375827936L
- Serialized Fields
  - workbook
```
org.apache.poi.ss.usermodel.Workbook workbook
```
  - sheet
```
org.apache.poi.ss.usermodel.Sheet sheet
```
  - dataformat
```
org.apache.poi.ss.usermodel.DataFormat dataformat
```
  - style
```
org.apache.poi.ss.usermodel.CellStyle style
```
  - out
```
OutputStream out
```
  - writingStarted
```
boolean writingStarted
```
  - fileExtension
```
String fileExtension
```

Class ambit2.db.reporters.xlsx.StructureRecordXLSXReporter extends AbstractXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable

serialVersionUID:: -2075636527988009741L

Serialized Fields

drawing

org.apache.poi.ss.usermodel.Drawing<T extends org.apache.poi.ss.usermodel.Shape> drawing

imageReporter

ImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> imageReporter

component
```
ProcessorStructureRetrieval component
```
d
```
Dimension d
```
offset
```
int offset
```
rowIndex
```
int rowIndex
```
formatter
```
StudyFormatter formatter
```
mergedProperties
```
Map<K,V> mergedProperties
```

style

org.apache.poi.ss.usermodel.CellStyle style

hstyle

org.apache.poi.ss.usermodel.CellStyle hstyle

blueStyle

org.apache.poi.ss.usermodel.CellStyle blueStyle

blackFont

org.apache.poi.ss.usermodel.Font blackFont

blueFont

org.apache.poi.ss.usermodel.Font blueFont

redFont

org.apache.poi.ss.usermodel.Font redFont

autosizecolumn
```
boolean autosizecolumn
```
imgHelper
```
AddDimensionedImage imgHelper
```

Class ambit2.db.reporters.xlsx.SubstanceRecordXLSXReporter extends AbstractXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable

serialVersionUID:: 3258781396076442458L

Serialized Fields

rowIndex
```
int rowIndex
```
substanceIndex
```
int substanceIndex
```
formatter
```
StudyFormatter formatter
```

sectionStyle

org.apache.poi.ss.usermodel.CellStyle sectionStyle

hstyle

org.apache.poi.ss.usermodel.CellStyle hstyle

tableStyle

org.apache.poi.ss.usermodel.CellStyle tableStyle

blackFont

org.apache.poi.ss.usermodel.Font blackFont

blueFont

org.apache.poi.ss.usermodel.Font blueFont

redFont

org.apache.poi.ss.usermodel.Font redFont

Package ambit2.db.results
- Class ambit2.db.results.AmbitRows extends net.idea.modbcum.p.AbstractDBProcessor<T,net.idea.modbcum.i.IQueryRetrieval> implements Serializable
  
  serialVersionUID:
  
  -4124120461604514413L
  - Serialized Fields
    - query
```
net.idea.modbcum.i.IQueryRetrieval<ResultType> query
```
    - rowset
```
CachedRowSet rowset
```
    - executor
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> executor
```
    - propertyname
```
String propertyname
```
    - ready
```
boolean ready
```
- Class ambit2.db.results.DictionaryRows extends AmbitRows<Dictionary> implements Serializable
- Class ambit2.db.results.MemoryRowsModel extends AbstractListModel implements Serializable
  
  serialVersionUID:
  
  -5034323147503404064L
  - Serialized Fields
    - rows
```
AmbitRows<T> rows
```
    - content
```
List<E> content
```
- Class ambit2.db.results.PropertyRows extends AmbitRows<Property> implements Serializable
  
  serialVersionUID:
  
  9120339076353090040L
- Class ambit2.db.results.QueryChangeEvent extends PropertyChangeEvent implements Serializable
  
  serialVersionUID:
  
  8430039223408120160L
- Class ambit2.db.results.ResultSetTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  2273479288973954063L
  - Serialized Fields
    - connection
```
Connection connection
```
    - records
```
ResultSet records
```
    - maxRecords
```
int maxRecords
```
- Class ambit2.db.results.RowsModel extends AbstractListModel implements Serializable
  
  serialVersionUID:
  
  -5034323147503404064L
  - Serialized Fields
    - rows
```
AmbitRows<T> rows
```
- Class ambit2.db.results.StoredQueryTableModel extends ResultSetTableModel implements Serializable
  
  serialVersionUID:
  
  -7273714299667490819L
  - Serialized Fields
    - selectionMode
```
ISelectableRecords.SELECTION_MODE selectionMode
```
    - storedResults
```
AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition> storedResults
```
    - retrieveMolecule
```
RetrieveAtomContainer retrieveMolecule
```
    - retrieveField
```
RetrieveField<ResultType> retrieveField
```
    - fields
```
TypedListModel<P> fields
```
    - properties
```
Hashtable<K,V> properties
```
    - order
```
Hashtable<K,V> order
```
    - updateExecutor
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> updateExecutor
```
    - queryMolecule
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> queryMolecule
```
    - queryExecutor
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> queryExecutor
```
    - queryFieldExecutor
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> queryFieldExecutor
```
    - propertyListener
```
PropertyChangeListener propertyListener
```
    - statsProcessor
```
StructureStatisticsProcessor statsProcessor
```
    - queryFields
```
net.idea.modbcum.i.IQueryRetrieval<ResultType>[] queryFields
```
    - workingRecord
```
StructureRecord workingRecord
```
Package ambit2.db.search
- Class ambit2.db.search.AbstractQuery extends Object implements Serializable
  
  serialVersionUID:
  
  3120118597644963365L
  - Serialized Fields
    - fieldname
```
Object fieldname
```
    - value
```
Object value
```
    - condition
```
net.idea.modbcum.i.IQueryCondition condition
```
    - selected
```
boolean selected
```
    - name
```
String name
```
    - id
```
Integer id
```
    - maxRecords
```
long maxRecords
```
    - page
```
int page
```
- Class ambit2.db.search.DictionaryObjectQuery extends DictionaryQuery<Dictionary> implements Serializable
  
  serialVersionUID:
  
  -7844553625486670502L
- Class ambit2.db.search.DictionaryQuery extends AbstractQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,T extends Dictionary> implements Serializable
  
  serialVersionUID:
  
  -7315142224794511557L
- Class ambit2.db.search.DictionarySubjectQuery extends DictionaryQuery<Dictionary> implements Serializable
  
  serialVersionUID:
  
  -4370465438653357188L
- Class ambit2.db.search.QueryCombined extends Object implements Serializable
  
  serialVersionUID:
  
  -2233255580366294449L
  - Serialized Fields
    - queries
```
ArrayList<E> queries
```
    - id
```
Integer id
```
    - scope
```
net.idea.modbcum.i.IQueryObject<ResultType> scope
```
    - combine_queries
```
QueryCombined.COMBINE combine_queries
```
- Class ambit2.db.search.QueryExecutor extends StatementExecutor<Q extends net.idea.modbcum.i.IQueryObject,ResultSet> implements Serializable
  
  serialVersionUID:
  
  5821244671560506456L
  - Serialized Fields
    - sresults
```
PreparedStatement sresults
```
    - statement
```
Statement statement
```
    - paged_limit
```
String paged_limit
```
    - LIMIT
```
String LIMIT
```
    - resultType
```
int resultType
```
    - resultTypeConcurency
```
int resultTypeConcurency
```
- Class ambit2.db.search.QueryExperiment extends AbstractQuery<Template,net.idea.modbcum.i.IQueryObject,C extends net.idea.modbcum.i.IQueryCondition,ResultType> implements Serializable
  
  serialVersionUID:
  
  -6805975633668595736L
- Class ambit2.db.search.QuerySmilesByID extends AbstractQuery<String,IStructureRecord,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -4024101219917942351L
  - Serialized Fields
    - maxValue
```
IStructureRecord maxValue
```
- Class ambit2.db.search.QueryUser extends AbstractQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,AmbitUser> implements Serializable
  
  serialVersionUID:
  
  -1174549562613435168L
- Class ambit2.db.search.SQLFileQueryParams extends net.idea.modbcum.q.query.SQLFileQuery<com.fasterxml.jackson.databind.node.ObjectNode> implements Serializable
  
  serialVersionUID:
  
  -2420284940751695905L
  - Serialized Fields
    - queryParams
```
List<E> queryParams
```
    - psql
```
String psql
```
    - jsonParams
```
String jsonParams
```
- Class ambit2.db.search.StoredQuery extends Object implements Serializable
  
  serialVersionUID:
  
  -4144504244895601171L
  - Serialized Fields
    - licenseURI
```
String licenseURI
```
    - rightsHolder
```
String rightsHolder
```
    - maintainer
```
String maintainer
```
    - stars
```
int stars
```
    - id
```
Integer id
```
    - name
```
String name
```
    - content
```
String content
```
    - template
```
Template template
```
    - query
```
net.idea.modbcum.i.IQueryObject<ResultType> query
```
    - rows
```
int rows
```
Package ambit2.db.search.property
- Class ambit2.db.search.property.AbstractPropertyRetrieval extends AbstractQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition,Property> implements Serializable
  
  serialVersionUID:
  
  -6129319550824253087L
  - Serialized Fields
    - chemicalsOnly
```
boolean chemicalsOnly
```
- Class ambit2.db.search.property.FilteredCount extends Object implements Serializable
  
  serialVersionUID:
  
  -9049403419636975159L
  - Serialized Fields
    - id
```
Integer id
```
    - property
```
Property property
```
    - query
```
IStoredQuery query
```
    - metric
```
Range<T extends Comparable<T>> metric
```
    - value
```
Range<T extends Comparable<T>> value
```
- Class ambit2.db.search.property.FilteredCountNominal extends FilteredCount<String> implements Serializable
  
  serialVersionUID:
  
  -8082889518227668528L
  - Serialized Fields
    - sql
```
String sql
```
    - sql_query
```
String sql_query
```
    - sql_value
```
String sql_value
```
    - sql_metric
```
String sql_metric
```
- Class ambit2.db.search.property.FilteredCountNumeric extends FilteredCount<Double> implements Serializable
  
  serialVersionUID:
  
  -8780107461721242518L
  - Serialized Fields
    - sql
```
String sql
```
    - sql_query
```
String sql_query
```
    - sql_value
```
String sql_value
```
    - sql_metric
```
String sql_metric
```
- Class ambit2.db.search.property.FreeTextPropertyQuery extends AbstractPropertyRetrieval<String[],String[],net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  7694873254695069097L
- Class ambit2.db.search.property.ModelTemplates extends AbstractPropertyRetrieval<ModelQueryResults,String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  4888110865139617053L
  - Serialized Fields
    - sql
```
String sql
```
    - where
```
String where
```
    - whereName
```
String whereName
```
- Class ambit2.db.search.property.PropertiesByDataset extends AbstractPropertyRetrieval<Template,SourceDataset,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -7265871901186884735L
- Class ambit2.db.search.property.PropertiesByQuery extends AbstractPropertyRetrieval<Template,IStoredQuery,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -7265871901186884735L
- Class ambit2.db.search.property.PropertyCount extends AbstractQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,PropertyTemplateStats> implements Serializable
  
  serialVersionUID:
  
  5610950555709854734L
- Class ambit2.db.search.property.PropertyRange extends AbstractQuery<Property,Integer,net.idea.modbcum.q.conditions.NumberCondition,Range> implements Serializable
  
  serialVersionUID:
  
  -2385531620133212366L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.property.PropertyStatsNumeric extends AbstractQuery<Property,String,net.idea.modbcum.q.conditions.StringCondition,PropertyStats> implements Serializable
  
  serialVersionUID:
  
  8369867048140756850L
- Class ambit2.db.search.property.PropertyStatsString extends AbstractQuery<Property,String,net.idea.modbcum.q.conditions.StringCondition,String> implements Serializable
  
  serialVersionUID:
  
  6364182865662239013L
- Class ambit2.db.search.property.QueryMetricRange extends AbstractQuery<IStoredQuery,Integer,net.idea.modbcum.q.conditions.NumberCondition,Range<Double>> implements Serializable
  
  serialVersionUID:
  
  415109938169483765L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.property.QueryOntology extends AbstractQuery<Boolean,Dictionary,net.idea.modbcum.q.conditions.StringCondition,Property> implements Serializable
  
  serialVersionUID:
  
  -6711409305156505699L
  - Serialized Fields
    - sqlParent
```
String sqlParent
```
    - sqlChild
```
String sqlChild
```
    - includeParent
```
boolean includeParent
```
- Class ambit2.db.search.property.QueryPairwiseTanimoto extends AbstractQuery<ISourceDataset,ISourceDataset,net.idea.modbcum.q.conditions.BooleanCondition,SimilarityRelation> implements Serializable
  
  serialVersionUID:
  
  -5148418049120426363L
  - Serialized Fields
    - relation
```
SimilarityRelation relation
```
    - threshold
```
double threshold
```
- Class ambit2.db.search.property.QueryPairwiseTanimotoAndProperty extends QueryPairwiseTanimoto implements Serializable
  
  serialVersionUID:
  
  -364452746280384698L
  - Serialized Fields
    - property
```
Property property
```
- Class ambit2.db.search.property.RetieveFeatures extends AbstractPropertyRetrieval<String,IStructureRecord,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  6723083165416521349L
- Class ambit2.db.search.property.RetrieveFieldNames extends AbstractPropertyRetrieval<String,Property,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  8369867048140756850L
- Class ambit2.db.search.property.RetrieveFieldNamesByAlias extends AbstractPropertyRetrieval<IStructureRecord,String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  8369867048140756850L
  - Serialized Fields
    - searchMode
```
AbstractPropertyRetrieval.SearchMode searchMode
```
- Class ambit2.db.search.property.RetrieveFieldNamesByType extends AbstractPropertyRetrieval<String,Boolean,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  8369867048140756850L
- Class ambit2.db.search.property.RetrieveProfile extends AbstractPropertyRetrieval<String,Profile<Property>,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -347765028858989655L
- Class ambit2.db.search.property.TemplateQuery extends AbstractPropertyRetrieval<String,String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  6746077496508519227L
- Class ambit2.db.search.property.ValuesReader extends ValuesByTemplateReader<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3678652087132468828L
  - Serialized Fields
    - reader
```
ProcessorStructureRetrieval reader
```
    - profile
```
Profile<P extends Property> profile
```
Package ambit2.db.search.qlabel
- Class ambit2.db.search.qlabel.QueryConsensus extends AbstractQuery<IStructureRecord,String,net.idea.modbcum.q.conditions.StringCondition,String> implements Serializable
  
  serialVersionUID:
  
  -6574002693997936309L
- Class ambit2.db.search.qlabel.QueryQLabel extends AbstractQuery<AmbitUser,IStructureRecord,net.idea.modbcum.q.conditions.NumberCondition,QLabel> implements Serializable
  
  serialVersionUID:
  
  -6574002693997936309L
Package ambit2.db.search.structure
- Class ambit2.db.search.structure.AbstractStructureQuery extends AbstractQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  3149398052063483705L
  - Serialized Fields
    - order_descendant
```
boolean order_descendant
```
    - chemicalsOnly
```
boolean chemicalsOnly
```
    - nanomaterial
```
boolean nanomaterial
```
- Class ambit2.db.search.structure.ChemicalByQueryFolder extends AbstractStructureQuery<String[],Integer,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  1888965075376808332L
- Class ambit2.db.search.structure.FingerprintsByStatus extends AbstractStructureQuery<FPTable,String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -8554160549010780854L
- Class ambit2.db.search.structure.FreeTextQuery extends AbstractStructureQuery<String[],String[],net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  4221828356692625890L
- Class ambit2.db.search.structure.MissingFingerprintsQuery extends AbstractStructureQuery<FPTable,String,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  -8554160549010780854L
- Class ambit2.db.search.structure.MissingInChIsQuery extends AbstractStructureQuery<String,String,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  7898392932554642629L
- Class ambit2.db.search.structure.NumberQuery extends AbstractStructureQuery<F,Double,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -1495455998753952442L
  - Serialized Fields
    - maxValue
```
Double maxValue
```
- Class ambit2.db.search.structure.QueryAtomEnvironment extends QuerySimilarity<String,HashIntDescriptorResult,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -7235494968515516274L
  - Serialized Fields
    - qe
```
QueryAtomEnvironment.q_modifier qe
```
- Class ambit2.db.search.structure.QueryByIdentifierWithStructureFallback extends AbstractStructureQuery<IStructureKey,IStructureRecord,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -2227075383236154179L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.structure.QueryCombinedStructure extends QueryCombined<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - maxRecords
```
long maxRecords
```
    - page
```
int page
```
    - chemicalsOnly
```
boolean chemicalsOnly
```
- Class ambit2.db.search.structure.QueryComplement extends QueryCombinedStructure implements Serializable
  
  serialVersionUID:
  
  -2818316465477137764L
- Class ambit2.db.search.structure.QueryDataset extends AbstractStructureQuery<String,SourceDataset,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
- Class ambit2.db.search.structure.QueryDatasetByID extends AbstractStructureQuery<String,Integer,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
- Class ambit2.db.search.structure.QueryDistance extends AbstractStructureQuery<org.openscience.cdk.interfaces.IBond,Double,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -5464266255373802342L
  - Serialized Fields
    - maxValue
```
Double maxValue
```
- Class ambit2.db.search.structure.QueryExactStructure extends AbstractStructureQuery<String,org.openscience.cdk.interfaces.IAtomContainer,net.idea.modbcum.q.conditions.BooleanCondition> implements Serializable
  
  serialVersionUID:
  
  -4140784963337312377L
  - Serialized Fields
    - screening
```
QueryPrescreenBitSet screening
```
      Deprecated.
    - smartsProperty
```
Property smartsProperty
```
      Deprecated.
- Class ambit2.db.search.structure.QueryField extends QueryFieldAbstract<String,net.idea.modbcum.q.conditions.StringCondition,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -5810564793012596407L
- Class ambit2.db.search.structure.QueryFieldAbstract extends AbstractStructureQuery<Property,T,C extends net.idea.modbcum.i.IQueryCondition> implements Serializable
  
  serialVersionUID:
  
  -8153311734801503300L
  - Serialized Fields
    - retrieveProperties
```
boolean retrieveProperties
```
    - caseSensitive
```
boolean caseSensitive
```
    - nameCondition
```
net.idea.modbcum.i.IQueryCondition nameCondition
```
    - searchMode
```
AbstractPropertyRetrieval.SearchMode searchMode
```
- Class ambit2.db.search.structure.QueryFieldMultiple extends QueryFieldAbstract<List<String>,net.idea.modbcum.q.conditions.SetCondition,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -731666271442110526L
- Class ambit2.db.search.structure.QueryFieldNumeric extends AbstractStructureQuery<Property,Number,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  1096544914170183549L
  - Serialized Fields
    - where_all
```
String where_all
```
    - where_equal
```
String where_equal
```
    - where_name
```
String where_name
```
    - searchMode
```
AbstractPropertyRetrieval.SearchMode searchMode
```
    - maxValue
```
Number maxValue
```
- Class ambit2.db.search.structure.QueryFunctionalGroups extends AbstractStructureQuery<List<PropertyTemplateStats>,Boolean,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  5310078588280973557L
  - Serialized Fields
    - query
```
QueryCombinedStructure query
```
- Class ambit2.db.search.structure.QueryLookupStructure extends AbstractStructureQuery<IStructureKey,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  960145706994951798L
  - Serialized Fields
    - query
```
QueryStructure query
```
    - reader
```
MoleculeReader reader
```
    - smiles
```
SmilesKey smiles
```
- Class ambit2.db.search.structure.QueryMissingDescriptor extends AbstractStructureQuery<ILiteratureEntry,String,net.idea.modbcum.q.conditions.BooleanCondition> implements Serializable
  
  serialVersionUID:
  
  -8610455060315105098L
- Class ambit2.db.search.structure.QueryMissingDistances extends AbstractStructureQuery<String,org.openscience.cdk.interfaces.IBond,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  8633296656332829455L
- Class ambit2.db.search.structure.QueryMissingProperty extends AbstractStructureQuery<ISourceDataset,Property,net.idea.modbcum.q.conditions.BooleanCondition> implements Serializable
  
  serialVersionUID:
  
  -8610455060315105098L
  - Serialized Fields
    - pageSize
```
long pageSize
```
      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
- Class ambit2.db.search.structure.QueryPrescreenBitSet extends AbstractStructureQuery<BitSet,BitSet,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -4995229206173686206L
  - Serialized Fields
    - sql_struc
```
String sql_struc
```
    - sql_chemical
```
String sql_chemical
```
    - sk_prescreen
```
String sk_prescreen
```
    - fp_prescreen
```
String fp_prescreen
```
    - sql_all
```
String sql_all
```
    - sql_prescreen
```
String sql_prescreen
```
    - sql_exact
```
String sql_exact
```
    - chemicalsOnly
```
boolean chemicalsOnly
```
- Class ambit2.db.search.structure.QuerySimilarity extends AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition> implements Serializable
  
  serialVersionUID:
  
  -3509155736213435907L
  - Serialized Fields
    - threshold
```
double threshold
```
    - forceOrdering
```
boolean forceOrdering
```
- Class ambit2.db.search.structure.QuerySimilarityBitset extends QuerySimilarity<String,BitSet,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  6862334340898438441L
  - Serialized Fields
    - mode
```
FPTable mode
```
    - order
```
String order
```
    - sql_similarity
```
String sql_similarity
```
- Class ambit2.db.search.structure.QuerySimilarityStructure extends QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -7669825969508301397L
  - Serialized Fields
    - query
```
AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition> query
```
    - g
```
FingerprintGenerator<FGenerator extends org.openscience.cdk.fingerprint.IFingerprinter> g
```
    - molReader
```
MoleculeReader molReader
```
    - uit
```
org.openscience.cdk.isomorphism.UniversalIsomorphismTester uit
```
- Class ambit2.db.search.structure.QuerySMARTS extends AbstractStructureQuery<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition> implements Serializable
  
  serialVersionUID:
  
  -4539445262832597492L
  - Serialized Fields
    - smartsToChemObject
```
SmartsToChemObject smartsToChemObject
```
    - screening
```
QueryPrescreenBitSet screening
```
    - smartsProperty
```
Property smartsProperty
```
    - fp1024_screening
```
boolean fp1024_screening
```
    - sk1024_screening
```
boolean sk1024_screening
```
    - usePrecalculatedAtomProperties
```
boolean usePrecalculatedAtomProperties
```
    - builder
```
org.openscience.cdk.interfaces.IChemObjectBuilder builder
```
- Class ambit2.db.search.structure.QueryStoredResults extends AbstractStructureQuery<IStoredQuery,Boolean,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  4597129739347497000L
- Class ambit2.db.search.structure.QueryStoredResultsByName extends AbstractStructureQuery<IStoredQuery,String,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  4597129739347497000L
- Class ambit2.db.search.structure.QueryStructure extends AbstractStructureQuery<ExactStructureSearchMode,String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  1446001922520148275L
  - Serialized Fields
    - smilesKey
```
SmilesKey smilesKey
```
    - configurator
```
AtomConfigurator configurator
```
- Class ambit2.db.search.structure.QueryStructureByID extends AbstractStructureQuery<ISourceDataset,IStructureRecord,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -2227075383236154179L
  - Serialized Fields
    - maxValue
```
IStructureRecord maxValue
```
    - metric
```
int metric
```
    - text
```
String text
```
- Class ambit2.db.search.structure.QueryStructureByQuality extends AbstractStructureQuery<ISourceDataset,QLabel,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -3232148472829083139L
- Class ambit2.db.search.structure.QueryStructureByQualityPairLabel extends AbstractStructureQuery<ISourceDataset,ConsensusLabel,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -3232148472829083139L
- Class ambit2.db.search.structure.QueryStructureByValueQuality extends AbstractStructureQuery<String,QLabel,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -3232148472829083139L
- Class ambit2.db.search.structure.QueryStructureType extends AbstractStructureQuery<ISourceDataset,IStructureRecord.STRUC_TYPE,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  -3232148472829083139L
- Class ambit2.db.search.structure.QueryStrucType extends AbstractStructureQuery<IStructureRecord,IStructureRecord.STRUC_TYPE[],net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  1725564560950361449L
- Class ambit2.db.search.structure.ScopeQuery extends AbstractQuery<SCOPE,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,net.idea.modbcum.q.conditions.EQCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8782175098760501557L
Package ambit2.db.search.structure.byproperty
- Class ambit2.db.search.structure.byproperty.QueryStructureByProperty extends AbstractStructureQuery<Profile,Q extends AbstractStructureQuery,net.idea.modbcum.q.conditions.SetCondition> implements Serializable
  
  serialVersionUID:
  
  4056680895955934165L
- Class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInCompounds extends QueryStructureByProperty<QueryStructureByID> implements Serializable
  
  serialVersionUID:
  
  -5478831682253837878L
- Class ambit2.db.search.structure.byproperty.QueryStructureByPropertyInDataset extends QueryStructureByProperty<QueryDatasetByID> implements Serializable
  
  serialVersionUID:
  
  2211443189914356410L
- Class ambit2.db.search.structure.byproperty.QueryStructuresByPropertyInResults extends QueryStructureByProperty<QueryStoredResults> implements Serializable
  
  serialVersionUID:
  
  -8622643751238845834L
Package ambit2.db.search.structure.pairwise
- Class ambit2.db.search.structure.pairwise.ChemicalSpaceQuery extends AbstractQuery<ISourceDataset,Property,net.idea.modbcum.q.conditions.BooleanCondition,ChemSpaceCell> implements Serializable
  
  serialVersionUID:
  
  169838296668703784L
  - Serialized Fields
    - cell
```
ChemSpaceCell cell
```
    - method
```
ChemicalSpaceQuery.ChemSpaceMethod method
```
    - threshold_similarity
```
double threshold_similarity
```
    - threshold_dactivity
```
double threshold_dactivity
```
    - maxPoints
```
int maxPoints
```
    - sql
```
String sql
```
- Class ambit2.db.search.structure.pairwise.ChemSpaceCell extends Object implements Serializable
  
  serialVersionUID:
  
  7933062037070427670L
  - Serialized Fields
    - index
```
int[] index
```
    - left
```
double[] left
```
    - right
```
double[] right
```
    - distance
```
double distance
```
- Class ambit2.db.search.structure.pairwise.PairPropertiesWriter extends AbstractRepositoryWriter<IStructureRecord[],IStructureRecord[]> implements Serializable
  
  serialVersionUID:
  
  941417486755990227L
  - Serialized Fields
    - writer
```
PropertyValuesWriter writer
```
- Class ambit2.db.search.structure.pairwise.ProcessorStructurePairsRetrieval extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord[],IStructureRecord[]> implements Serializable
  
  serialVersionUID:
  
  2086055435347535113L
  - Serialized Fields
    - query
```
net.idea.modbcum.i.IQueryRetrieval<ResultType> query
```
    - exec
```
QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> exec
```
- Class ambit2.db.search.structure.pairwise.QueryStructurePairs extends AbstractQuery<Dataset1,Dataset2,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord[]> implements Serializable
  
  serialVersionUID:
  
  1306709480084311651L
  - Serialized Fields
    - records
```
IStructureRecord[] records
```
- Class ambit2.db.search.structure.pairwise.QueryStructurePairsDataset extends QueryStructurePairs<SourceDataset,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  -526806487145457640L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.structure.pairwise.QueryStructurePairsMixed extends QueryStructurePairs<SourceDataset,IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  -526806487145457640L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset extends QueryStructurePairs<IStoredQuery,IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  -526806487145457640L
  - Serialized Fields
    - sql
```
String sql
```
- Class ambit2.db.search.structure.pairwise.RetrieveStructurePair extends AbstractQuery<IStructureRecord,IStructureRecord,net.idea.modbcum.q.conditions.EQCondition,IStructureRecord[]> implements Serializable
  
  serialVersionUID:
  
  3952654869210259121L
  - Serialized Fields
    - sql1
```
String sql1
```
    - sql2
```
String sql2
```
    - records
```
IStructureRecord[] records
```
Package ambit2.db.simiparity.space
- Class ambit2.db.simiparity.space.QMap extends Object implements Serializable
  
  serialVersionUID:
  
  7229458825361028794L
  - Serialized Fields
    - id
```
int id
```
    - dataset
```
ISourceDataset dataset
```
    - property
```
Property property
```
    - activityThreshold
```
double activityThreshold
```
    - similarityThreshold
```
double similarityThreshold
```
- Class ambit2.db.simiparity.space.QMapSpace extends Object implements Serializable
  
  serialVersionUID:
  
  -888827119842958432L
  - Serialized Fields
    - qmap
```
QMap<P extends Property> qmap
```
    - record
```
IStructureRecord record
```
    - g2
```
double g2
```
    - a
```
double a
```
    - b
```
double b
```
    - c
```
double c
```
    - d
```
double d
```
    - fisher
```
double fisher
```
- Class ambit2.db.simiparity.space.QueryQMap extends AbstractQuery<IStructureRecord,QMap,net.idea.modbcum.q.conditions.StringCondition,QMap> implements Serializable
  
  serialVersionUID:
  
  -5648740520878436166L
  - Serialized Fields
    - condition
```
StringBuilder condition
```
- Class ambit2.db.simiparity.space.QueryQMapSpace extends AbstractQuery<IStructureRecord,QMap,net.idea.modbcum.q.conditions.StringCondition,QMapSpace> implements Serializable
  
  serialVersionUID:
  
  -5648740520878436166L
  - Serialized Fields
    - qmap
```
QMap<P extends Property> qmap
```
    - qspace
```
QMapSpace qspace
```
    - threshold_a
```
int threshold_a
```
    - conditionString
```
StringBuilder conditionString
```
- Class ambit2.db.simiparity.space.QueryQMapStructures extends AbstractStructureQuery<String,Integer,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
Package ambit2.db.substance
- Class ambit2.db.substance.AbstractReadSubstance extends AbstractQuery<F,T,net.idea.modbcum.q.conditions.EQCondition,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  8441610930610137578L
- Class ambit2.db.substance.FacetedSearchSubstance extends AbstractReadSubstance<List<ProtocolApplication<Protocol,Params,String,Params,String>>,String> implements Serializable
  
  serialVersionUID:
  
  -9142126306356090595L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.QueryCountBundles extends QueryCount implements Serializable
  
  serialVersionUID:
  
  -4268694398905885170L
- Class ambit2.db.substance.QueryCountEndpoints extends QueryCount<ResultsCountFacet<E extends EffectRecord<String,Object,String>>> implements Serializable
  
  serialVersionUID:
  
  -3168195512257461022L
  - Serialized Fields
    - endpoint
```
String endpoint
```
- Class ambit2.db.substance.QueryCountInterpretationResults extends QueryCount<ResultsCountFacet<ProtocolApplication<Protocol,Params,String,Params,String>>> implements Serializable
  
  serialVersionUID:
  
  -3168195512257461022L
  - Serialized Fields
    - interpretation_result
```
String interpretation_result
```
- Class ambit2.db.substance.QueryCountProtocolApplications extends QueryCount<F extends SubstanceByCategoryFacet> implements Serializable
  
  serialVersionUID:
  
  -6001454887114379950L
  - Serialized Fields
    - mode
```
QueryCountProtocolApplications._mode_related mode
```
    - bundle
```
SubstanceEndpointsBundle bundle
```
- Class ambit2.db.substance.QueryCountSubstances extends QueryCount implements Serializable
  
  serialVersionUID:
  
  -3168195512257461022L
- Class ambit2.db.substance.QueryCountSubstanceTypes extends QueryCount<ambit2.db.substance.SubstanceTypefacet> implements Serializable
- Class ambit2.db.substance.ReadByReliabilityFlags extends AbstractReadSubstance<String,String> implements Serializable
  
  serialVersionUID:
  
  -8701796200692548800L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.ReadSubstance extends AbstractReadSubstance<CompositionRelation,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  -3661558183996204387L
  - Serialized Fields
    - retrieveComposition
```
boolean retrieveComposition
```
- Class ambit2.db.substance.ReadSubstanceByExternalIDentifier extends AbstractReadSubstance<String,String> implements Serializable
  
  serialVersionUID:
  
  -5352529378365800440L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.ReadSubstanceByName extends AbstractReadSubstance<String,String> implements Serializable
  
  serialVersionUID:
  
  -8701796200692548800L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
    - condition
```
ReadSubstanceByName._namecondition condition
```
- Class ambit2.db.substance.ReadSubstanceByOwner extends AbstractReadSubstance<ReadSubstanceByOwner._ownersearchmode,String> implements Serializable
  
  serialVersionUID:
  
  -7362476423007097726L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.ReadSubstanceByStudy extends AbstractReadSubstance<ReadSubstanceByStudy._studysearchmode,String> implements Serializable
  
  serialVersionUID:
  
  -5352529378365800440L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.ReadSubstanceByType extends AbstractReadSubstance<String,String> implements Serializable
  
  serialVersionUID:
  
  -2198459948257520650L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.ReadSubstances extends AbstractReadSubstance<CompositionRelation,String[]> implements Serializable
  
  serialVersionUID:
  
  6355365745488149195L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
Package ambit2.db.substance.ids
- Class ambit2.db.substance.ids.ReadChemIdentifiersByComposition extends ReadChemPropertiesByComposition implements Serializable
  
  serialVersionUID:
  
  -8810690686530660839L
- Class ambit2.db.substance.ids.ReadSubstanceIdentifiers extends AbstractQuery<SubstanceRecord,ExternalIdentifier,net.idea.modbcum.q.conditions.EQCondition,ExternalIdentifier> implements Serializable
  
  serialVersionUID:
  
  -2268008311829764871L

Package ambit2.db.substance.processor

Class ambit2.db.substance.processor.DBBundleStudyWriter extends DBSubstanceWriter implements Serializable

serialVersionUID:

7474604799923342029L
- Serialized Fields
  - rq
```
ReadSubstance rq
```
  - qx
```
net.idea.modbcum.p.QueryExecutor<Q extends net.idea.modbcum.i.IQueryObject> qx
```
  - bundle
```
SubstanceEndpointsBundle bundle
```
Class ambit2.db.substance.processor.DBMatrixValueMarker extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord> implements Serializable

serialVersionUID:

1630263508460590694L
- Serialized Fields
  - writer
```
net.idea.modbcum.p.UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> writer
```
  - query_effectrecord
```
DeleteMatrixValue<VALUE> query_effectrecord
```
  - query_interpretation_result
```
DeleteMatrixProtocolApplicationValue<VALUE> query_interpretation_result
```

Class ambit2.db.substance.processor.DBSubstanceWriter extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord> implements Serializable

serialVersionUID:: -2237399197958151808L

Serialized Fields

i5mode
```
boolean i5mode
```
q
```
CreateSubstance q
```

qids

UpdateSubstanceIdentifiers<C extends SubstanceRecord> qids

qr
```
UpdateSubstanceRelation qr
```
qss
```
UpdateSubstanceStudy qss
```
qeffr
```
UpdateEffectRecords qeffr
```
deffr
```
DeleteEffectRecords deffr
```

x

UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> x

deleteStudy
```
DeleteStudy deleteStudy
```

deleteComposition

DeleteSubstanceRelation deleteComposition

qbundles
```
AddSubstanceToBundle qbundles
```
bundles

qchembundles

AddAllChemicalsperSubstanceToBundle qchembundles

writer
```
RepositoryWriter writer
```
clearMeasurements
```
boolean clearMeasurements
```
importBundles
```
boolean importBundles
```
keepEffectRecordsForDocUUID
```
boolean keepEffectRecordsForDocUUID
```
componentsMatch
```
PropertyKey<Result> componentsMatch
```
clearComposition
```
boolean clearComposition
```
splitRecord
```
boolean splitRecord
```
importedRecord
```
SubstanceRecord importedRecord
```

Package ambit2.db.substance.properties
- Class ambit2.db.substance.properties.ReadChemPropertiesByComposition extends net.idea.modbcum.q.query.AbstractQuery<SubstanceRecord,IStructureRecord,net.idea.modbcum.q.conditions.SetCondition,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8810690686530660839L
  - Serialized Fields
    - record
```
IStructureRecord record
```
Package ambit2.db.substance.relation
- Class ambit2.db.substance.relation.ChemicalBySubstanceRelation extends AbstractStructureQuery<STRUCTURE_RELATION,String,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
- Class ambit2.db.substance.relation.ReadSubstanceComposition extends AbstractQuery<SubstanceRecord,CompositionRelation,net.idea.modbcum.q.conditions.EQCondition,CompositionRelation> implements Serializable
  
  serialVersionUID:
  
  -1980335091441168568L
  - Serialized Fields
    - record
```
CompositionRelation record
```
    - excludeHidden
```
boolean excludeHidden
```
    - bundle
```
SubstanceEndpointsBundle bundle
```
- Class ambit2.db.substance.relation.ReadSubstanceRelation extends AbstractStructureQuery<STRUCTURE_RELATION,SubstanceRecord,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
Package ambit2.db.substance.study
- Class ambit2.db.substance.study.ReadEffectRecord extends ReadEffectRecordAbstract<ProtocolApplication,EffectRecord<String,String,String>> implements Serializable
  
  serialVersionUID:
  
  -5430387137460722198L
- Class ambit2.db.substance.study.ReadEffectRecordAbstract extends AbstractQuery<F,ER extends EffectRecord<String,String,String>,net.idea.modbcum.q.conditions.EQCondition,ER extends EffectRecord<String,String,String>> implements Serializable
  
  serialVersionUID:
  
  2277250526632665919L
- Class ambit2.db.substance.study.ReadEffectRecordBySubstance extends ReadEffectRecordAbstract<SubstanceRecord,ProtocolEffectRecord<String,String,String>> implements Serializable
  
  serialVersionUID:
  
  -3708679134698941319L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
    - _sql
```
String _sql
```
- Class ambit2.db.substance.study.ReadSubstanceProperty extends AbstractPropertyRetrieval<SubstanceProperty,Profile<Property>,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  6014257070546479407L
- Class ambit2.db.substance.study.ReadSubstanceStudy extends AbstractQuery<String,PA extends ProtocolApplication<Protocol,String,String,IParams,String>,net.idea.modbcum.q.conditions.EQCondition,PA extends ProtocolApplication<Protocol,String,String,IParams,String>> implements Serializable
  
  serialVersionUID:
  
  -1980335091441168568L
  - Serialized Fields
    - record
```
ProtocolApplication<PROTOCOL,PARAMS,ENDPOINT,CONDITIONS,UNIT> record
```
- Class ambit2.db.substance.study.ReadSubstanceStudyFlat extends Object implements Serializable
  
  serialVersionUID:
  
  8662401515570688215L
  - Serialized Fields
    - flatQuery
```
SubstanceStudyFlatQuery flatQuery
```
    - effectQuery
```
ReadEffectRecord effectQuery
```
    - paQuery
```
ReadSubstanceStudy<PA extends ProtocolApplication<Protocol,String,String,IParams,String>> paQuery
```
    - measurements
```
List<E> measurements
```
    - fieldname
```
SubstanceRecord fieldname
```
- Class ambit2.db.substance.study.SubstanceStudyDetailsProcessor extends net.idea.modbcum.p.MasterDetailsProcessor<SubstanceRecord,List<ProtocolApplication>,net.idea.modbcum.i.IQueryCondition> implements Serializable
  
  serialVersionUID:
  
  2258609350382277827L
- Class ambit2.db.substance.study.SubstanceStudyFlatQuery extends SQLFileQueryParams implements Serializable
  
  serialVersionUID:
  
  5304176321951306089L
  - Serialized Fields
    - dx
```
com.fasterxml.jackson.databind.ObjectMapper dx
```
Package ambit2.db.substance.study.facet
- Class ambit2.db.substance.study.facet.FacetAnnotator extends AbstractAnnotator<net.idea.modbcum.i.facet.IFacet,net.idea.modbcum.i.facet.IFacet> implements Serializable
  
  serialVersionUID:
  
  -6993550791423851737L
- Class ambit2.db.substance.study.facet.OwnerFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  5464948093969109879L
  - Serialized Fields
    - name
```
String name
```
- Class ambit2.db.substance.study.facet.OwnerSubstanceStats extends net.idea.modbcum.q.facet.AbstractFacetQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,OwnerFacet> implements Serializable
  
  serialVersionUID:
  
  -8910197148842469398L
  - Serialized Fields
    - sql
```
String sql
```
    - record
```
OwnerFacet record
```
- Class ambit2.db.substance.study.facet.ProtocolApplicationSummaryFacet extends SubstanceByCategoryFacet implements Serializable
  
  serialVersionUID:
  
  8084077562134464946L
  - Serialized Fields
    - guidance
```
String guidance
```
    - interpretation_result
```
String interpretation_result
```
- Class ambit2.db.substance.study.facet.ResultsCountFacet extends SubstanceByCategoryFacet implements Serializable
  
  serialVersionUID:
  
  -1301400016402834823L
  - Serialized Fields
    - result
```
Object result
```
- Class ambit2.db.substance.study.facet.SubstanceByCategoryFacet extends AbstractFacet<String> implements Serializable
  
  serialVersionUID:
  
  3229573174462112181L
  - Serialized Fields
    - bundleRole
```
BundleRoleFacet bundleRole
```
    - subcategory
```
String subcategory
```
    - endpoint
```
Protocol._categories endpoint
```
    - substancesCount
```
int substancesCount
```
    - bundles
```
List<E> bundles
```
- Class ambit2.db.substance.study.facet.SubstanceDataAvailabilityFacet extends SubstanceByCategoryFacet implements Serializable
  
  serialVersionUID:
  
  -7344551689563932326L
  - Serialized Fields
    - record
```
SubstanceRecord record
```
- Class ambit2.db.substance.study.facet.SubstanceStudyFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<SubstanceRecord,String,net.idea.modbcum.q.conditions.StringCondition,SubstanceStudyFacet> implements Serializable
  
  serialVersionUID:
  
  -8910197148842469398L
  - Serialized Fields
    - record
```
SubstanceStudyFacet record
```
    - groupByInterpretationResult
```
boolean groupByInterpretationResult
```
    - topcategory
```
String topcategory
```
    - facetURL
```
String facetURL
```
    - reuseRecord
```
boolean reuseRecord
```
    - category
```
String category
```
Package ambit2.db.update.bookmark
- Class ambit2.db.update.bookmark.ReadAnnotation extends AbstractQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,Bookmark> implements Serializable
  
  serialVersionUID:
  
  -8595708937489941431L
  - Serialized Fields
    - queryExpansion
```
boolean queryExpansion
```
- Class ambit2.db.update.bookmark.ReadBookmark extends AbstractQuery<Bookmark,Integer,net.idea.modbcum.q.conditions.StringCondition,Bookmark> implements Serializable
  
  serialVersionUID:
  
  -8595708937489941431L
Package ambit2.db.update.bundle
- Class ambit2.db.update.bundle.BundleOwnerByNumber extends net.idea.modbcum.q.query.AbstractQuery<String,String,net.idea.modbcum.q.conditions.EQCondition,Integer> implements Serializable
  
  serialVersionUID:
  
  4045644505492454127L
- Class ambit2.db.update.bundle.ReadBundle extends AbstractReadDataset<String,SubstanceEndpointsBundle> implements Serializable
  
  serialVersionUID:
  
  -5560670663328542819L
  - Serialized Fields
    - status
```
Set<E> status
```
    - _idmode
```
ambit2.db.update.bundle.ReadBundle._IDMODE _idmode
```
- Class ambit2.db.update.bundle.ReadBundleVersion extends ReadBundle implements Serializable
  
  serialVersionUID:
  
  -988961563705675581L
Package ambit2.db.update.bundle.chemicals
- Class ambit2.db.update.bundle.chemicals.ReadChemicalsByBundle extends AbstractStructureQuery<SubstanceEndpointsBundle,StructureRecord,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  3139508348246513746L
  - Serialized Fields
    - enableFeatures
```
boolean enableFeatures
```
Package ambit2.db.update.bundle.effects
- Class ambit2.db.update.bundle.effects.BundleStudyFacetQuery extends net.idea.modbcum.q.facet.AbstractFacetQuery<SubstanceEndpointsBundle,String,net.idea.modbcum.q.conditions.StringCondition,SubstanceByCategoryFacet> implements Serializable
  
  serialVersionUID:
  
  -8910197148842469398L
  - Serialized Fields
    - facet
```
SubstanceByCategoryFacet facet
```
- Class ambit2.db.update.bundle.effects.ReadEffectRecordByBundle extends ReadEffectRecordBySubstance implements Serializable
  
  serialVersionUID:
  
  -1885870102248748663L
  - Serialized Fields
    - bundle
```
SubstanceEndpointsBundle bundle
```
    - b_sql
```
String b_sql
```
Package ambit2.db.update.bundle.endpoints
- Class ambit2.db.update.bundle.endpoints.ReadEndpointsByBundle extends AbstractPropertyRetrieval<SubstanceEndpointsBundle,SubstanceProperty,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  661276311247312738L
Package ambit2.db.update.bundle.matrix
- Class ambit2.db.update.bundle.matrix.ReadEffectRecordByBundleMatrix extends ReadEffectRecordBySubstance implements Serializable
  
  serialVersionUID:
  
  -1885870102248748663L
  - Serialized Fields
    - bundle
```
SubstanceEndpointsBundle bundle
```
    - matrix
```
ReadEffectRecordByBundleMatrix._matrix matrix
```
Package ambit2.db.update.bundle.substance
- Class ambit2.db.update.bundle.substance.ReadSubstanceChemicalsUnionByBundle extends ReadSubstancesByBundle implements Serializable
  
  serialVersionUID:
  
  -5710747152479311181L
- Class ambit2.db.update.bundle.substance.ReadSubstancesByBundle extends AbstractReadSubstance<SubstanceEndpointsBundle,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  661276311247312738L
  - Serialized Fields
    - enableFeatures
```
boolean enableFeatures
```
- Class ambit2.db.update.bundle.substance.ReadSubstancesByBundleCompounds extends AbstractReadSubstance<SubstanceEndpointsBundle,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  4301930849084992853L
Package ambit2.db.update.chemical
- Class ambit2.db.update.chemical.InChIChemicalsWriter extends AbstractUpdateProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -5985642442961325777L
Package ambit2.db.update.dataset
- Class ambit2.db.update.dataset.AbstractReadDataset extends AbstractQuery<T,M extends ISourceDataset,net.idea.modbcum.q.conditions.StringCondition,M extends ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  -6358006970038485516L
- Class ambit2.db.update.dataset.DatasetQueryFieldGeneric extends AbstractStructureQuery<ISourceDataset,PropertyValue<T>,net.idea.modbcum.i.IQueryCondition> implements Serializable
  
  serialVersionUID:
  
  4878852850705024770L
- Class ambit2.db.update.dataset.DatasetQueryFieldNumeric extends DatasetQueryFieldGeneric<Double,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  4878852850705024770L
- Class ambit2.db.update.dataset.DatasetQueryFieldString extends DatasetQueryFieldGeneric<String,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  4878852850705024770L
- Class ambit2.db.update.dataset.QueryCount extends net.idea.modbcum.q.facet.AbstractFacetQuery<String,String,net.idea.modbcum.q.conditions.StringCondition,FACET extends net.idea.modbcum.i.facet.IFacet<String>> implements Serializable
  
  serialVersionUID:
  
  8759287056069662442L
  - Serialized Fields
    - facet
```
net.idea.modbcum.i.facet.IFacet<T> facet
```
    - QR_PREFIX
```
String QR_PREFIX
```
- Class ambit2.db.update.dataset.QueryCountChemicalInDataset extends QueryCount<AbstractFacet<String>> implements Serializable
  
  serialVersionUID:
  
  6955218726720517180L
- Class ambit2.db.update.dataset.QueryCountDataset extends QueryCount implements Serializable
  
  serialVersionUID:
  
  -4268694398905885170L
- Class ambit2.db.update.dataset.QueryCountDatasetIntersection extends QueryCount<FACET extends net.idea.modbcum.i.facet.IFacet<String>> implements Serializable
  
  serialVersionUID:
  
  -2679397674845722288L
  - Serialized Fields
    - fieldname_dataset
```
boolean fieldname_dataset
```
    - value_dataset
```
boolean value_dataset
```
- Class ambit2.db.update.dataset.QueryCountProperties extends QueryCount implements Serializable
  
  serialVersionUID:
  
  3762221213334168489L
- Class ambit2.db.update.dataset.QueryCountValues extends QueryCount implements Serializable
  
  serialVersionUID:
  
  -4680217024248382081L
- Class ambit2.db.update.dataset.QueryDatasetByFeatures extends AbstractReadDataset<Property,ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  -3278861415939066571L
  - Serialized Fields
    - structure
```
IStructureRecord structure
```
    - sql
```
String sql
```
    - sql_chemical
```
String sql_chemical
```
    - sql_structure
```
String sql_structure
```
    - sql_datasetid
```
String sql_datasetid
```
- Class ambit2.db.update.dataset.ReadDataset extends AbstractReadDataset<String,SourceDataset> implements Serializable
  
  serialVersionUID:
  
  -5560670663328542819L
- Class ambit2.db.update.dataset.ReadDatasetLicense extends AbstractQuery<String,Integer,net.idea.modbcum.q.conditions.StringCondition,String> implements Serializable
  
  serialVersionUID:
  
  -5560670663328542819L
Package ambit2.db.update.fp
- Class ambit2.db.update.fp.Fingerprint extends Object implements Serializable
  
  serialVersionUID:
  
  5550890711527303929L
  - Serialized Fields
    - type
```
Object type
```
    - bits
```
Object bits
```
    - frequency
```
int frequency
```
- Class ambit2.db.update.fp.QueryFingerprints extends AbstractQuery<String,IFingerprint<FPTable,String>,net.idea.modbcum.q.conditions.StringCondition,IFingerprint<FPTable,String>> implements Serializable
  
  serialVersionUID:
  
  -2637272084357419722L
  - Serialized Fields
    - order
```
QueryFingerprints._order order
```
    - sql
```
String sql
```
- Class ambit2.db.update.fp.ReadStructuresByFingerprint extends AbstractStructureQuery<String,IFingerprint<FPTable,String>,net.idea.modbcum.q.conditions.StringCondition> implements Serializable
  
  serialVersionUID:
  
  2852604942293779318L
Package ambit2.db.update.fpae
- Class ambit2.db.update.fpae.AtomEnvironmentMatrixWriter extends AbstractUpdateProcessor<IStructureRecord,S> implements Serializable
  
  serialVersionUID:
  
  -5985642442961325777L
- Class ambit2.db.update.fpae.AtomEnvironmentWriter extends AbstractUpdateProcessor<IStructureRecord,S> implements Serializable
  
  serialVersionUID:
  
  -5985642442961325777L
  - Serialized Fields
    - g
```
CreateAtomEnvironment g
```
      Deprecated.
Package ambit2.db.update.model
- Class ambit2.db.update.model.AbstractModelQuery extends AbstractQuery<F,V,net.idea.modbcum.q.conditions.StringCondition,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -5670785871072092628L
- Class ambit2.db.update.model.QueryModel extends AbstractModelQuery<String,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -5485707611740260825L
- Class ambit2.db.update.model.ReadModel extends AbstractModelQuery<String,Integer> implements Serializable
  
  serialVersionUID:
  
  -8595708937489941431L
Package ambit2.db.update.property
- Class ambit2.db.update.property.ReadProperty extends AbstractPropertyRetrieval<IStructureRecord,Integer,net.idea.modbcum.q.conditions.EQCondition> implements Serializable
  
  serialVersionUID:
  
  6247086921731939782L
Package ambit2.db.update.propertyannotations
- Class ambit2.db.update.propertyannotations.ReadPropertyAnnotations extends AbstractQuery<Property,Integer,net.idea.modbcum.q.conditions.EQCondition,PropertyAnnotation> implements Serializable
  
  serialVersionUID:
  
  -4470430491847500096L
  - Serialized Fields
    - sql
```
String sql
```
Package ambit2.db.update.qlabel.smarts
- Class ambit2.db.update.qlabel.smarts.SMARTSAcceleratorWriter extends AbstractUpdateProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -5985642442961325777L
  - Serialized Fields
    - g
```
CreateSMARTSData g
```
Package ambit2.db.update.queryfolder
- Class ambit2.db.update.queryfolder.ReadQueryFolder extends AbstractQuery<AmbitUser,SessionID,net.idea.modbcum.q.conditions.StringCondition,SessionID> implements Serializable
  
  serialVersionUID:
  
  -8595708937489941431L
Package ambit2.db.update.reference
- Class ambit2.db.update.reference.ReadReference extends AbstractQuery<String,Integer,net.idea.modbcum.q.conditions.EQCondition,ILiteratureEntry> implements Serializable
  
  serialVersionUID:
  
  -8595708937489941431L
Package ambit2.db.update.storedquery
- Class ambit2.db.update.storedquery.ReadStoredQuery extends AbstractQuery<String,IStoredQuery,net.idea.modbcum.q.conditions.StringCondition,ISourceDataset> implements Serializable
  
  serialVersionUID:
  
  1485698692883271843L
- Class ambit2.db.update.storedquery.SearchStoredQueries extends AbstractQuery<SessionID,String,net.idea.modbcum.q.conditions.StringCondition,IStoredQuery> implements Serializable
  
  serialVersionUID:
  
  5945313962492375417L
Package ambit2.db.update.structure
- Class ambit2.db.update.structure.ChemicalByDataset extends AbstractStructureQuery<String,Integer,net.idea.modbcum.q.conditions.NumberCondition> implements Serializable
  
  serialVersionUID:
  
  -8329798753353233477L
Package ambit2.db.version
- Class ambit2.db.version.AmbitDBVersion extends Object implements Serializable
  
  serialVersionUID:
  
  -810148258205916153L
  - Serialized Fields
    - dbname
```
String dbname
```
    - major
```
int major
```
    - minor
```
int minor
```
    - created
```
long created
```
    - comments
```
String comments
```
- Class ambit2.db.version.DBVersionQuery extends AbstractQuery<String,String,net.idea.modbcum.q.conditions.NumberCondition,AmbitDBVersion> implements Serializable
  
  serialVersionUID:
  
  -915159203431471645L
Package ambit2.dbui
- Class ambit2.dbui.CachedRowSetTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  -5428865165072188779L
  - Serialized Fields
    - records
```
CachedRowSet records
```
    - page
```
int page
```
- Class ambit2.dbui.LoginInfoBean extends com.jgoodies.binding.beans.Model implements Serializable
  
  serialVersionUID:
  
  -6318006747221999109L
  - Serialized Fields
    - loginInfo
```
LoginInfo loginInfo
```
- Class ambit2.dbui.ProfileEditor extends net.idea.modbcum.p.AbstractDBProcessor<Profile<Property>,Profile<Property>> implements Serializable
  
  serialVersionUID:
  
  6665474866800960721L
  - Serialized Fields
    - profile
```
Profile<P extends Property> profile
```
    - panel
```
DictionaryQueryPanel panel
```
- Class ambit2.dbui.QueryChemicalEditor extends QueryEditor<ExactStructureSearchMode,String,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryStructure> implements Serializable
  
  serialVersionUID:
  
  3727097962149438857L
- Class ambit2.dbui.QueryCombinedEditor extends net.idea.modbcum.p.AbstractDBProcessor<net.idea.modbcum.i.IQueryRetrieval<Property>,QueryCombinedStructure> implements Serializable
  
  serialVersionUID:
  
  2731638693126278344L
  - Serialized Fields
    - listEditor
```
ListEditor listEditor
```
    - model
```
com.jgoodies.binding.PresentationModel<B> model
```
- Class ambit2.dbui.QueryDatasetEditor extends QueryEditor<String,SourceDataset,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryDataset> implements Serializable
  
  serialVersionUID:
  
  -3741781796086220256L
  - Serialized Fields
    - datasets
```
AmbitRows<T> datasets
```
- Class ambit2.dbui.QueryEditor extends net.idea.modbcum.p.AbstractDBProcessor<net.idea.modbcum.i.IQueryRetrieval<Property>,Q extends AbstractQuery<F,T,C,ResultType>> implements Serializable
  
  serialVersionUID:
  
  -4697669908562921410L
  - Serialized Fields
    - mainPanel
```
JComponent mainPanel
```
    - presentationModel
```
com.jgoodies.binding.PresentationModel<B> presentationModel
```
- Class ambit2.dbui.QueryFieldEditor extends QueryEditor<Property,String,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryField> implements Serializable
  
  serialVersionUID:
  
  4483885648170842874L
  - Serialized Fields
    - properties
```
AmbitRows<T> properties
```
    - stats
```
AmbitRows<T> stats
```
    - queryStringStartsWith
```
PropertyStatsString queryStringStartsWith
```
- Class ambit2.dbui.QueryFieldNumericEditor extends QueryEditor<Property,Number,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord,QueryFieldNumeric> implements Serializable
  
  serialVersionUID:
  
  3347607199840621061L
  - Serialized Fields
    - properties
```
AmbitRows<T> properties
```
    - stats
```
AmbitRows<T> stats
```
    - statsQuery
```
PropertyStatsNumeric statsQuery
```
    - propertyStats
```
PropertyStats<T extends Comparable<T>> propertyStats
```
    - statsAdapter
```
com.jgoodies.binding.PresentationModel<B> statsAdapter
```
- Class ambit2.dbui.QueryFunctionalGroupsEditor extends QueryEditor<List<PropertyTemplateStats>,Boolean,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryFunctionalGroups> implements Serializable
  
  serialVersionUID:
  
  6825082093596853959L
  - Serialized Fields
    - table
```
JTable table
```
- Class ambit2.dbui.QueryInfoEditor extends JPanel implements Serializable
  
  serialVersionUID:
  
  4337363916900586486L
  - Serialized Fields
    - object
```
QueryInfo object
```
    - detailsModel
```
ambit2.dbui.QueryInfoModel detailsModel
```
    - tf_identifier1
```
JTextField tf_identifier1
```
    - tf_identifier2
```
JTextField tf_identifier2
```
    - tf_identifier3
```
JTextField tf_identifier3
```
    - tf_formula
```
JTextField tf_formula
```
    - tf_smiles
```
JTextField tf_smiles
```
    - tf_inchi
```
JTextField tf_inchi
```
    - threshold
```
JComboBox<E> threshold
```
    - dataset
```
JComboBox<E> dataset
```
    - fieldnames1
```
JComboBox<E> fieldnames1
```
    - fieldnames2
```
JComboBox<E> fieldnames2
```
    - fieldnames3
```
JComboBox<E> fieldnames3
```
    - method
```
JComboBox<E> method
```
    - scope
```
JComboBox<E> scope
```
    - cond1
```
JComboBox<E> cond1
```
    - cond2
```
JComboBox<E> cond2
```
    - cond3
```
JComboBox<E> cond3
```
    - and
```
JComboBox<E> and
```
    - panel2d
```
Panel2D<A extends IMoleculeEditAction> panel2d
```
- Class ambit2.dbui.QueryScopeEditor extends net.idea.modbcum.p.AbstractDBProcessor<ScopeQuery,ScopeQuery> implements Serializable
  
  serialVersionUID:
  
  1745393417109602866L
  - Serialized Fields
    - editor
```
ListEditor editor
```
    - model
```
ambit2.dbui.ScopeListModel model
```
- Class ambit2.dbui.QuerySimilarityEditor extends QueryEditor<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord,QuerySimilarityStructure> implements Serializable
  
  serialVersionUID:
  
  -7423741371866787902L
- Class ambit2.dbui.QuerySmartsEditor extends QueryEditor<String,FunctionalGroup,net.idea.modbcum.q.conditions.BooleanCondition,IStructureRecord,QuerySMARTS> implements Serializable
  
  serialVersionUID:
  
  -9201007230031542807L
  - Serialized Fields
    - smartsToChemObject
```
SmartsToChemObject smartsToChemObject
```
- Class ambit2.dbui.QueryStoredResultsEditor extends QueryEditor<IStoredQuery,Boolean,net.idea.modbcum.q.conditions.EQCondition,IStructureRecord,QueryStoredResults> implements Serializable
  
  serialVersionUID:
  
  -2851443117151701351L
  - Serialized Fields
    - queries
```
AmbitRows<T> queries
```
    - searchStoredQuery
```
SearchStoredQueries searchStoredQuery
```
- Class ambit2.dbui.QueryStructureByQualityEditor extends QueryEditor<ISourceDataset,QLabel,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryStructureByQuality> implements Serializable
  
  serialVersionUID:
  
  -5588226956876509820L
- Class ambit2.dbui.QueryStructureByValueQualityEditor extends QueryEditor<String,QLabel,net.idea.modbcum.q.conditions.StringCondition,IStructureRecord,QueryStructureByValueQuality> implements Serializable
  
  serialVersionUID:
  
  4778074204901236208L
Package ambit2.dbui.dictionary
- Class ambit2.dbui.dictionary.AmbitRowsPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  2854619268267349642L
  - Serialized Fields
    - srtm
```
CachedRowSetTableModel srtm
```
    - editable
```
boolean editable
```
    - browser
```
QueryBrowser<T extends TableModel> browser
```
- Class ambit2.dbui.dictionary.DictionaryQueryPanel extends QueryEditor<String,String,net.idea.modbcum.q.conditions.StringCondition,Dictionary,DictionaryQuery<Dictionary>> implements Serializable
  
  serialVersionUID:
  
  7515359779806114282L
  - Serialized Fields
    - parents
```
AmbitRows<T> parents
```
    - details
```
AmbitRows<T> details
```
    - path
```
List<E> path
```
    - profile
```
Profile<P extends Property> profile
```
- Class ambit2.dbui.dictionary.OntologyEditor extends net.idea.modbcum.p.AbstractDBProcessor<Object,Dictionary> implements Serializable
  
  serialVersionUID:
  
  6900524455040663939L
  - Serialized Fields
    - buttons
```
List<E> buttons
```
    - processor
```
ProcessorOntology processor
```
    - query
```
QueryOntology[] query
```
    - listEditor
```
ListEditor[] listEditor
```
    - rows
```
AmbitRows<T>[] rows
```
    - folderIcon
```
ImageIcon folderIcon
```
    - component
```
JComponent component
```
- Class ambit2.dbui.dictionary.TemplatePropertyPanel extends AmbitRowsPanel<Property,PropertyRows> implements Serializable
  
  serialVersionUID:
  
  2786094438980343162L
Package ambit2.descriptors
- Class ambit2.descriptors.AtomEnvironment extends Object implements Serializable
  
  serialVersionUID:
  
  596283081660825735L
  - Serialized Fields
    - levels
```
int levels
```
    - atomno
```
int atomno
```
    - central_atom
```
String central_atom
```
    - atom_environment
```
int[] atom_environment
```
    - time_elapsed
```
long time_elapsed
```
    - status
```
int status
```
    - frequency
```
int frequency
```
- Class ambit2.descriptors.FuncGroupsDescriptorFactory extends net.idea.modbcum.p.DefaultAmbitProcessor<String,List<FunctionalGroup>> implements Serializable
  
  serialVersionUID:
  
  -3836212586696127104L
- Class ambit2.descriptors.FunctionalGroup extends AmbitBean implements Serializable
  
  serialVersionUID:
  
  9069207547772781160L
  - Serialized Fields
    - properties
```
Hashtable<K,V> properties
```
    - query
```
ISmartsPattern<T> query
```
    - enabled
```
boolean enabled
```
    - verboseMatch
```
boolean verboseMatch
```
- Class ambit2.descriptors.VerboseDescriptorResult extends Object implements Serializable
  
  serialVersionUID:
  
  1098522687701012760L
  - Serialized Fields
    - trace
```
Object trace
```
    - result
```
org.openscience.cdk.qsar.result.IDescriptorResult result
```
Package ambit2.descriptors.processors
- Class ambit2.descriptors.processors.AbstractDescriptorCalculationProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<ITEM,org.openscience.cdk.qsar.DescriptorValue> implements Serializable
  
  serialVersionUID:
  
  471269379672309986L
  - Serialized Fields
    - descriptor
```
org.openscience.cdk.qsar.IDescriptor descriptor
```
- Class ambit2.descriptors.processors.AbstractDescriptorFactory extends net.idea.modbcum.p.DefaultAmbitProcessor<String,Result> implements Serializable
  
  serialVersionUID:
  
  275242996048077139L
- Class ambit2.descriptors.processors.AtomEnvironmentGenerator extends AbstractPropertyGenerator<AtomEnvironmentList> implements Serializable
  
  serialVersionUID:
  
  7279981279903286909L
  - Serialized Fields
    - hAdder
```
org.openscience.cdk.tools.CDKHydrogenAdder hAdder
```
    - aeDescriptor
```
AtomEnvironmentDescriptor aeDescriptor
```
    - aeParams
```
Object[] aeParams
```
    - useHydrogens
```
boolean useHydrogens
```
    - maxLevels
```
Integer maxLevels
```
    - createSubLevels
```
boolean createSubLevels
```
    - noDuplicates
```
boolean noDuplicates
```
    - fpmode
```
FPTable fpmode
```
- Class ambit2.descriptors.processors.AtomEnvironmentList extends ArrayList<AtomEnvironment> implements Serializable
  
  serialVersionUID:
  
  -8190211422146555342L
  - Serialized Fields
    - title
```
String title
```
    - noDuplicates
```
boolean noDuplicates
```
- Class ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator extends AbstractPropertyGenerator<HashIntDescriptorResult> implements Serializable
  
  serialVersionUID:
  
  7279981279903286909L
  - Serialized Fields
    - hAdder
```
org.openscience.cdk.tools.CDKHydrogenAdder hAdder
```
    - matrix
```
AtomEnvironentMatrix matrix
```
    - fpmode
```
FPTable fpmode
```
- Class ambit2.descriptors.processors.BitSetGenerator extends AbstractPropertyGenerator<BitSet> implements Serializable
  
  serialVersionUID:
  
  -1046795418089401843L
  - Serialized Fields
    - smartsProperty
```
Property smartsProperty
```
    - processor
```
net.idea.modbcum.i.processors.IProcessor<Target,Result> processor
```
    - fpmode
```
FPTable fpmode
```
- Class ambit2.descriptors.processors.DescriptorCalculationProcessor extends AbstractDescriptorCalculationProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.qsar.IMolecularDescriptor> implements Serializable
  
  serialVersionUID:
  
  -3399104328409649302L
  - Serialized Fields
    - imageSize
```
Dimension imageSize
```
- Class ambit2.descriptors.processors.DescriptorEngineProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,List<org.openscience.cdk.IImplementationSpecification>> implements Serializable
  
  serialVersionUID:
  
  -3482009837842377453L
  - Serialized Fields
    - engine
```
org.openscience.cdk.qsar.DescriptorEngine engine
```
- Class ambit2.descriptors.processors.DescriptorResultFormatter extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.qsar.DescriptorValue,Object> implements Serializable
  
  serialVersionUID:
  
  -8879440610070527255L
  - Serialized Fields
    - convertToString
```
boolean convertToString
```
    - format
```
NumberFormat format
```
    - index
```
int index
```
- Class ambit2.descriptors.processors.DescriptorsFactory extends AbstractDescriptorFactory<Profile<Property>> implements Serializable
  
  serialVersionUID:
  
  275242996048077139L
- Class ambit2.descriptors.processors.DescriptorValue2Property extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.qsar.DescriptorValue,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -5299954753073067252L
  - Serialized Fields
    - structure
```
IStructureRecord structure
```
- Class ambit2.descriptors.processors.PropertyCalculationProcessor extends DescriptorCalculationProcessor implements Serializable
  
  serialVersionUID:
  
  4826827029980497125L
  - Serialized Fields
    - property
```
Property property
```
    - cache
```
Map<K,V> cache
```
    - useCache
```
boolean useCache
```
Package ambit2.domain.stats.datastructures
- Class ambit2.domain.stats.datastructures.Histogram extends TreeMap<T extends Comparable,MutableInt> implements Serializable
Package ambit2.domain.stats.transforms.densityestimation
- Class ambit2.domain.stats.transforms.densityestimation.KCEpanechnikov extends Kernel implements Serializable
- Class ambit2.domain.stats.transforms.densityestimation.KDensity1D extends Object implements Serializable
  - Serialized Fields
    - Fmin
```
double Fmin
```
    - Fmax
```
double Fmax
```
    - FStep
```
double FStep
```
    - Resolution
```
double Resolution
```
    - kernelH
```
double kernelH
```
    - FGrid
```
double[] FGrid
```
    - FInterpolate
```
boolean FInterpolate
```
- Class ambit2.domain.stats.transforms.densityestimation.Kernel extends Object implements Serializable
  
  serialVersionUID:
  
  4014631502430481861L
  - Serialized Fields
    - KernelName
```
String KernelName
```
    - multiplier
```
double multiplier
```
    - R
```
double R
```
- Class ambit2.domain.stats.transforms.densityestimation.KLaplacian extends Kernel implements Serializable
- Class ambit2.domain.stats.transforms.densityestimation.KNormal extends Kernel implements Serializable
Package ambit2.domain.stats.transforms.transformfilters
- Class ambit2.domain.stats.transforms.transformfilters.OrthogonalTransform extends TransformFilter implements Serializable
  - Serialized Fields
    - FMeanVector
```
double[] FMeanVector
```
    - FScaleVector
```
double[] FScaleVector
```
    - FIndices
```
int[] FIndices
```
    - EigenValues
```
double[] EigenValues
```
    - EigenVectors
```
Jama.Matrix EigenVectors
```
    - EigenVectorsInverse
```
Jama.Matrix EigenVectorsInverse
```
    - FScaleInverse
```
double[] FScaleInverse
```
- Class ambit2.domain.stats.transforms.transformfilters.TransformFilter extends Object implements Serializable
  
  serialVersionUID:
  
  373435065193751882L
  - Serialized Fields
    - FMinVector
```
double[] FMinVector
```
    - FMaxVector
```
double[] FMaxVector
```
    - FInputDescriptorNumber
```
int FInputDescriptorNumber
```
    - FOutputDescriptorNumber
```
int FOutputDescriptorNumber
```
    - FEnabled
```
boolean FEnabled
```
    - FDescriptorsRankThreshold
```
double FDescriptorsRankThreshold
```
    - TransformError
```
int[] TransformError
```
Package ambit2.dragon
- Class ambit2.dragon.AbstractDescriptorShell extends CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  846520553482086575L
- Class ambit2.dragon.DragonShell extends AbstractDescriptorShell implements Serializable
  
  serialVersionUID:
  
  3357377118450137010L
  - Serialized Fields
    - descriptors
```
DragonDescriptorDictionary descriptors
```
    - inFile
```
String[] inFile
```
    - outFile
```
String[] outFile
```
Package ambit2.export.isa.v1_0
- Class ambit2.export.isa.v1_0.ISAJsonExporter1_0 extends Object implements Serializable
  
  serialVersionUID:
  
  1052243240384487847L
  - Serialized Fields
    - enabled
```
boolean enabled
```
    - outputDir
```
File outputDir
```
    - exportConfig
```
File exportConfig
```
    - xmlISAConfig
```
File xmlISAConfig
```
    - externalDataFile
```
File externalDataFile
```
    - extDataManager
```
ExternalDataFileManager extDataManager
```
    - ontologyManager
```
OntologyManager1_0 ontologyManager
```
    - cfg
```
ISAJsonExportConfig cfg
```
    - investigation
```
Investigation investigation
```
    - isaMapper
```
ISAJsonMapper1_0 isaMapper
```
Package ambit2.jchempaint.editor
- Class ambit2.jchempaint.editor.AbstractMoleculeAction extends AbstractAction implements Serializable
  - Serialized Fields
    - molecule
```
org.openscience.cdk.interfaces.IAtomContainer molecule
```
- Class ambit2.jchempaint.editor.JChemPaintDialog extends JDialog implements Serializable
  
  serialVersionUID:
  
  8382571970782141100L
  - Serialized Fields
    - jcpep
```
org.openscience.jchempaint.JChemPaintPanel jcpep
```
    - result
```
int result
```
- Class ambit2.jchempaint.editor.MoleculeEditAction extends AbstractMoleculeAction implements Serializable
  
  serialVersionUID:
  
  5166718649430988452L
  - Serialized Fields
    - molecules
```
org.openscience.cdk.interfaces.IAtomContainerSet molecules
```
    - jcpModel
```
org.openscience.cdk.interfaces.IChemModel jcpModel
```
    - sdg
```
org.openscience.cdk.layout.StructureDiagramGenerator sdg
```
    - parentComponent
```
Component parentComponent
```
    - jcpDialog
```
JChemPaintDialog jcpDialog
```
    - modal
```
boolean modal
```
Package ambit2.markush
- Class ambit2.markush.MarkushException extends Exception implements Serializable
  
  serialVersionUID:
  
  583453585294567201L
Package ambit2.model.builder
- Class ambit2.model.builder.AbstractModelBuilder extends net.idea.modbcum.p.DefaultAmbitProcessor<A extends Algorithm,Model extends ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  3721710990307131078L
  - Serialized Fields
    - targetURI
```
String[] targetURI
```
    - parameters
```
String[] parameters
```
    - trainingData
```
Object trainingData
```
Package ambit2.model.numeric
- Class ambit2.model.numeric.DataCoverage extends Object implements Serializable
  
  serialVersionUID:
  
  5355137220284907331L
  - Serialized Fields
    - appDomainMethodType
```
ADomainMethodType appDomainMethodType
```
    - threshold
```
double threshold
```
    - pThreshold
```
double pThreshold
```
- Class ambit2.model.numeric.DataCoverageDensity extends DataCoverageDescriptors implements Serializable
  
  serialVersionUID:
  
  -4530499526801051110L
  - Serialized Fields
    - theKernel
```
Kernel theKernel
```
    - kdeList
```
KDensity1D[] kdeList
```
    - nGrid
```
int nGrid
```
- Class ambit2.model.numeric.DataCoverageDescriptors extends DataCoverage<Jama.Matrix> implements Serializable
  
  serialVersionUID:
  
  730617163278629469L
  - Serialized Fields
    - datasetCenterPoint
```
DatasetCenterPoint datasetCenterPoint
```
    - scale
```
boolean scale
```
    - pca
```
boolean pca
```
    - boxcox
```
boolean boxcox
```
    - mindata
```
double[] mindata
```
    - maxdata
```
double[] maxdata
```
    - pcaTransform
```
OrthogonalTransform pcaTransform
```
- Class ambit2.model.numeric.DataCoverageDistance extends DataCoverageDescriptors implements Serializable
  
  serialVersionUID:
  
  4288804703751436528L
  - Serialized Fields
    - meandata
```
double[] meandata
```
- Class ambit2.model.numeric.DataCoverageLeverage extends DataCoverage<Jama.Matrix> implements Serializable
  
  serialVersionUID:
  
  -8841985800478607411L
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException
```
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
```
private void writeObject(ObjectOutputStream stream)
                  throws IOException
```
      Throws:
      
      IOException
  - Serialized Fields
    - X
```
Jama.Matrix X
```
- Class ambit2.model.numeric.DataCoverageLeverageHatMatrix extends DataCoverage<Jama.Matrix> implements Serializable
  
  serialVersionUID:
  
  -8841985800478607411L
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException
```
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
```
private void writeObject(ObjectOutputStream stream)
                  throws IOException
```
      Throws:
      
      IOException
  - Serialized Fields
    - X
```
Jama.Matrix X
```
Package ambit2.model.numeric.distance
- Class ambit2.model.numeric.distance.DataCoverageDistanceCityBlock extends DataCoverageDistance implements Serializable
  
  serialVersionUID:
  
  4750791138097501986L
- Class ambit2.model.numeric.distance.DataCoverageDistanceEuclidean extends DataCoverageDistance implements Serializable
  
  serialVersionUID:
  
  6182394064995003521L
- Class ambit2.model.numeric.distance.DataCoverageDistanceMahalanobis extends DataCoverageDistance implements Serializable
  
  serialVersionUID:
  
  545962040271628450L
Package ambit2.model.structure
- Class ambit2.model.structure.DataCoverageFingeprintsMissingFragments extends DataCoverageFingerprints implements Serializable
  
  serialVersionUID:
  
  -732145918036578793L
- Class ambit2.model.structure.DataCoverageFingerprints extends DataCoverage<List<BitSet>> implements Serializable
  
  serialVersionUID:
  
  8338115538206282818L
  - Serialized Fields
    - fingerPrintLength
```
int fingerPrintLength
```
    - fingerprintsCalculated
```
int fingerprintsCalculated
```
    - consensusFingerprint
```
BitSet consensusFingerprint
```
    - fpProfile
```
double[] fpProfile
```
- Class ambit2.model.structure.DataCoverageFingerprintsTanimoto extends DataCoverageFingerprints implements Serializable
  
  serialVersionUID:
  
  -2253589622326446088L
Package ambit2.mopac
- Class ambit2.mopac.AbstractMopacShell extends CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -5948332340539224507L
  - Serialized Fields
    - maxHeavyAtoms
```
int maxHeavyAtoms
```
    - maxAllAtoms
```
int maxAllAtoms
```
    - mopac_commands
```
String mopac_commands
```
    - useOriginalStructure
```
boolean useOriginalStructure
```
    - optimize
```
boolean optimize
```
    - inFile
```
String inFile
```
    - outFiles
```
String[] outFiles
```
    - errorIfDisconnected
```
boolean errorIfDisconnected
```
    - table
```
String[] table
```
- Class ambit2.mopac.MopacShell extends AbstractMopacShell implements Serializable
  
  serialVersionUID:
  
  -8813390861716760573L
  - Serialized Fields
    - smi2sdf
```
ShellSmi2SDF smi2sdf
```
    - mengine
```
ShellMengine mengine
```
- Class ambit2.mopac.MopacShellBalloon extends AbstractMopacShell implements Serializable
  
  serialVersionUID:
  
  3625737861693976094L
  - Serialized Fields
    - shellBalloon
```
ShellBalloon shellBalloon
```
- Class ambit2.mopac.MopacShellOB extends AbstractMopacShell implements Serializable
  
  serialVersionUID:
  
  -2622221792381035489L
  - Serialized Fields
    - shell
```
OpenBabelGen3D shell
```
Package ambit2.namestructure
- Class ambit2.namestructure.Name2StructureFinder extends AbstractFinder<Name2StructureProcessor,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -3159036024126147810L
  - Serialized Fields
    - record
```
IStructureRecord record
```
- Class ambit2.namestructure.Name2StructureProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<String,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -6157770369957204199L
  - Serialized Fields
    - nameToStructure
```
uk.ac.cam.ch.wwmm.opsin.NameToStructure nameToStructure
```
Package ambit2.pubchem
- Class ambit2.pubchem.BatchRetrievePubChem extends net.idea.modbcum.p.DefaultAmbitProcessor<String,Integer> implements Serializable
  
  serialVersionUID:
  
  3658928227952234163L
  - Serialized Fields
    - resultDir
```
String resultDir
```
    - logfile
```
String logfile
```
- Class ambit2.pubchem.DepictRequest extends net.idea.modbcum.p.DefaultAmbitProcessor<String,BufferedImage> implements Serializable
  
  serialVersionUID:
  
  -8933763425306077100L
  - Serialized Fields
    - root
```
String root
```
    - server
```
String server
```
    - form
```
String form
```
    - imagesrc
```
String imagesrc
```
- Class ambit2.pubchem.EntrezESearchParser extends net.idea.modbcum.p.DefaultAmbitProcessor<InputStream,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  1147135155708179050L
- Class ambit2.pubchem.EntrezSearchProcessor extends HTTPRequest<String,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  -8215370335359483817L
  - Serialized Fields
    - parser
```
EntrezESearchParser parser
```
    - pug
```
PUGProcessor pug
```
    - retrieve_sdf
```
boolean retrieve_sdf
```
- Class ambit2.pubchem.FileNotFoundException extends ProcessorException implements Serializable
  
  serialVersionUID:
  
  8657450659186925103L
- Class ambit2.pubchem.HTTPRequest extends net.idea.modbcum.p.DefaultAmbitProcessor<Target,Result> implements Serializable
  
  serialVersionUID:
  
  -3444405772335211466L
  - Serialized Fields
    - timeout
```
int timeout
```
    - maxretry
```
int maxretry
```
    - url
```
String url
```
    - httpMethod
```
String httpMethod
```
    - cancelled
```
boolean cancelled
```
- Class ambit2.pubchem.NCISearchProcessor extends HTTPRequest<String,String> implements Serializable
  
  serialVersionUID:
  
  1503961338542812463L
  - Serialized Fields
    - wait_ms
```
long wait_ms
```
    - nci_url
```
String nci_url
```
    - host
```
String host
```
    - option
```
NCISearchProcessor.METHODS option
```
- Class ambit2.pubchem.PubchemFinder extends AbstractFinder<EntrezSearchProcessor,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  1681833725212826604L
- Class ambit2.pubchem.PUGProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<List<IStructureRecord>,List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  4410271093960202855L
  - Serialized Fields
    - support
```
QuerySupport<Target,Result> support
```
    - retrieveConformers
```
boolean retrieveConformers
```
- Class ambit2.pubchem.ServerError extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  -2702476035421353328L
  - Serialized Fields
    - status
```
int status
```
Package ambit2.pubchem.rest
- Class ambit2.pubchem.rest.PubChemRestFinder extends AbstractFinder<PUGRestCompoundRequest,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  1681833725212826604L
- Class ambit2.pubchem.rest.PUGRestCompoundRequest extends PUGRestRequest<List<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  7930190885253688770L
- Class ambit2.pubchem.rest.PUGRestImageRequest extends PUGRestRequest<BufferedImage> implements Serializable
  
  serialVersionUID:
  
  8697178762300415861L
  - Serialized Fields
    - imageSize
```
PUGRestImageRequest.IMAGE_SIZE imageSize
```
    - recordType
```
PUGRestImageRequest.RECORD_TYPE recordType
```
    - width
```
int width
```
    - height
```
int height
```
- Class ambit2.pubchem.rest.PUGRestRequest extends AbstractSearchRequest<R> implements Serializable
  
  serialVersionUID:
  
  -4821305383980518514L
  - Serialized Fields
    - input
```
PUGRestRequest.COMPOUND_DOMAIN_INPUT input
```
    - operation
```
PUGRestRequest.COMPOUND_DOMAIN_OPERATION operation
```
    - output
```
PUGRestRequest.COMPOUND_DOMAIN_OUTPUT output
```
Package ambit2.rendering
- Class ambit2.rendering.StructureEditorProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,String> implements Serializable
  
  serialVersionUID:
  
  -6384602483929803381L
  - Serialized Fields
    - command
```
StructureEditorProcessor._commands command
```
Package ambit2.rest
- Class ambit2.rest.QueryStaXReporter extends net.idea.modbcum.r.QueryReporter<T,Q extends net.idea.modbcum.i.IQueryRetrieval<T>,XMLStreamWriter> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - uriReporter
```
net.idea.restnet.db.QueryURIReporter<T,Q extends net.idea.modbcum.i.IQueryRetrieval<T>> uriReporter
```
    - recordWriter
```
AbstractStaxRDFWriter<INPUT,OUTPUT> recordWriter
```
    - compoundInDatasetPrefix
```
String compoundInDatasetPrefix
```
- Class ambit2.rest.RDFBatchParser extends net.idea.modbcum.p.batch.AbstractBatchProcessor<org.restlet.data.Reference,Item> implements Serializable
  
  serialVersionUID:
  
  -8921517639325859050L
  - Serialized Fields
    - rdfObjectIterator
```
RDFObjectIterator<Item> rdfObjectIterator
```
    - baseReference
```
String baseReference
```
    - objectToParse
```
String objectToParse
```
    - mediaType
```
org.restlet.data.MediaType mediaType
```
- Class ambit2.rest.RemoteStreamConvertor extends net.idea.modbcum.p.DefaultAmbitProcessor<ByteArrayOutputStream,org.restlet.representation.Representation> implements Serializable
  
  serialVersionUID:
  
  4450496053693119759L
  - Serialized Fields
    - query
```
WrappedService<C extends org.apache.http.auth.Credentials> query
```
    - media
```
org.restlet.data.MediaType media
```
    - entityType
```
org.restlet.data.MediaType entityType
```
    - entity
```
ByteArrayOutputStream entity
```
    - method
```
org.restlet.data.Method method
```
    - fileNamePrefix
```
String fileNamePrefix
```
    - fileExtension
```
String fileExtension
```
- Class ambit2.rest.StreamConvertor extends net.idea.restnet.c.RepresentationConvertor<T,Q,OutputStream,R extends net.idea.modbcum.i.reporter.Reporter<Q,OutputStream>> implements Serializable
  
  serialVersionUID:
  
  1652253598534818669L
Package ambit2.rest.algorithm
- Class ambit2.rest.algorithm.AlgorithmURIReporter extends CatalogURIReporter<Algorithm> implements Serializable
  
  serialVersionUID:
  
  4802490674242368703L
Package ambit2.rest.dataset
- Class ambit2.rest.dataset.AbstractStaxRDFWriter extends net.idea.modbcum.p.DefaultAmbitProcessor<INPUT,OUTPUT> implements Serializable
  
  serialVersionUID:
  
  446909136995475303L
  - Serialized Fields
    - output
```
XMLStreamWriter output
```
    - uriReporter
```
net.idea.restnet.db.QueryURIReporter<T,Q extends net.idea.modbcum.i.IQueryRetrieval<T>> uriReporter
```
- Class ambit2.rest.dataset.DatasetRDFStaxReporter extends QueryStaXReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,DatasetRDFWriter> implements Serializable
  
  serialVersionUID:
  
  1676895914680469360L
- Class ambit2.rest.dataset.DatasetRDFWriter extends AbstractStaxRDFWriter<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -1825074197173628894L
  - Serialized Fields
    - datasetIndividual
```
String datasetIndividual
```
    - header
```
List<E> header
```
    - propertyReporter
```
PropertyURIReporter propertyReporter
```
    - compoundReporter
```
CompoundURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter
```
    - comp
```
Comparator<T> comp
```
    - groupProperties
```
Profile<P extends Property> groupProperties
```
    - licenseURI
```
String licenseURI
```
    - template
```
Template template
```
- Class ambit2.rest.dataset.DatasetURIReporter extends net.idea.restnet.db.QueryURIReporter<M extends ISourceDataset,Q extends net.idea.modbcum.i.IQueryRetrieval<M>> implements Serializable
  
  serialVersionUID:
  
  3648376868814044783L
- Class ambit2.rest.dataset.RDFFileWriter extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -7626753873168651075L
  - Serialized Fields
    - recordWriter
```
DatasetRDFWriter recordWriter
```
- Class ambit2.rest.dataset.RDFInstancesParser extends RDFBatchParser<weka.core.Instance> implements Serializable
  
  serialVersionUID:
  
  5276450707875380321L
  - Serialized Fields
    - referer
```
String referer
```
- Class ambit2.rest.dataset.RDFStructuresReader extends RDFBatchParser<IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  7079139854857529405L
  - Serialized Fields
    - referer
```
String referer
```
Package ambit2.rest.exception
- Class ambit2.rest.exception.ImportSubstanceException extends org.restlet.resource.ResourceException implements Serializable
  
  serialVersionUID:
  
  8559378742531504299L
  - Serialized Fields
    - details
```
String details
```
- Class ambit2.rest.exception.RResourceException extends org.restlet.resource.ResourceException implements Serializable
  
  serialVersionUID:
  
  6405322729021154626L
  - Serialized Fields
    - variant
```
org.restlet.representation.Variant variant
```
- Class ambit2.rest.exception.TaskException extends org.restlet.resource.ResourceException implements Serializable
  
  serialVersionUID:
  
  5060840500563021260L
  - Serialized Fields
    - URL
```
String URL
```
    - subtasksStatus
```
List<E> subtasksStatus
```
Package ambit2.rest.legacy
- Class ambit2.rest.legacy.OTAlgorithm extends OTProcessingResource implements Serializable
  
  serialVersionUID:
  
  -2661587415132661190L
- Class ambit2.rest.legacy.OTAlgorithms extends OTProcessingContainers<OTAlgorithm> implements Serializable
  
  serialVersionUID:
  
  -8743429754894223373L
- Class ambit2.rest.legacy.OTCompound extends OTObject implements Serializable
  
  serialVersionUID:
  
  -979314615579855647L
  - Serialized Fields
    - identifiers
```
Hashtable<K,V> identifiers
```
      Deprecated.
- Class ambit2.rest.legacy.OTContainers extends OTProcessingResource implements Serializable
  
  serialVersionUID:
  
  -461676329820947445L
  - Serialized Fields
    - items
```
List<E> items
```
      Deprecated.
- Class ambit2.rest.legacy.OTDataset extends OTObject implements Serializable
  - Serialized Fields
    - isEmpty
```
OTDataset.dataset_size isEmpty
```
      Deprecated.
    - license
```
String license
```
      Deprecated.
    - source
```
String source
```
      Deprecated.
    - seeAlso
```
String seeAlso
```
      Deprecated.
- Class ambit2.rest.legacy.OTDatasets extends OTContainers<OTDataset> implements Serializable
  
  serialVersionUID:
  
  7638982655806506900L
- Class ambit2.rest.legacy.OTFeature extends OTProcessingResource implements Serializable
  - Serialized Fields
    - algorithm
```
OTAlgorithm algorithm
```
      Deprecated.
    - isNumeric
```
boolean isNumeric
```
      Deprecated.
    - isNominal
```
boolean isNominal
```
      Deprecated.
    - units
```
String units
```
      Deprecated.
- Class ambit2.rest.legacy.OTFeatures extends OTProcessingContainers<OTFeature> implements Serializable
  
  serialVersionUID:
  
  -5711791565860384883L
- Class ambit2.rest.legacy.OTModel extends OTProcessingResource implements Serializable
  - Serialized Fields
    - endpointName
```
String endpointName
```
      Deprecated.
    - supportsPredictedVarURI
```
boolean supportsPredictedVarURI
```
      Deprecated.
    - endpointURI
```
String endpointURI
```
      Deprecated.
    - independentVariables
```
OTFeatures independentVariables
```
      Deprecated.
    - creator
```
String creator
```
      Deprecated.
    - trainingData
```
OTDataset trainingData
```
      Deprecated.
    - algorithm
```
OTAlgorithm algorithm
```
      Deprecated.
    - dependentVariables
```
OTFeatures dependentVariables
```
      Deprecated.
    - predictedVariables
```
OTFeatures predictedVariables
```
      Deprecated.
- Class ambit2.rest.legacy.OTObject extends Object implements Serializable
  
  serialVersionUID:
  
  1085797924363749090L
  - Serialized Fields
    - selected
```
boolean selected
```
      Deprecated.
    - forbidden
```
boolean forbidden
```
      Deprecated.
    - name
```
String name
```
      Deprecated.
    - form
```
org.restlet.data.Form form
```
      Deprecated.
    - pollInterval
```
long pollInterval
```
      Deprecated.
    - pollTimeout
```
long pollTimeout
```
      Deprecated.
- Class ambit2.rest.legacy.OTOntologyService extends OTObject implements Serializable
  
  serialVersionUID:
  
  -8906409505260761688L
- Class ambit2.rest.legacy.OTProcessingContainers extends OTContainers<T extends OTProcessingResource> implements Serializable
  
  serialVersionUID:
  
  -2923678513191494188L
- Class ambit2.rest.legacy.OTProcessingResource extends OTObject implements Serializable
  
  serialVersionUID:
  
  -3483706848787877937L
  - Serialized Fields
    - referer
```
String referer
```
      Deprecated.
- Class ambit2.rest.legacy.OTRemoteTask extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - url
```
org.restlet.data.Reference url
```
      Deprecated.
    - status
```
org.restlet.data.Status status
```
      Deprecated.
    - result
```
org.restlet.data.Reference result
```
      Deprecated.
    - error
```
Exception error
```
      Deprecated.
- Class ambit2.rest.legacy.OTSuperModel extends OTModel implements Serializable
Package ambit2.rest.model
- Class ambit2.rest.model.ModelURIReporter extends net.idea.restnet.db.QueryURIReporter<ModelQueryResults,Q extends net.idea.modbcum.i.IQueryRetrieval<ModelQueryResults>> implements Serializable
  
  serialVersionUID:
  
  3648376868814044783L
Package ambit2.rest.model.builder
- Class ambit2.rest.model.builder.AbstractStructuresModelBuilder extends ModelBuilder<DATA,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -5510875688817299687L
- Class ambit2.rest.model.builder.CoverageModelBuilder extends ModelBuilder<weka.core.Instances,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  4281612770780436429L
  - Serialized Fields
    - predictedFeatureURI
```
String predictedFeatureURI
```
- Class ambit2.rest.model.builder.ExpertModelBuilder extends SimpleModelBuilder implements Serializable
  
  serialVersionUID:
  
  -2375350593328937076L
  - Serialized Fields
    - modelHidden
```
boolean modelHidden
```
    - userName
```
String userName
```
    - datasetURI
```
String datasetURI
```
- Class ambit2.rest.model.builder.FingerprintsModelBuilder extends ModelBuilder<List<BitSet>,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  4281612770780436429L
  - Serialized Fields
    - predictedFeatureURI
```
String predictedFeatureURI
```
- Class ambit2.rest.model.builder.ModelBuilder extends AbstractModelBuilder<DATA,A extends Algorithm,Model extends ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  3721710990307131078L
  - Serialized Fields
    - model_reporter
```
ModelURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<ModelQueryResults>> model_reporter
```
    - alg_reporter
```
AlgorithmURIReporter alg_reporter
```
    - applicationRootReference
```
org.restlet.data.Reference applicationRootReference
```
    - referer
```
String referer
```
- Class ambit2.rest.model.builder.SimpleModelBuilder extends ModelBuilder<Object,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -2827461619547962205L
  - Serialized Fields
    - modelHidden
```
boolean modelHidden
```
    - parameters
```
String[] parameters
```
- Class ambit2.rest.model.builder.SMSDModelBuilder extends AbstractStructuresModelBuilder<ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -3199396535541771758L
Package ambit2.rest.model.predictor
- Class ambit2.rest.model.predictor.AbstractStructureProcessor extends ModelPredictor<Predictor,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  861458621962435019L
  - Serialized Fields
    - updateStructure
```
UpdateStructure updateStructure
```
    - exec
```
UpdateExecutor<Q extends net.idea.modbcum.i.query.IQueryUpdate> exec
```
- Class ambit2.rest.model.predictor.CoveragePredictor extends ModelPredictor<DataCoverage,Input> implements Serializable
  
  serialVersionUID:
  
  2227441480460487334L
- Class ambit2.rest.model.predictor.DescriptorPredictor extends ModelPredictor<C extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord>,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8106073411946010587L
  - Serialized Fields
    - mopac_commands
```
String mopac_commands
```
    - calculator
```
net.idea.modbcum.p.AbstractDBProcessor<Target,Result> calculator
```
- Class ambit2.rest.model.predictor.ExpertModelpredictor extends ModelPredictor<Predictor,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -5270628252984937908L
  - Serialized Fields
    - value
```
Object value
```
- Class ambit2.rest.model.predictor.ExternalModel extends Object implements Serializable
  
  serialVersionUID:
  
  9072575012057496754L
  - Serialized Fields
    - model
```
Object model
```
- Class ambit2.rest.model.predictor.ExternalModelPredictor extends ModelPredictor<C extends ExternalModel,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -9183148308530951202L
  - Serialized Fields
    - predictedProperties
```
List<E> predictedProperties
```
- Class ambit2.rest.model.predictor.FingerprintsPredictor extends CoveragePredictor<IStructureRecord,List<BitSet>> implements Serializable
  
  serialVersionUID:
  
  -5981058745327200642L
  - Serialized Fields
    - fpgen
```
FingerprintGenerator<FGenerator extends org.openscience.cdk.fingerprint.IFingerprinter> fpgen
```
    - reader
```
MoleculeReader reader
```
    - bitsets
```
List<E> bitsets
```
- Class ambit2.rest.model.predictor.ModelPredictor extends net.idea.modbcum.p.AbstractDBProcessor<NativeTypeItem,IStructureRecord> implements Serializable
  
  serialVersionUID:
  
  -8267727629802363087L
  - Serialized Fields
    - model
```
ModelQueryResults model
```
    - imageSize
```
Dimension imageSize
```
    - structureRequired
```
boolean structureRequired
```
    - valuesRequired
```
boolean valuesRequired
```
    - predictor
```
Object predictor
```
    - classIndex
```
int classIndex
```
    - header
```
weka.core.Instances header
```
    - filter
```
weka.filters.Filter filter
```
    - targetURI
```
String[] targetURI
```
    - modelReporter
```
ModelURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<ModelQueryResults>> modelReporter
```
    - propertyReporter
```
PropertyURIReporter propertyReporter
```
    - applicationRootReference
```
org.restlet.data.Reference applicationRootReference
```
    - compoundURITemplate
```
org.restlet.routing.Template compoundURITemplate
```
    - conformerURITemplate
```
org.restlet.routing.Template conformerURITemplate
```
    - record
```
IStructureRecord record
```
- Class ambit2.rest.model.predictor.NumericADPredictor extends CoveragePredictor<IStructureRecord,Jama.Matrix> implements Serializable
  
  serialVersionUID:
  
  4940602547639105140L
  - Serialized Fields
    - propertyReporter
```
PropertyURIReporter propertyReporter
```
- Class ambit2.rest.model.predictor.Structure2DProcessor extends AbstractStructureProcessor<CompoundImageTools> implements Serializable
  
  serialVersionUID:
  
  2666994533139041193L
- Class ambit2.rest.model.predictor.StructureProcessor extends AbstractStructureProcessor<AbstractMopacShell> implements Serializable
  
  serialVersionUID:
  
  -8106073411946010587L
Package ambit2.rest.property
- Class ambit2.rest.property.PropertyURIReporter extends net.idea.restnet.db.QueryURIReporter<Property,net.idea.modbcum.i.IQueryRetrieval<Property>> implements Serializable
  
  serialVersionUID:
  
  711954935147788056L
Package ambit2.rest.reporters
- Class ambit2.rest.reporters.CatalogRDFReporter extends ListReporter<T,Writer> implements Serializable
  
  serialVersionUID:
  
  1805248585197091514L
  - Serialized Fields
    - mediaType
```
org.restlet.data.MediaType mediaType
```
    - jenaModel
```
com.hp.hpl.jena.ontology.OntModel jenaModel
```
- Class ambit2.rest.reporters.CatalogURIReporter extends ListReporter<T,Writer> implements Serializable
  
  serialVersionUID:
  
  2871865183499748866L
  - Serialized Fields
    - request
```
org.restlet.Request request
```
    - baseReference
```
org.restlet.data.Reference baseReference
```
- Class ambit2.rest.reporters.TaskRDFReporter extends CatalogRDFReporter<UUID> implements Serializable
  
  serialVersionUID:
  
  3789102915378513270L
  - Serialized Fields
    - storage
```
net.idea.restnet.i.task.ITaskStorage<USERID> storage
```
    - baseRef
```
org.restlet.data.Reference baseRef
```
    - urireporter
```
TaskURIReporter<USERID> urireporter
```
- Class ambit2.rest.reporters.TaskURIReporter extends CatalogURIReporter<UUID> implements Serializable
  
  serialVersionUID:
  
  9136099541989811170L
  - Serialized Fields
    - storage
```
net.idea.restnet.i.task.ITaskStorage<USERID> storage
```
Package ambit2.rest.structure
- Class ambit2.rest.structure.CompoundURIReporter extends net.idea.restnet.db.QueryURIReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  3648376868814044783L
  - Serialized Fields
    - readStructure
```
boolean readStructure
```
    - prefix
```
String prefix
```
- Class ambit2.rest.structure.ConformerURIReporter extends CompoundURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> implements Serializable
  
  serialVersionUID:
  
  -3240656616658257198L
Package ambit2.rest.study
- Class ambit2.rest.study.BucketJson2CSVConvertor extends net.idea.modbcum.p.DefaultAmbitProcessor<InputStream,OutputStream> implements Serializable
  
  serialVersionUID:
  
  -4805381027500815039L
  - Serialized Fields
    - delimiter
```
String delimiter
```
    - dx
```
com.fasterxml.jackson.databind.ObjectMapper dx
```
    - out
```
OutputStream out
```
    - headers
```
List<E> headers
```
    - paramHeaders
```
List<E> paramHeaders
```
    - studyHeaders
```
List<E> studyHeaders
```
    - conditionHeaders
```
List<E> conditionHeaders
```
    - moreHeaders
```
List<E> moreHeaders
```
    - _dontadd
```
String[] _dontadd
```
Package ambit2.rest.substance
- Class ambit2.rest.substance.SubstanceBundleStAXReporter extends QueryStaXReporter<SubstanceRecord,net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>,SubstanceRecordStaxWriter> implements Serializable
  
  serialVersionUID:
  
  4249582934025698175L
- Class ambit2.rest.substance.SubstanceRDFReporter extends net.idea.restnet.db.convertors.QueryRDFReporter<SubstanceRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> implements Serializable
  
  serialVersionUID:
  
  -4522513627076425922L
  - Serialized Fields
    - base
```
String base
```
    - propertyReporter
```
PropertyURIReporter propertyReporter
```
    - compoundReporter
```
CompoundURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter
```
    - dx
```
com.fasterxml.jackson.databind.ObjectMapper dx
```
- Class ambit2.rest.substance.SubstanceRecordStaxWriter extends AbstractStaxRDFWriter<SubstanceRecord,SubstanceRecord> implements Serializable
  
  serialVersionUID:
  
  5591294383381439253L
- Class ambit2.rest.substance.SubstanceURIReporter extends net.idea.restnet.db.QueryURIReporter<SubstanceRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<SubstanceRecord>> implements Serializable
  
  serialVersionUID:
  
  3811264823419677254L
Package ambit2.rest.task
- Class ambit2.rest.task.Task extends Object implements Serializable
  
  serialVersionUID:
  
  -646087833848914553L
  - Serialized Fields
    - result
```
Object result
```
    - name
```
String name
```
    - started
```
long started
```
    - completed
```
long completed
```
    - internal
```
boolean internal
```
    - percentCompleted
```
float percentCompleted
```
    - userid
```
Object userid
```
    - uuid
```
UUID uuid
```
    - error
```
org.restlet.resource.ResourceException error
```
    - policyError
```
Exception policyError
```
    - status
```
net.idea.restnet.i.task.TaskStatus status
```
- Class ambit2.rest.task.TaskJSONReporter extends TaskURIReporter<USERID> implements Serializable
  
  serialVersionUID:
  
  9136099541989811170L
  - Serialized Fields
    - comma
```
String comma
```
Package ambit2.rest.task.dsl
- Class ambit2.rest.task.dsl.OTDatasetComparisonReport extends OTObject implements Serializable
  - Serialized Fields
    - ontology_service
```
org.restlet.data.Reference ontology_service
```
    - application
```
org.restlet.data.Reference application
```
    - datasets1
```
OTDatasets datasets1
```
    - datasets2
```
OTDatasets datasets2
```
    - datasetReportRef
```
org.restlet.data.Reference datasetReportRef
```
- Class ambit2.rest.task.dsl.OTDatasetRDFReport extends OTObject implements Serializable
  - Serialized Fields
    - jenaModel
```
com.hp.hpl.jena.rdf.model.Model jenaModel
```
    - application
```
String application
```
    - dataset
```
OTDataset dataset
```
    - page
```
int page
```
    - pageSize
```
int pageSize
```
    - showEndpoints
```
boolean showEndpoints
```
    - showFeatures
```
boolean showFeatures
```
    - requestref
```
org.restlet.data.Reference requestref
```
- Class ambit2.rest.task.dsl.OTDatasetReport extends OTObject implements Serializable
  - Serialized Fields
    - header
```
List<E> header
```
    - values
```
List<E> values
```
    - application
```
String application
```
    - dataset
```
OTDataset dataset
```
    - features
```
OTFeatures features
```
    - page
```
int page
```
    - pageSize
```
int pageSize
```
    - requestref
```
org.restlet.data.Reference requestref
```
- Class ambit2.rest.task.dsl.OTDatasetScrollableReport extends OTDatasetReport implements Serializable
- Class ambit2.rest.task.dsl.OTDatasetTableReport extends OTDatasetReport implements Serializable
Package ambit2.rest.task.weka
- Class ambit2.rest.task.weka.FilteredWekaModelBuilder extends ModelBuilder<weka.core.Instances,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -4372904815135663667L
  - Serialized Fields
    - fclusterer
```
weka.clusterers.FilteredClusterer fclusterer
```
    - fclassifier
```
weka.classifiers.meta.FilteredClassifier fclassifier
```
    - pca
```
weka.attributeSelection.PrincipalComponents pca
```
- Class ambit2.rest.task.weka.FilteredWekaPredictor extends ModelPredictor<T,weka.core.Instance> implements Serializable
  
  serialVersionUID:
  
  1394180227835161276L
  - Serialized Fields
    - classifier
```
weka.classifiers.Classifier classifier
```
    - clusterer
```
weka.clusterers.Clusterer clusterer
```
    - pca
```
weka.attributeSelection.PrincipalComponents pca
```
- Class ambit2.rest.task.weka.WekaModelBuilder extends ModelBuilder<weka.core.Instances,Algorithm,ModelQueryResults> implements Serializable
  
  serialVersionUID:
  
  -4372904815135663667L
  - Serialized Fields
    - clusterer
```
weka.clusterers.Clusterer clusterer
```
    - classifier
```
weka.classifiers.Classifier classifier
```
    - pca
```
weka.attributeSelection.PrincipalComponents pca
```
- Class ambit2.rest.task.weka.WekaPredictor extends ModelPredictor<T,weka.core.Instance> implements Serializable
  
  serialVersionUID:
  
  1394180227835161276L
  - Serialized Fields
    - classifier
```
weka.classifiers.Classifier classifier
```
    - clusterer
```
weka.clusterers.Clusterer clusterer
```
    - pca
```
weka.attributeSelection.PrincipalComponents pca
```
Package ambit2.search
- Class ambit2.search.AllSourcesFinder extends AbstractFinder<net.idea.modbcum.i.processors.IProcessor<String,String>,String> implements Serializable
  
  serialVersionUID:
  
  -7059985528732316425L
Package ambit2.search.chemidplus
- Class ambit2.search.chemidplus.AbstractSearchRequest extends net.idea.modbcum.p.DefaultAmbitProcessor<String,R> implements Serializable
  
  serialVersionUID:
  
  -5629570446572417364L
- Class ambit2.search.chemidplus.ChemIdPlusRequest extends AbstractSearchRequest<String> implements Serializable
  
  serialVersionUID:
  
  4023235628557946550L
Package ambit2.search.csls
- Class ambit2.search.csls.CSLSImageRequest extends CSLSRequest<BufferedImage> implements Serializable
  
  serialVersionUID:
  
  8697178762300415861L
  - Serialized Fields
    - width
```
int width
```
    - height
```
int height
```
- Class ambit2.search.csls.CSLSRequest extends AbstractSearchRequest<R> implements Serializable
  
  serialVersionUID:
  
  -4821305383980518514L
  - Serialized Fields
    - representation
```
NCISearchProcessor.METHODS representation
```
- Class ambit2.search.csls.CSLSStringRequest extends CSLSRequest<String> implements Serializable
  
  serialVersionUID:
  
  6645197141747700467L
Package ambit2.search.opentox
- Class ambit2.search.opentox.OpenToxRequest extends AbstractSearchRequest<String> implements Serializable
  
  serialVersionUID:
  
  4186581307201678996L
  - Serialized Fields
    - opentoxservice
```
String opentoxservice
```
Package ambit2.similarity.knn
- Class ambit2.similarity.knn.NearestNeighborsSearch extends ArrayList<DistanceComparable<T>> implements Serializable
  - Serialized Fields
    - distanceFunction
```
IDistanceFunction<T> distanceFunction
```
    - lowestDistanceIsClosest
```
boolean lowestDistanceIsClosest
```
Package ambit2.similarity.stats
- Class ambit2.similarity.stats.ConfusionMatrix extends AbstractTableModel implements Serializable
  - Serialized Fields
    - observed
```
ArrayList<E> observed
```
    - predicted
```
ArrayList<E> predicted
```
    - histogram
```
Histogram<T extends Comparable> histogram
```
    - vp
```
SelfBin<T extends Comparable> vp
```
- Class ambit2.similarity.stats.Histogram extends TreeMap<T extends Comparable,MutableInt> implements Serializable
Package ambit2.smarts
- Class ambit2.smarts.SmartsToChemObject extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -5893878673124511317L
  - Serialized Fields
    - forceAromaticBondsAlways
```
boolean forceAromaticBondsAlways
```
    - forceAromaticBondsForNonRingAtoms
```
boolean forceAromaticBondsForNonRingAtoms
```
    - mFlagConfirmAromaticBond
```
boolean mFlagConfirmAromaticBond
```
    - mSubAtomType
```
int mSubAtomType
```
    - mSubAromaticity
```
int mSubAromaticity
```
    - mCurSubArom
```
int mCurSubArom
```
    - mRecCurSubArom
```
int mRecCurSubArom
```
    - mSubAtomCharge
```
int mSubAtomCharge
```
    - mCurSubAtCharge
```
int mCurSubAtCharge
```
    - mSubBondType
```
int mSubBondType
```
    - mSubBoAromaticity
```
int mSubBoAromaticity
```
    - mCurSubBoArom
```
int mCurSubBoArom
```
    - builder
```
org.openscience.cdk.interfaces.IChemObjectBuilder builder
```
Package ambit2.smarts.processors
- Class ambit2.smarts.processors.NeutraliseProcessor extends SMIRKSProcessor implements Serializable
  
  serialVersionUID:
  
  8550598539258019431L
- Class ambit2.smarts.processors.SMARTSPropertiesGenerator extends AbstractPropertyGenerator<String> implements Serializable
  
  serialVersionUID:
  
  -3259442103743490512L
  - Serialized Fields
    - utils
```
CMLUtilities utils
```
    - config
```
AtomConfigurator config
```
- Class ambit2.smarts.processors.SMARTSPropertiesReader extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -2900200524126295738L
  - Serialized Fields
    - util
```
CMLUtilities util
```
- Class ambit2.smarts.processors.SMIRKSProcessor extends AbstractStructureProcessor implements Serializable
  
  serialVersionUID:
  
  5540483406795033374L
  - Serialized Fields
    - loadExamples
```
boolean loadExamples
```
    - transformationasproperties
```
boolean transformationasproperties
```
    - transformations
```
List<E> transformations
```
    - smrkMan
```
SMIRKSManager smrkMan
```
- Class ambit2.smarts.processors.StructureKeysBitSetGenerator extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,BitSet> implements Serializable
  
  serialVersionUID:
  
  696373923085520847L
  - Serialized Fields
    - isoTester
```
IsomorphismTester isoTester
```
    - cfg
```
AtomConfigurator cfg
```
    - aromaticDetector
```
CDKHueckelAromaticityDetector aromaticDetector
```
    - cleanKekuleBonds
```
boolean cleanKekuleBonds
```
Package ambit2.smarts.query
- Class ambit2.smarts.query.AbstractSmartsPattern extends Object implements Serializable
  
  serialVersionUID:
  
  -771113251398072451L
  - Serialized Fields
    - negate
```
boolean negate
```
    - smarts
```
String smarts
```
    - name
```
String name
```
    - hint
```
String hint
```
- Class ambit2.smarts.query.FastSmartsMatcher extends AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -437122688052917294L
  - Serialized Fields
    - isoTester
```
IsomorphismTester isoTester
```
    - sp
```
SmartsParser sp
```
    - query
```
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query
```
    - reader
```
SMARTSPropertiesReader reader
```
- Class ambit2.smarts.query.SMARTSException extends net.idea.modbcum.i.exceptions.AmbitException implements Serializable
  
  serialVersionUID:
  
  -7931318487728176912L
- Class ambit2.smarts.query.SmartsPatternAmbit extends AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  4400701166436805492L
  - Serialized Fields
    - useCDKIsomorphism
```
boolean useCDKIsomorphism
```
- Class ambit2.smarts.query.SmartsPatternCDK extends AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -63030468038251612L
  - Serialization Methods
    - readObject
```
private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException
```
      Throws:
      
      IOException
      
      ClassNotFoundException
Package ambit2.smi23d
- Class ambit2.smi23d.ShellMengine extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  9089097054499846056L
- Class ambit2.smi23d.ShellSmi2SDF extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  7647984144381286155L
  - Serialized Fields
    - dropHydrogens
```
boolean dropHydrogens
```
Package ambit2.some
- Class ambit2.some.SOMEShell extends CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -5948332340539224507L
  - Serialized Fields
    - useOriginalStructure
```
boolean useOriginalStructure
```
    - inFile
```
String inFile
```
    - outFile
```
String[] outFile
```
- Class ambit2.some.SOMEVisualizer extends SOMEResultsParser implements Serializable
  
  serialVersionUID:
  
  -2863301348491350336L
  - Serialized Fields
    - selected
```
org.openscience.cdk.interfaces.IAtomContainer selected
```
    - imageSize
```
Dimension imageSize
```
    - ruleid
```
String ruleid
```
    - mol
```
org.openscience.cdk.interfaces.IAtomContainer mol
```
Package ambit2.tautomers.processor
- Class ambit2.tautomers.processor.StructureStandardizer extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -2600599340740351460L
  - Serialized Fields
    - tags
```
Map<K,V> tags
```
    - generateInChI
```
boolean generateInChI
```
    - generateSMILES_Canonical
```
boolean generateSMILES_Canonical
```
    - generateSMILES_Aromatic
```
boolean generateSMILES_Aromatic
```
    - splitFragments
```
boolean splitFragments
```
    - generateTautomers
```
boolean generateTautomers
```
    - generateSMILES
```
boolean generateSMILES
```
    - neutralise
```
boolean neutralise
```
    - generate2D
```
boolean generate2D
```
    - implicitHydrogens
```
boolean implicitHydrogens
```
    - generateStereofrom2D
```
boolean generateStereofrom2D
```
    - clearIsotopes
```
boolean clearIsotopes
```
    - options
```
List<E> options
```
- Class ambit2.tautomers.processor.TautomerProcessor extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  -6493329018044361388L
  - Serialized Fields
    - tautomerManager
```
TautomerManager tautomerManager
```
    - callback
```
net.idea.modbcum.i.processors.IProcessor<Target,Result> callback
```
Package ambit2.ui
- Class ambit2.ui.AbstractAmbitAction extends AbstractAction implements Serializable
  
  serialVersionUID:
  
  -6078241510121388340L
- Class ambit2.ui.AbstractPanel extends JToolBar implements Serializable
  
  serialVersionUID:
  
  3963305539191739942L
- Class ambit2.ui.BrowserModeCellRenderer extends DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  4027149275232536325L
  - Serialized Fields
    - mode
```
IBrowserMode.BrowserMode mode
```
- Class ambit2.ui.ColorTableCellRenderer extends DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  -8469636566374238630L
  - Serialized Fields
    - oddColor
```
Color oddColor
```
- Class ambit2.ui.DelimitersPanel extends JPanel implements Serializable
  - Serialized Fields
    - boxes
```
JRadioButton[] boxes
```
    - field
```
JFormattedTextField field
```
    - delimiter
```
String delimiter
```
    - border
```
TitledBorder border
```
- Class ambit2.ui.EditableHeader extends JTableHeader implements Serializable
  
  serialVersionUID:
  
  8173999492561440990L
  - Serialized Fields
    - HEADER_ROW
```
int HEADER_ROW
```
- Class ambit2.ui.EditableHeaderTableColumn extends TableColumn implements Serializable
  
  serialVersionUID:
  
  3641111865722454282L
  - Serialized Fields
    - headerEditor
```
TableCellEditor headerEditor
```
    - isHeaderEditable
```
boolean isHeaderEditable
```
- Class ambit2.ui.HeaderComboBoxModel extends AbstractListModel implements Serializable
  
  serialVersionUID:
  
  -4586230477632082997L
  - Serialized Fields
    - table
```
JTable table
```
    - column
```
int column
```
    - selectedObject
```
Object selectedObject
```
    - actions
```
IHeaderAction[] actions
```
    - values
```
List<E> values
```
- Class ambit2.ui.ImageCellRenderer extends DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  -4507345423562728344L
  - Serialized Fields
    - imageTools
```
ICompoundImageTools imageTools
```
    - icon
```
ImageIcon icon
```
- Class ambit2.ui.NumberCellRenderer extends ColorTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  6134329163642859855L
  - Serialized Fields
    - nf
```
NumberFormat nf
```
- Class ambit2.ui.Panel2D extends JPanel implements Serializable
  
  serialVersionUID:
  
  -6293533800645578594L
  - Serialized Fields
    - tools
```
CompoundImageTools tools
```
    - atomContainer
```
org.openscience.cdk.interfaces.IAtomContainer atomContainer
```
    - selector
```
IAtomContainerHighlights selector
```
    - image
```
Image image
```
    - generate2d
```
boolean generate2d
```
    - editable
```
boolean editable
```
    - editAction
```
IMoleculeEditAction editAction
```
    - atomrendermode
```
Panel2D._atomrendermode atomrendermode
```
- Class ambit2.ui.QueryBrowser extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - browser_table
```
JTable browser_table
```
    - headerActions
```
IHeaderAction[] headerActions
```
    - imageRenderers
```
Hashtable<K,V> imageRenderers
```
    - cellRenderer
```
BrowserModeCellRenderer cellRenderer
```
    - editable
```
boolean editable
```
- Class ambit2.ui.WizardPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -4624498162154536082L
  - Serialized Fields
    - dialog
```
JDialog dialog
```
    - answer
```
WizardPanel.ANSWER_MODE answer
```
    - dlu
```
String dlu
```
Package ambit2.ui.editors
- Class ambit2.ui.editors.EditorPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  4466287344655179932L
  - Serialized Fields
    - component
```
JComponent component
```
    - editor
```
IAmbitEditor<T> editor
```
    - noDataText
```
String noDataText
```
    - nodatalabel
```
JLabel nodatalabel
```
- Class ambit2.ui.editors.FileSelector extends JPanel implements Serializable
  
  serialVersionUID:
  
  5574703583284875026L
  - Serialized Fields
    - detailsModel
```
com.jgoodies.binding.PresentationModel<B> detailsModel
```
    - editable
```
boolean editable
```
    - filestate
```
FileState filestate
```
    - filename
```
JTextField filename
```
    - browse
```
JButton browse
```
- Class ambit2.ui.editors.SelectFieldsPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -256267185521731191L
  - Serialized Fields
    - buttons
```
List<E> buttons
```
    - fields
```
TypedListModel<P> fields
```
    - fieldsModel
```
TypedListModel<P>[] fieldsModel
```
    - tables
```
JList<E>[] tables
```
    - help
```
String help
```
Package ambit2.ui.jmol
- Class ambit2.ui.jmol.ImageTools3D extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,BufferedImage> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentSize
```
Dimension currentSize
```
    - viewer
```
org.jmol.api.JmolViewer viewer
```
    - jmolpopup
```
org.jmol.popup.JmolPopup jmolpopup
```
    - adapter
```
org.jmol.api.JmolAdapter adapter
```
    - moleculeSet
```
org.openscience.cdk.interfaces.IAtomContainerSet moleculeSet
```
    - model
```
org.openscience.cdk.interfaces.IChemModel model
```
    - sequence
```
org.openscience.cdk.interfaces.IChemSequence sequence
```
    - chemFile
```
org.openscience.cdk.interfaces.IChemFile chemFile
```
- Class ambit2.ui.jmol.Panel3D extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - painter3D
```
ImageTools3D painter3D
```
Package ambit2.ui.table
- Class ambit2.ui.table.BrowsableTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  -1948964692310621358L
  - Serialized Fields
    - ps
```
PropertyChangeSupport ps
```
    - dataModel
```
TableModel dataModel
```
    - pageSize
```
int pageSize
```
    - page
```
int page
```
    - record
```
int record
```
    - idColumn
```
int idColumn
```
    - zoomFactor
```
double[] zoomFactor
```
    - selectedIcon
```
ImageIcon selectedIcon
```
    - currentIcon
```
ImageIcon currentIcon
```
    - selectedAndCurrentIcon
```
ImageIcon selectedAndCurrentIcon
```
    - browserMode
```
IBrowserMode.BrowserMode browserMode
```
- Class ambit2.ui.table.BrowserModeNavigator extends AbstractPanel<IBrowserMode> implements Serializable
  
  serialVersionUID:
  
  -8336772938262715397L
  - Serialized Fields
    - button
```
JToggleButton[] button
```
    - zoomIn
```
JButton zoomIn
```
    - zoomOut
```
JButton zoomOut
```
- Class ambit2.ui.table.FindNavigator extends AbstractPanel<IFindNavigator> implements Serializable
  
  serialVersionUID:
  
  -4228397553276899404L
  - Serialized Fields
    - label
```
JLabel label
```
    - prevPage
```
JButton prevPage
```
    - nextPage
```
JButton nextPage
```
    - findValue
```
JTextField findValue
```
- Class ambit2.ui.table.PageNavigator extends AbstractPanel<IPageNavigator> implements Serializable
  
  serialVersionUID:
  
  -4228397553276899404L
  - Serialized Fields
    - label
```
JLabel label
```
    - prevPage
```
JButton prevPage
```
    - nextPage
```
JButton nextPage
```
    - currentPage
```
JTextField currentPage
```
    - allPages
```
JTextField allPages
```
    - pageSize
```
JTextField pageSize
```
- Class ambit2.ui.table.RecordNavigator extends AbstractPanel<IRecordNavigator> implements Serializable
  
  serialVersionUID:
  
  -4228397553276899404L
  - Serialized Fields
    - label
```
JLabel label
```
    - prevPage
```
JButton prevPage
```
    - nextPage
```
JButton nextPage
```
    - currentPage
```
JTextField currentPage
```
    - allPages
```
JTextField allPages
```
- Class ambit2.ui.table.StructureRecordsTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  -635680060021212861L
  - Serialized Fields
    - records
```
List<E> records
```
    - selected
```
Hashtable<K,V> selected
```
    - fields
```
TypedListModel<P> fields
```
    - properties
```
Hashtable<K,V> properties
```
    - propertyListener
```
PropertyChangeListener propertyListener
```
    - offset
```
int offset
```
    - transform
```
MoleculeReader transform
```
Package ambit2.vega
- Class ambit2.vega.ExternalModelVega extends ExternalModel<VegaShell,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable
  
  serialVersionUID:
  
  6049936082079982901L
  - Serialized Fields
    - reader
```
MoleculeReader reader
```
- Class ambit2.vega.VegaShell extends AbstractDescriptorShell implements Serializable
  
  serialVersionUID:
  
  -4109994330375555731L
  - Serialized Fields
    - properties
```
Map<K,V> properties
```
    - config
```
String config
```
    - inFile
```
String[] inFile
```
    - outFile
```
String[] outFile
```

Serialized Form

Package ambit2.balloon

Class ambit2.balloon.ShellBalloon extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer> implements Serializable

Serialized Fields

hydrogens

Class ambit2.balloon.ShellBalloonWeb extends ShellBalloon implements Serializable

Package ambit2.base.data

Class ambit2.base.data.AbstractDataset extends Object implements Serializable

Serialized Fields

ID

stars

properties

Class ambit2.base.data.AbstractLabel extends AmbitBean implements Serializable

Serialized Fields

label

user

text

Class ambit2.base.data.AmbitBean extends Object implements Serializable

Class ambit2.base.data.Bookmark extends Object implements Serializable

Serialized Fields

uuid

relevance

type

id

creator

recalls

hasTopic

title

description

created

date

Class ambit2.base.data.ConsensusLabel extends AbstractLabel<ConsensusLabel.CONSENSUS_LABELS> implements Serializable

Class ambit2.base.data.Dictionary extends Property implements Serializable

Serialized Fields

relationship

Class ambit2.base.data.Endpoints extends Template implements Serializable

Class ambit2.base.data.LiteratureEntry extends AmbitBean implements Serializable

Serialized Fields

title

URL

id

editable

type

Class ambit2.base.data.PredictedVarsTemplate extends Template implements Serializable

Class ambit2.base.data.Profile extends Object implements Serializable

Serialized Fields

container

name

Class ambit2.base.data.ProfileListModel extends AbstractListModel implements Serializable

Serialized Fields

fields

visibleIndex

visibility

Class ambit2.base.data.PropertiesTableModel extends AbstractTableModel implements Serializable

Serialized Fields

visibleFields

visibility

columns

Class ambit2.base.data.Property extends Object implements Serializable

Serialized Fields

annotations

isNominal

name

label

units

id

order

clazz

enabled

reference

allowedValues

Class ambit2.base.data.PropertyAnnotation extends Object implements Serializable

Serialized Fields

idproperty

type

predicate

object

Class ambit2.base.data.PropertyAnnotations extends ArrayList<PropertyAnnotation> implements Serializable

Class ambit2.base.data.QLabel extends AbstractLabel<QLabel.QUALITY> implements Serializable

Class ambit2.base.data.SelectionBean extends AmbitBean implements Serializable