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Serialized Form

Package ambit2.core.data.distances

Class ambit2.core.data.distances.AtomDistanceProcessor extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.util.List<AtomDistance>> implements Serializable

serialVersionUID: -2602737581794155267L

Package ambit2.core.data.experiment

Class ambit2.core.data.experiment.AQUIREStudy extends Study implements Serializable

Class ambit2.core.data.experiment.Study extends ambit2.base.data.AmbitBean implements Serializable

serialVersionUID: -1502943233991253317L

Serialized Fields

template

ambit2.base.data.Template template

studyResults

java.util.Hashtable<K,V> studyResults

name

java.lang.String name

id

int id

Class ambit2.core.data.experiment.StudyList extends java.util.ArrayList<Study> implements Serializable

serialVersionUID: -5279829130669439132L

Class ambit2.core.data.experiment.StudyTemplate extends java.util.ArrayList<TemplateField> implements Serializable

serialVersionUID: -9152728910421949089L

Serialized Fields

source

java.lang.String source

query

TemplateField query

name

java.lang.String name

id

int id

Class ambit2.core.data.experiment.TemplateField extends ambit2.base.data.AmbitBean implements Serializable

serialVersionUID: 7598061386536935899L

Serialized Fields

units

java.lang.String units

numeric

boolean numeric

isResult

boolean isResult

name

java.lang.String name

id

int id

Package ambit2.core.external

Class ambit2.core.external.ShellSDFoutput extends ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule> 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

java.util.List<E> atoms

bonds

java.util.List<E> bonds

number

int number

Class ambit2.core.groups.AbstractGroup$SelfIterable$1 extends java.lang.Object implements Serializable

Class ambit2.core.groups.ComponentGroup extends AbstractGroup implements Serializable

serialVersionUID: -2031261520924881915L

Serialized Fields

order

java.lang.Integer order

Class ambit2.core.groups.ContainerGroup extends AbstractGroup implements Serializable

serialVersionUID: -557546576995848521L

Serialized Fields

components

java.util.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 java.lang.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

java.util.List<E> parentAtoms

parentBonds

java.util.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

java.util.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

java.util.List<E> lonePairs

singleElectrons

java.util.List<E> singleElectrons

Internal array of single electrons.

atomParities

java.util.Map<K,V> atomParities

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

Class ambit2.core.io.FileOutputState extends FileState implements Serializable

Class ambit2.core.io.FileState extends com.jgoodies.binding.beans.Model implements Serializable

serialVersionUID: -9098389880881547516L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

responseType

java.lang.String responseType

supportedExtensions

java.lang.String[] supportedExtensions

extensionDescriptions

java.lang.String[] extensionDescriptions

filename

java.lang.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.processors

Class ambit2.core.processors.AbstractRepresentationConvertor extends ambit2.base.processors.DefaultAmbitProcessor<Content,R> implements Serializable

serialVersionUID: 3205584753771251514L

Serialized Fields

reporter

ambit2.base.processors.Reporter<Content,Output> reporter

mediaType

java.lang.Object mediaType

Class ambit2.core.processors.ProcessorFileExport extends ambit2.base.processors.DefaultAmbitProcessor<Content,FileOutputState> implements Serializable

serialVersionUID: -5006607500469902058L

Serialized Fields

output

FileOutputState output

Package ambit2.core.processors.batch

Class ambit2.core.processors.batch.DefaultInputState extends DefaultIOState implements Serializable

serialVersionUID: 8642417087199310257L

Class ambit2.core.processors.batch.DefaultIOState extends java.lang.Object implements Serializable

Serialized Fields

currentRecord

long currentRecord

responseType

java.lang.String responseType

Package ambit2.core.processors.quality

Class ambit2.core.processors.quality.ChemicalStructureQualityCheck extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IMolecule,ambit2.base.data.QLabel> implements Serializable

serialVersionUID: -518931054923701570L

Serialized Fields

qualityVerifier

ambit2.base.data.AmbitUser qualityVerifier

groundTruth

org.openscience.cdk.interfaces.IMolecule groundTruth

isoTester

org.openscience.cdk.isomorphism.IsomorphismTester isoTester

Package ambit2.core.processors.structure

Class ambit2.core.processors.structure.AbstractPropertyGenerator extends ambit2.base.processors.DefaultAmbitProcessor<ambit2.base.interfaces.IStructureRecord,ambit2.base.interfaces.IStructureRecord> implements Serializable

serialVersionUID: 6923827535809255431L

Serialized Fields

reader

MoleculeReader reader

Class ambit2.core.processors.structure.AtomConfigurator extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable

serialVersionUID: -1245226849382037921L

Class ambit2.core.processors.structure.CloneProcessor extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable

serialVersionUID: -3628034858252983090L

Class ambit2.core.processors.structure.FingerprintGenerator extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.util.BitSet> implements Serializable

serialVersionUID: 3905797414723139887L

Serialized Fields

FPLength

int FPLength

fingerprinter

org.openscience.cdk.fingerprint.Fingerprinter fingerprinter

hydrogens

boolean hydrogens

hAdder

org.openscience.cdk.tools.HydrogenAdder 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 ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.inchi.InChIGenerator> implements Serializable

serialVersionUID: -9052892261511104974L

Class ambit2.core.processors.structure.MoleculeReader extends ambit2.base.processors.DefaultAmbitProcessor<ambit2.base.interfaces.IStructureRecord,org.openscience.cdk.interfaces.IAtomContainer> implements Serializable

serialVersionUID: 1811923574213153916L

Class ambit2.core.processors.structure.MoleculeWriter extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.lang.String> implements Serializable

serialVersionUID: 7007704004927846803L

Class ambit2.core.processors.structure.StructureTypeProcessor extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,AmbitCONSTANTS.STRUC_TYPE> implements Serializable

serialVersionUID: 470417245691484159L

Package ambit2.core.processors.structure.key

Class ambit2.core.processors.structure.key.CASKey extends PropertyKey<java.lang.String> implements Serializable

serialVersionUID: 3848970585289051369L

Serialized Fields

key

ambit2.base.data.Property key

Class ambit2.core.processors.structure.key.DSSToxCID extends PropertyKey<java.lang.Number> implements Serializable

serialVersionUID: -5172763951258433726L

Class ambit2.core.processors.structure.key.DSSToxRID extends PropertyKey<java.lang.Number> implements Serializable

serialVersionUID: 2117618200041344844L

Class ambit2.core.processors.structure.key.EINECSKey extends PropertyKey implements Serializable

serialVersionUID: -9098011521397491242L

Class ambit2.core.processors.structure.key.EmptyKey extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.lang.String> implements Serializable

serialVersionUID: -2365056130992400384L

Class ambit2.core.processors.structure.key.InchiKey extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.lang.String> implements Serializable

serialVersionUID: -4957862884677389524L

Serialized Fields

inchi

InchiProcessor inchi

key

java.lang.Object key

Class ambit2.core.processors.structure.key.InchiPropertyKey extends PropertyKey<java.lang.String> implements Serializable

serialVersionUID: 1718062022783509128L

Class ambit2.core.processors.structure.key.PropertyKey extends ambit2.base.processors.DefaultAmbitProcessor<ambit2.base.interfaces.IStructureRecord,Result> implements Serializable

serialVersionUID: 6393097111823664858L

Serialized Fields

key

ambit2.base.data.Property key

Class ambit2.core.processors.structure.key.PubchemCID extends PropertyKey<java.lang.Number> implements Serializable

serialVersionUID: -5172763951258433726L

Class ambit2.core.processors.structure.key.SmilesKey extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,java.lang.String> implements Serializable

serialVersionUID: 8319267963784553472L

Serialized Fields

gen

org.openscience.cdk.smiles.SmilesGenerator gen

key

java.lang.Object key

Package ambit2.core.smiles

Class ambit2.core.smiles.OpenBabelShell extends ShellSDFoutput<java.lang.String> implements Serializable

serialVersionUID: -89551999366481056L

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