A B C D E F G H I J K L M N O P Q R S T U V W X _

A

AbstractGroup - Class in ambit2.core.groups

AbstractGroup() - Constructor for class ambit2.core.groups.AbstractGroup

AbstractGroup(String) - Constructor for class ambit2.core.groups.AbstractGroup

AbstractGroup(String, int) - Constructor for class ambit2.core.groups.AbstractGroup

AbstractGroup.EmptyIterator<T> - Class in ambit2.core.groups

AbstractGroup.EmptyIterator() - Constructor for class ambit2.core.groups.AbstractGroup.EmptyIterator

AbstractGroup.SelfIterable<T> - Class in ambit2.core.groups

AbstractGroup.SelfIterable(T) - Constructor for class ambit2.core.groups.AbstractGroup.SelfIterable

AbstractPropertyGenerator<P> - Class in ambit2.core.processors.structure

Transforms IStructureRecord into IAtomContainer , calculates some property and assigns it to IStructureRecord

AbstractPropertyGenerator() - Constructor for class ambit2.core.processors.structure.AbstractPropertyGenerator

AbstractRepresentationConvertor<Item,Content,Output,R,Media,ItemReporter extends ambit2.base.processors.Reporter<Content,Output>> - Class in ambit2.core.processors

An abstract IProcessor , converting between arbitrary Content and arbitrary Representation.

AbstractRepresentationConvertor(ItemReporter) - Constructor for class ambit2.core.processors.AbstractRepresentationConvertor

AbstractRepresentationConvertor(ItemReporter, Media) - Constructor for class ambit2.core.processors.AbstractRepresentationConvertor

accepts(Class) - Method in class ambit2.core.io.DelimitedFileReader

accepts(Class) - Method in class ambit2.core.io.DelimitedFileWriter

accepts(Class) - Method in class ambit2.core.io.IteratingFileReader

accepts(Class) - Method in class ambit2.core.io.MDLReader

accepts(Class) - Method in class ambit2.core.io.MDLV2000ReaderExtended

accepts(Class) - Method in class ambit2.core.io.MDLWriter

accepts(Class) - Method in class ambit2.core.io.PDFWriter

accepts(Class) - Method in class ambit2.core.io.RawIteratingWrapper

accepts(Class) - Method in class ambit2.core.io.XLSFileWriter

activeList - Variable in class ambit2.core.groups.FilteredList

add(T) - Method in class ambit2.core.groups.FilteredList

add(int, T) - Method in class ambit2.core.groups.FilteredList

add(IAtomContainer) - Method in class ambit2.core.groups.SuppleAtomContainer

add(Object) - Method in class ambit2.core.io.RandomAccessReader

addAll(Collection<? extends T>) - Method in class ambit2.core.groups.FilteredList

addAll(int, Collection<? extends T>) - Method in class ambit2.core.groups.FilteredList

addAtom(IAtom) - Method in class ambit2.core.groups.AbstractGroup

addAtom(IAtom) - Method in interface ambit2.core.groups.ISGroup

addAtom(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

addAtomParity(IAtomParity) - Method in class ambit2.core.groups.SuppleAtomContainer

addBond(IBond) - Method in class ambit2.core.groups.AbstractGroup

addBond(IBond) - Method in interface ambit2.core.groups.ISGroup

addBond(IBond) - Method in class ambit2.core.groups.SuperAtom

addBond(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

addBond(int, int, IBond.Order, int) - Method in class ambit2.core.groups.SuppleAtomContainer

addBond(int, int, IBond.Order) - Method in class ambit2.core.groups.SuppleAtomContainer

addBondsConnected2Atoms(IAtomContainer, List<IAtom>, List<IBond>) - Method in class ambit2.core.groups.AbstractGroup

addBrackets(double, double, double, double) - Method in class ambit2.core.groups.AbstractGroup

addBrackets(double, double, double, double) - Method in interface ambit2.core.groups.ISGroup

addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.IteratingFileReader

addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RandomAccessReader

addChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RawIteratingWrapper

addEexplicitHydrogens - Variable in class ambit2.core.processors.structure.HydrogenAdderProcessor

addElectronContainer(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer

adder - Static variable in class ambit2.core.data.MoleculeTools

adder - Variable in class ambit2.core.processors.structure.HydrogenAdderProcessor

addFields(String, String, boolean, boolean) - Method in class ambit2.core.data.experiment.StudyTemplate

addGroupAtom(ISGroup, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

addGroupBond(ISGroup, IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

addHeaderColumn(String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

addLonePair(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer

addLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer

addParentAtom(IAtom) - Method in class ambit2.core.groups.MultipleGroup

addProperties(Map) - Method in class ambit2.core.io.MolPropertiesIOSetting

addSingleElectron(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer

addSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer

addToFilter(T) - Method in class ambit2.core.groups.FilteredList

addToFilter(int) - Method in class ambit2.core.groups.FilteredList

addToFilter(T) - Method in interface ambit2.core.groups.IFiltered

addToFilter(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

addToFilter(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

AESimilarity - Static variable in class ambit2.core.config.AmbitCONSTANTS

Atom environment similarity

ambit2.core.config - package ambit2.core.config

User preferences and other configuration options

ambit2.core.data - package ambit2.core.data

ambit2.core.data.distances - package ambit2.core.data.distances

ambit2.core.data.experiment - package ambit2.core.data.experiment

Classes to handle experimental data.

ambit2.core.data.model - package ambit2.core.data.model

ambit2.core.external - package ambit2.core.external

Launching external applications by command shell

ambit2.core.groups - package ambit2.core.groups

ambit2.core.io - package ambit2.core.io

Input output support.

ambit2.core.io.bcf - package ambit2.core.io.bcf

ambit2.core.processors - package ambit2.core.processors

ambit2.core.processors.batch - package ambit2.core.processors.batch

ambit2.core.processors.quality - package ambit2.core.processors.quality

ambit2.core.processors.structure - package ambit2.core.processors.structure

ambit2.core.processors.structure.key - package ambit2.core.processors.structure.key

ambit2.core.smiles - package ambit2.core.smiles

SMILES tools, additional to CDK smiles functionality

AMBIT_IDSTRUCTURE - Static variable in class ambit2.core.config.AmbitCONSTANTS

the database field structure.idstructure

AMBIT_IDSUBSTANCE - Static variable in class ambit2.core.config.AmbitCONSTANTS

the database field substance.idsubstance

AmbitCONSTANTS - Class in ambit2.core.config

Constants

AmbitCONSTANTS.STRUC_TYPE - Enum in ambit2.core.config

analyzeSubstance(IAtomContainer) - Static method in class ambit2.core.data.MoleculeTools

AQUIRE - Static variable in class ambit2.core.config.AmbitCONSTANTS

AQUIRE data (TO DO)

AQUIREConditions - Static variable in class ambit2.core.data.experiment.AquireTemplate

AQUIREResults - Static variable in class ambit2.core.data.experiment.AquireTemplate

AQUIREStudy - Class in ambit2.core.data.experiment

AQUIREStudy(boolean) - Constructor for class ambit2.core.data.experiment.AQUIREStudy

AQUIREStudy(String, boolean) - Constructor for class ambit2.core.data.experiment.AQUIREStudy

AQUIREStudy(String, int, Template) - Constructor for class ambit2.core.data.experiment.AQUIREStudy

AquireTemplate - Class in ambit2.core.data.experiment

AquireTemplate() - Constructor for class ambit2.core.data.experiment.AquireTemplate

AquireTemplate(boolean) - Constructor for class ambit2.core.data.experiment.AquireTemplate

ArrayResult<T> - Class in ambit2.core.data

ArrayResult() - Constructor for class ambit2.core.data.ArrayResult

ArrayResult(T[]) - Constructor for class ambit2.core.data.ArrayResult

assignCASRN(IStructureRecord) - Method in class ambit2.core.io.RawIteratingFolderReader

atom - Variable in class ambit2.core.groups.AbstractGroup.SelfIterable

AtomConfigurator - Class in ambit2.core.processors.structure

AtomConfigurator() - Constructor for class ambit2.core.processors.structure.AtomConfigurator

atomContainers - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper

AtomDistance - Class in ambit2.core.data.distances

AtomDistance() - Constructor for class ambit2.core.data.distances.AtomDistance

AtomDistanceProcessor - Class in ambit2.core.data.distances

AtomDistanceProcessor() - Constructor for class ambit2.core.data.distances.AtomDistanceProcessor

AtomEnvironment - Static variable in class ambit2.core.config.AmbitCONSTANTS

Atom environment (circular fingerprints)

atomParities - Variable in class ambit2.core.groups.SuppleAtomContainer

Internal list of atom parities.

atoms - Variable in class ambit2.core.groups.AbstractGroup

atoms - Variable in class ambit2.core.groups.SuppleAtomContainer

atoms() - Method in class ambit2.core.groups.SuppleAtomContainer

B

b - Variable in class ambit2.core.io.RandomAccessReader

babel - Variable in class ambit2.core.smiles.SmilesParserWrapper

background - Variable in class ambit2.core.io.CompoundImageTools

bitset2bigint16(BitSet, int, BigInteger[]) - Static method in class ambit2.core.data.MoleculeTools

bitset2Long(BitSet) - Static method in class ambit2.core.data.MoleculeTools

bonds - Variable in class ambit2.core.groups.AbstractGroup

bonds - Variable in class ambit2.core.groups.SuppleAtomContainer

bonds() - Method in class ambit2.core.groups.SuppleAtomContainer

borderColor - Variable in class ambit2.core.io.CompoundImageTools

borderWidth - Variable in class ambit2.core.io.CompoundImageTools

bracketLeft - Static variable in class ambit2.core.data.MoleculeTools

bracketRight - Static variable in class ambit2.core.data.MoleculeTools

buildDocument() - Method in class ambit2.core.data.experiment.StudyTemplate

builder - Variable in class ambit2.core.io.RandomAccessReader

C

CASKey - Class in ambit2.core.processors.structure.key

Returns CAS number given the structure and its properties

CASKey() - Constructor for class ambit2.core.processors.structure.key.CASKey

CASRN - Static variable in class ambit2.core.config.AmbitCONSTANTS

CAS RN

casTransformer - Variable in class ambit2.core.io.RawIteratingFolderReader

cdkParser - Variable in class ambit2.core.smiles.SmilesParserWrapper

cell - Variable in class ambit2.core.io.PDFWriter

ChemicalStructureQualityCheck - Class in ambit2.core.processors.quality

Verifies consistency between multiple structures, coming from different origins 2)coherence of multiple origins - compare all structures of same idchemical - assign OK if same, notOK if not same retrieve a chemical (by idchemical) retrieve structures per chemical calculate fingerprints per structure compare structure fingerprints with fingerprints from fp1024 (per chemical), if different, assign "ERROR", otherwise assign "ProbablyOK" (slow) select one structure and compare all other structures (same chemical) with isomrphism test; assign "ERROR" if not same.

ChemicalStructureQualityCheck() - Constructor for class ambit2.core.processors.quality.ChemicalStructureQualityCheck

chemObject - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper

chemObjectReader - Variable in class ambit2.core.io.RandomAccessReader

clear() - Method in class ambit2.core.data.experiment.Study

clear() - Method in class ambit2.core.groups.FilteredList

clearFilter() - Method in class ambit2.core.groups.FilteredList

clearFilter() - Method in interface ambit2.core.groups.IFiltered

clearFilter() - Method in class ambit2.core.groups.SuppleAtomContainer

clone() - Method in class ambit2.core.data.experiment.Study

clone() - Method in class ambit2.core.groups.SuppleAtomContainer

CloneProcessor - Class in ambit2.core.processors.structure

Clones IAtomContainer.

CloneProcessor() - Constructor for class ambit2.core.processors.structure.CloneProcessor

close() - Method in class ambit2.core.io.DelimitedFileReader

close() - Method in class ambit2.core.io.DelimitedFileWriter

close() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper

close() - Method in class ambit2.core.io.IteratingDelimitedFileReader

close() - Method in class ambit2.core.io.IteratingFileReader

close() - Method in class ambit2.core.io.IteratingFolderReader

close() - Method in class ambit2.core.io.IteratingXLSReader

close() - Method in class ambit2.core.io.MDLReader

close() - Method in class ambit2.core.io.MDLV2000ReaderExtended

close() - Method in class ambit2.core.io.MDLWriter

Flushes the output and closes this object.

close() - Method in class ambit2.core.io.MyIteratingMDLReader

close() - Method in class ambit2.core.io.PDFWriter

close() - Method in class ambit2.core.io.RandomAccessReader

close() - Method in class ambit2.core.io.RawIteratingReader

close() - Method in class ambit2.core.io.RawIteratingWrapper

close() - Method in class ambit2.core.io.XLSFileWriter

closeItemReader(ItemReader) - Method in class ambit2.core.io.IteratingFolderReader

CML_INDEX - Static variable in class ambit2.core.io.FileInputState

CML_INDEX - Static variable in class ambit2.core.io.FileOutputState

compareTo(ISGroup) - Method in class ambit2.core.groups.AbstractGroup

ComponentGroup - Class in ambit2.core.groups

ComponentGroup(String, int) - Constructor for class ambit2.core.groups.ComponentGroup

components - Variable in class ambit2.core.groups.ContainerGroup

CompoundImageTools - Class in ambit2.core.io

Generates BufferedImage from smiles or compound.

CompoundImageTools() - Constructor for class ambit2.core.io.CompoundImageTools

CompoundImageTools(Dimension) - Constructor for class ambit2.core.io.CompoundImageTools

config - Variable in class ambit2.core.processors.structure.FingerprintGenerator

ContainerGroup - Class in ambit2.core.groups

ContainerGroup(String, int) - Constructor for class ambit2.core.groups.ContainerGroup

ContainerGroup(String, int, ContainerGroup.SGROUP_MIXTURE) - Constructor for class ambit2.core.groups.ContainerGroup

ContainerGroup.SGROUP_MIXTURE - Enum in ambit2.core.groups

contains(Object) - Method in class ambit2.core.groups.FilteredList

contains(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

contains(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

contains(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer

contains(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer

contains(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer

containsAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList

content - Variable in class ambit2.core.data.model.ModelWrapper

contractedBonds - Variable in class ambit2.core.groups.SuperAtom

convertFile(String) - Static method in class ambit2.core.io.SDFBrokenLineTerminationConverter

In Java, a line is considered terminated by any one of the following: a line feed \n, a carriage return \r, or a carriage return followed immediately by a line feed.

counter - Variable in class ambit2.core.io.SimpleIOListener

createChemObjectReader() - Method in class ambit2.core.io.RandomAccessReader

createChemObjectReader() - Method in class ambit2.core.io.RandomAccessSDFReader

createFile() - Method in class ambit2.core.io.FileState

createGroup(int, SGroupMDL2000Helper.SGROUP_TYPE) - Static method in class ambit2.core.io.SGroupMDL2000Helper

createReader(IChemFormat) - Method in class ambit2.core.io.ReaderFactoryExtended

CSV_INDEX - Static variable in class ambit2.core.io.FileInputState

CSV_INDEX - Static variable in class ambit2.core.io.FileOutputState

currentRecord - Variable in class ambit2.core.io.FileState

currentRecord - Variable in class ambit2.core.io.RandomAccessReader

currentRecord - Variable in class ambit2.core.processors.batch.DefaultIOState

customizeJob() - Method in class ambit2.core.io.MDLReader

customizeJob() - Method in class ambit2.core.io.MDLV2000ReaderExtended

D

dataformat - Variable in class ambit2.core.io.XLSFileWriter

DataGroup - Class in ambit2.core.groups

Corresponds to DAT group found in MOL files

DataGroup(String, int) - Constructor for class ambit2.core.groups.DataGroup

DataGroup.DGROUP_DISPLAY - Enum in ambit2.core.groups

DataGroup.SGROUP_FIELD - Enum in ambit2.core.groups

DATASET - Static variable in class ambit2.core.config.AmbitCONSTANTS

Dataset source (table struc_dataset)

dbt - Variable in class ambit2.core.smiles.SmilesParserWrapper

DeduceBondSystemTool - Class in ambit2.core.smiles

Tool that tries to deduce bond orders based on connectivity and hybridization for a number of common ring systems.

DeduceBondSystemTool() - Constructor for class ambit2.core.smiles.DeduceBondSystemTool

Constructor for the DeduceBondSystemTool object.

DEFAULT_DIR - Static variable in class ambit2.core.config.Resources

default dir

defaultImage - Variable in class ambit2.core.io.CompoundImageTools

DefaultInputState - Class in ambit2.core.processors.batch

DefaultInputState(IIteratingChemObjectReader) - Constructor for class ambit2.core.processors.batch.DefaultInputState

DefaultIOState - Class in ambit2.core.processors.batch

DefaultIOState() - Constructor for class ambit2.core.processors.batch.DefaultIOState

defaultSMILESHeader - Static variable in class ambit2.core.io.FilesWithHeaderWriter

defaultSMILESHeader - Static variable in class ambit2.core.io.FileWithHeaderWriter

defaultSMILESHeader - Static variable in class ambit2.core.io.IteratingDelimitedFileReader

defaultSMILESHeader - Static variable in class ambit2.core.io.IteratingFilesWithHeaderReader

DefaultTemplate - Class in ambit2.core.data.experiment

Default template.

DefaultTemplate() - Constructor for class ambit2.core.data.experiment.DefaultTemplate

DefaultTemplate(String) - Constructor for class ambit2.core.data.experiment.DefaultTemplate

delete(T) - Method in class ambit2.core.groups.FilteredList

delim - Static variable in class ambit2.core.data.MoleculeTools

DelimitedFileFormat - Class in ambit2.core.io

File format for delimited files

DelimitedFileFormat() - Constructor for class ambit2.core.io.DelimitedFileFormat

Default field delimiter ',' Default text delimiter '"'

DelimitedFileFormat(String, char) - Constructor for class ambit2.core.io.DelimitedFileFormat

DelimitedFileReader - Class in ambit2.core.io

Reads delimited files (CSV, TXT)

DelimitedFileReader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileReader

Default delimited file format - CSV

DelimitedFileReader(Reader) - Constructor for class ambit2.core.io.DelimitedFileReader

DelimitedFileReader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileReader

DelimitedFileReader(InputStream) - Constructor for class ambit2.core.io.DelimitedFileReader

DelimitedFileWriter - Class in ambit2.core.io

Writes delimited files

DelimitedFileWriter(Writer, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileWriter

DelimitedFileWriter(Writer) - Constructor for class ambit2.core.io.DelimitedFileWriter

DelimitedFileWriter(OutputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.DelimitedFileWriter

DelimitedFileWriter(OutputStream) - Constructor for class ambit2.core.io.DelimitedFileWriter

delimiter - Static variable in class ambit2.core.io.RawIteratingSDFReader

dependent - Variable in class ambit2.core.data.model.ModelWrapper

dontWriteAromatic() - Method in class ambit2.core.io.MDLWriter

Method does not do anything until now.

DSSToxCarcinogenicityTemplate - Class in ambit2.core.data.experiment

A template with fields extracted from DSSTox carcinogenicity database.

DSSToxCarcinogenicityTemplate(String) - Constructor for class ambit2.core.data.experiment.DSSToxCarcinogenicityTemplate

DSSToxCID - Class in ambit2.core.processors.structure.key

DSSTox_CID

DSSToxCID() - Constructor for class ambit2.core.processors.structure.key.DSSToxCID

DSSToxERBindingTemplate - Class in ambit2.core.data.experiment

A template with fields extracted from DSSTox estrogen binding database.

DSSToxERBindingTemplate(String) - Constructor for class ambit2.core.data.experiment.DSSToxERBindingTemplate

DSSToxLC50Template - Class in ambit2.core.data.experiment

A template with fields extracted from DSSTox EPA Fathead Minnow database.

DSSToxLC50Template(String) - Constructor for class ambit2.core.data.experiment.DSSToxLC50Template

DSSToxRID - Class in ambit2.core.processors.structure.key

DSSToxRID() - Constructor for class ambit2.core.processors.structure.key.DSSToxRID

duration - Static variable in class ambit2.core.data.experiment.DefaultTemplate

E

EINECS - Class in ambit2.core.data

EINECS() - Constructor for class ambit2.core.data.EINECS

EINECSKey - Class in ambit2.core.processors.structure.key

returns einecs rn, given structure and its properties

EINECSKey() - Constructor for class ambit2.core.processors.structure.key.EINECSKey

electronContainers() - Method in class ambit2.core.groups.SuppleAtomContainer

elements - Static variable in class ambit2.core.processors.structure.AtomConfigurator

EmptyKey - Class in ambit2.core.processors.structure.key

REturns null key

EmptyKey() - Constructor for class ambit2.core.processors.structure.key.EmptyKey

endpoint - Static variable in class ambit2.core.data.experiment.DefaultTemplate

equals(Object) - Method in class ambit2.core.data.experiment.Study

equals(Object) - Method in class ambit2.core.data.experiment.TemplateField

equals(Object) - Method in class ambit2.core.groups.AbstractGroup

equals(Object) - Method in class ambit2.core.io.FileState

err_invalidcas - Static variable in class ambit2.core.config.Resources

Invalid CAS

EURAS_INDEX - Static variable in class ambit2.core.io.FileInputState

EurasBCFReader - Class in ambit2.core.io.bcf

EurasBCFReader(InputStream, int) - Constructor for class ambit2.core.io.bcf.EurasBCFReader

EXPERIMENT - Static variable in class ambit2.core.config.AmbitCONSTANTS

Experimental data record

EXPERIMENT_LIST - Static variable in class ambit2.core.config.AmbitCONSTANTS

List of experiments

extensionDescription - Static variable in class ambit2.core.io.FileInputState

extensionDescription - Static variable in class ambit2.core.io.FileOutputState

extensionDescriptions - Variable in class ambit2.core.io.FileState

extensions - Static variable in class ambit2.core.io.FileInputState

extensions - Static variable in class ambit2.core.io.FileOutputState

extractRowKeyAndData(String) - Method in class ambit2.core.io.IteratingDelimitedFileReader

Extract values from a line

F

fieldDelimiter - Variable in class ambit2.core.io.DelimitedFileFormat

file - Variable in class ambit2.core.io.FileState

fileFormat - Variable in class ambit2.core.io.FileState

FileInputState - Class in ambit2.core.io

Use FileInputState.getReader(InputStream, String) to get a reader of the right type.

FileInputState() - Constructor for class ambit2.core.io.FileInputState

FileInputState(String) - Constructor for class ambit2.core.io.FileInputState

FileInputState(File) - Constructor for class ambit2.core.io.FileInputState

filename - Variable in class ambit2.core.io.FileState

filename - Variable in class ambit2.core.io.IteratingFileReader

FileOutputState - Class in ambit2.core.io

Use FileOutputState.getWriter(OutputStream, String) to get a writer of the right type.

FileOutputState() - Constructor for class ambit2.core.io.FileOutputState

FileOutputState(String) - Constructor for class ambit2.core.io.FileOutputState

FileOutputState(File) - Constructor for class ambit2.core.io.FileOutputState

files - Variable in class ambit2.core.io.IteratingFolderReader

FileState - Class in ambit2.core.io

This is to be able to verify if a file has changed since it has been last processed by FileBatchProcessing

FileState() - Constructor for class ambit2.core.io.FileState

FileState(String) - Constructor for class ambit2.core.io.FileState

FileState(File) - Constructor for class ambit2.core.io.FileState

FilesWithHeaderWriter - Class in ambit2.core.io

FilesWithHeaderWriter() - Constructor for class ambit2.core.io.FilesWithHeaderWriter

FileWithHeaderWriter - Class in ambit2.core.io

FileWithHeaderWriter() - Constructor for class ambit2.core.io.FileWithHeaderWriter

FilteredList<T> - Class in ambit2.core.groups

A list that can be filtered by setting a filter elements.

FilteredList() - Constructor for class ambit2.core.groups.FilteredList

FilteredMDLReader - Class in ambit2.core.io

FilteredMDLReader() - Constructor for class ambit2.core.io.FilteredMDLReader

FilteredMDLReader(InputStream) - Constructor for class ambit2.core.io.FilteredMDLReader

FilteredMDLReader(Reader) - Constructor for class ambit2.core.io.FilteredMDLReader

finalize() - Method in class ambit2.core.io.RandomAccessReader

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.AbstractGroup

does nothing

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.ComponentGroup

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.ContainerGroup

finalizeAtomList(IAtomContainer) - Method in interface ambit2.core.groups.ISGroup

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.MonomerGroup

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.MultipleGroup

finalizeAtomList(IAtomContainer) - Method in class ambit2.core.groups.SuperAtom

finalizeParentAtomList(IAtomContainer) - Method in class ambit2.core.groups.MultipleGroup

Fingerprint - Static variable in class ambit2.core.config.AmbitCONSTANTS

Daylight - like hashed fingerprint

fingerprinter - Static variable in class ambit2.core.data.MoleculeTools

fingerprinter - Variable in class ambit2.core.processors.structure.FingerprintGenerator

FingerprintGenerator - Class in ambit2.core.processors.structure

** Fingerprint generator processor.

FingerprintGenerator() - Constructor for class ambit2.core.processors.structure.FingerprintGenerator

FingerprintGenerator(int) - Constructor for class ambit2.core.processors.structure.FingerprintGenerator

FingerprintSTATUS - Static variable in class ambit2.core.config.AmbitCONSTANTS

fingerprint status invalid=1; valid=2; error = 3

FingerprintTIME - Static variable in class ambit2.core.config.AmbitCONSTANTS

Time to generate hashed fingerprint

first() - Method in class ambit2.core.io.RandomAccessReader

fixAromaticBondOrders(IMolecule) - Method in class ambit2.core.smiles.DeduceBondSystemTool

format - Variable in class ambit2.core.io.DelimitedFileReader

format - Variable in class ambit2.core.io.DelimitedFileWriter

format - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper

format - Variable in class ambit2.core.io.IteratingDelimitedFileReader

FORMULA - Static variable in class ambit2.core.config.AmbitCONSTANTS

Chemical Formula

FPLength - Variable in class ambit2.core.processors.structure.FingerprintGenerator

frameRead(ReaderEvent) - Method in class ambit2.core.io.SimpleIOListener

G

gen - Variable in class ambit2.core.processors.structure.key.SmilesKey

GENERATE2D - Static variable in class ambit2.core.config.Resources

generate 2D

generate2D(IAtomContainer, boolean, IMoleculeSet) - Static method in class ambit2.core.io.CompoundImageTools

generateImage(String) - Method in class ambit2.core.io.CompoundImageTools

generateProperty(IAtomContainer) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator

GenericGroup - Class in ambit2.core.groups

GenericGroup(String, int) - Constructor for class ambit2.core.groups.GenericGroup

get(int) - Method in class ambit2.core.data.ArrayResult

get(int) - Method in class ambit2.core.groups.FilteredList

getAtom(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getAtomContainer(IStructureRecord) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator

getAtomCount() - Method in class ambit2.core.groups.SuppleAtomContainer

getAtomNumber(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getAtomParity(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getAtoms(boolean) - Method in class ambit2.core.groups.AbstractGroup

getAtoms(boolean) - Method in interface ambit2.core.groups.ISGroup

getAtoms(boolean) - Method in class ambit2.core.groups.MultipleGroup

getAtoms(boolean) - Method in class ambit2.core.groups.SuperAtom

getAuthor(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getBackground() - Method in class ambit2.core.io.CompoundImageTools

getBond(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getBond(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getBondCount() - Method in class ambit2.core.groups.SuppleAtomContainer

getBondNumber(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

getBondNumber(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getBondOrderSum(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getBonds(boolean) - Method in class ambit2.core.groups.AbstractGroup

getBonds(boolean) - Method in interface ambit2.core.groups.ISGroup

getBonds(boolean) - Method in class ambit2.core.groups.MultipleGroup

getBonds(boolean) - Method in class ambit2.core.groups.SuperAtom

getBorderColor() - Method in class ambit2.core.io.CompoundImageTools

getBorderWidth() - Method in class ambit2.core.io.CompoundImageTools

getChemObjectReader() - Method in class ambit2.core.io.RandomAccessReader

getCitation(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getComponents() - Method in class ambit2.core.groups.ContainerGroup

getConnectedAtomsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedAtomsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedBondsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedBondsCount(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedBondsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedElectronContainersList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedLonePairsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedLonePairsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedSingleElectronsCount(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getConnectedSingleElectronsList(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getContent() - Method in class ambit2.core.data.model.ModelWrapper

getCurrentRecord() - Method in class ambit2.core.io.FileState

getCurrentRecord() - Method in class ambit2.core.io.RandomAccessReader

getCurrentRecord() - Method in class ambit2.core.processors.batch.DefaultIOState

getDefaultImage() - Method in class ambit2.core.io.CompoundImageTools

getDependent() - Method in class ambit2.core.data.model.ModelWrapper

getElectronContainer(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getElectronContainerCount() - Method in class ambit2.core.groups.SuppleAtomContainer

getElements() - Static method in class ambit2.core.processors.structure.AtomConfigurator

getField(Object) - Method in class ambit2.core.data.experiment.StudyTemplate

getFieldDelimiter() - Method in class ambit2.core.io.DelimitedFileFormat

getFieldFormat() - Method in class ambit2.core.groups.DataGroup

getFieldType() - Method in class ambit2.core.groups.DataGroup

getFile() - Method in class ambit2.core.io.FileState

getFilename() - Method in class ambit2.core.io.FileState

getFiles() - Method in class ambit2.core.io.IteratingFolderReader

getFingerPrint(String, int) - Static method in class ambit2.core.data.MoleculeTools

getFingerPrint(String) - Static method in class ambit2.core.data.MoleculeTools

getFirstAtom() - Method in class ambit2.core.groups.SuppleAtomContainer

getFormat() - Method in class ambit2.core.io.DelimitedFileReader

getFormat() - Method in class ambit2.core.io.DelimitedFileWriter

getFormat() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper

getFormat() - Method in class ambit2.core.io.IteratingDelimitedFileReader

getFormat() - Method in class ambit2.core.io.IteratingFileReader

getFormat() - Method in class ambit2.core.io.IteratingFolderReader

getFormat() - Method in class ambit2.core.io.IteratingXLSReader

getFormat() - Method in class ambit2.core.io.MDLReader

getFormat() - Method in class ambit2.core.io.MDLV2000ReaderExtended

getFormat() - Method in class ambit2.core.io.MDLWriter

getFormat() - Method in class ambit2.core.io.MyIteratingMDLReader

getFormat() - Method in class ambit2.core.io.PDFWriter

getFormat() - Method in class ambit2.core.io.RandomAccessSDFReader

getFormat() - Method in class ambit2.core.io.RawIteratingMOLReader

getFormat() - Method in class ambit2.core.io.RawIteratingReader

getFormat() - Method in class ambit2.core.io.RawIteratingSDFReader

getFormat() - Method in class ambit2.core.io.RawIteratingWrapper

getFormat() - Method in class ambit2.core.io.XLSFileWriter

getFormatName() - Method in class ambit2.core.io.DelimitedFileFormat

getFormatName() - Method in class ambit2.core.io.XLSFileFormat

getFPLength() - Method in class ambit2.core.processors.structure.FingerprintGenerator

getGroundTruth() - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

getHashCode() - Method in class ambit2.core.io.FileState

getHeader() - Method in class ambit2.core.io.FilesWithHeaderWriter

getHeader() - Method in class ambit2.core.io.FileWithHeaderWriter

getHeaderColumn(int) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

getId() - Method in class ambit2.core.data.experiment.Study

getId() - Method in class ambit2.core.data.experiment.StudyTemplate

getId() - Method in class ambit2.core.data.experiment.TemplateField

getId() - Method in class ambit2.core.data.model.ModelWrapper

getImage(Object) - Method in class ambit2.core.io.CompoundImageTools

getImage(String) - Method in class ambit2.core.io.CompoundImageTools

getImage(IAtomContainer) - Method in class ambit2.core.io.CompoundImageTools

getImage(IAtomContainer, IAtomContainer) - Method in class ambit2.core.io.CompoundImageTools

getImage(IAtomContainer, IAtomContainer, boolean) - Method in class ambit2.core.io.CompoundImageTools

getImage(ArrayList<?>) - Method in class ambit2.core.io.CompoundImageTools

getImageSize() - Method in class ambit2.core.io.CompoundImageTools

getIndexFile(String) - Static method in class ambit2.core.io.RandomAccessReader

getInstance(SmilesParserWrapper.SMILES_PARSER) - Static method in class ambit2.core.smiles.SmilesParserWrapper

getInstance() - Static method in class ambit2.core.smiles.SmilesParserWrapper

getIOSettings() - Method in class ambit2.core.io.DelimitedFileReader

getIOSettings() - Method in class ambit2.core.io.IteratingFileReader

getIOSettings() - Method in class ambit2.core.io.MDLReader

getIOSettings() - Method in class ambit2.core.io.MDLV2000ReaderExtended

getIOSettings() - Method in class ambit2.core.io.RawIteratingWrapper

getIssue(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getItemReader(int) - Method in class ambit2.core.io.IteratingFolderReader

getItemReader(int) - Method in class ambit2.core.io.IteratingMolFolderReader

getItemReader(int) - Method in class ambit2.core.io.RawIteratingFolderReader

getJournal(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getKey() - Method in class ambit2.core.processors.structure.key.EmptyKey

getKey() - Method in class ambit2.core.processors.structure.key.InchiKey

getKey() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey

getKey() - Method in interface ambit2.core.processors.structure.key.IStructureKey

getKey() - Method in class ambit2.core.processors.structure.key.PropertyKey

getKey() - Method in class ambit2.core.processors.structure.key.SmilesKey

getLastAtom() - Method in class ambit2.core.groups.SuppleAtomContainer

getLastModified() - Method in class ambit2.core.io.FileState

getLength() - Method in class ambit2.core.io.FileState

getLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getLonePairCount() - Method in class ambit2.core.groups.SuppleAtomContainer

getLonePairNumber(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer

getMaximumBondOrder(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getMediaType() - Method in class ambit2.core.processors.AbstractRepresentationConvertor

getMIMEType() - Method in class ambit2.core.io.DelimitedFileFormat

getMIMEType() - Method in class ambit2.core.io.XLSFileFormat

getMinimumBondOrder(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

getMode() - Method in class ambit2.core.data.experiment.TemplateField

getMolecule(String) - Static method in class ambit2.core.data.MoleculeTools

getMulticenter() - Method in class ambit2.core.groups.DataGroup

getMultiplier() - Method in class ambit2.core.groups.MultipleGroup

getName() - Method in class ambit2.core.data.experiment.Study

getName() - Method in class ambit2.core.data.experiment.StudyTemplate

getName() - Method in class ambit2.core.data.experiment.TemplateField

getName() - Method in class ambit2.core.data.model.ModelWrapper

getName() - Method in class ambit2.core.groups.DataGroup

getNameExtensions() - Method in class ambit2.core.io.DelimitedFileFormat

getNameExtensions() - Method in class ambit2.core.io.XLSFileFormat

getNextReader() - Method in class ambit2.core.io.IteratingFolderReader

getNumber() - Method in class ambit2.core.groups.AbstractGroup

getNumber(T) - Method in class ambit2.core.groups.FilteredList

getNumber() - Method in interface ambit2.core.groups.ISGroup

getNumberOfColumns() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

getNumberOfHeaderLines() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

getNumberOfRecords() - Method in class ambit2.core.io.RandomAccessReader

getObject(String) - Static method in class ambit2.core.config.Resources

getOffset() - Method in class ambit2.core.io.FileState

getOrder() - Method in class ambit2.core.groups.ComponentGroup

getOutput() - Method in class ambit2.core.processors.ProcessorFileExport

getPages(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getParser() - Method in class ambit2.core.smiles.SmilesParserWrapper

getPredictors() - Method in class ambit2.core.data.model.ModelWrapper

getPreferredNameExtension() - Method in class ambit2.core.io.DelimitedFileFormat

getPreferredNameExtension() - Method in class ambit2.core.io.XLSFileFormat

getProperties() - Method in class ambit2.core.io.SimpleIOListener

getProperty() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator

getProperty(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PropertyKey

getQueryKey() - Method in class ambit2.core.processors.structure.key.DSSToxCID

getQueryKey() - Method in class ambit2.core.processors.structure.key.DSSToxRID

getQueryKey() - Method in class ambit2.core.processors.structure.key.EmptyKey

getQueryKey() - Method in class ambit2.core.processors.structure.key.InchiKey

getQueryKey() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey

getQueryKey() - Method in interface ambit2.core.processors.structure.key.IStructureKey

getQueryKey() - Method in class ambit2.core.processors.structure.key.PropertyKey

getQueryKey() - Method in class ambit2.core.processors.structure.key.PubchemCID

getQueryKey() - Method in class ambit2.core.processors.structure.key.SmilesKey

getQueryOperator() - Method in class ambit2.core.groups.DataGroup

getQueryType() - Method in class ambit2.core.groups.DataGroup

getReader() - Method in class ambit2.core.io.FileInputState

getReader(InputStream, String) - Static method in class ambit2.core.io.FileInputState

getReader(InputStream, String, IChemFormat) - Static method in class ambit2.core.io.FileInputState

getReader() - Method in interface ambit2.core.io.IInputState

getReader() - Method in class ambit2.core.processors.batch.DefaultInputState

getReaderClassName() - Method in class ambit2.core.io.DelimitedFileFormat

getReaderClassName() - Method in class ambit2.core.io.XLSFileFormat

getReference() - Method in class ambit2.core.io.IteratingDelimitedFileReader

getReference() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

getReference() - Method in class ambit2.core.io.IteratingXLSReader

getReference() - Method in class ambit2.core.io.RawIteratingReader

getReference() - Method in class ambit2.core.io.RawIteratingWrapper

getReporter() - Method in class ambit2.core.processors.AbstractRepresentationConvertor

getRequiredDataFeatures() - Method in class ambit2.core.io.DelimitedFileFormat

getRequiredDataFeatures() - Method in class ambit2.core.io.XLSFileFormat

getResourceBundle() - Static method in class ambit2.core.config.Resources

getResponseType(String) - Static method in class ambit2.core.io.FileOutputState

getResponseType() - Method in class ambit2.core.io.FileState

getResponseType() - Method in class ambit2.core.processors.batch.DefaultIOState

getSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer

getSingleElectronCount() - Method in class ambit2.core.groups.SuppleAtomContainer

getSingleElectronNumber(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer

getSource() - Method in class ambit2.core.data.experiment.StudyTemplate

getString(String) - Static method in class ambit2.core.config.Resources

getStringArray(String) - Static method in class ambit2.core.config.Resources

getStudyConditions(Hashtable) - Method in class ambit2.core.data.experiment.StudyTemplate

getStudyResults() - Method in class ambit2.core.data.experiment.Study

getStudyResults(Hashtable) - Method in class ambit2.core.data.experiment.StudyTemplate

getSubscript() - Method in class ambit2.core.groups.AbstractGroup

getSubscript() - Method in interface ambit2.core.groups.ISGroup

getSubstanceType(String) - Static method in class ambit2.core.data.MoleculeTools

getSupportedDataFeatures() - Method in class ambit2.core.io.DelimitedFileFormat

getSupportedDataFeatures() - Method in class ambit2.core.io.DelimitedFileWriter

getSupportedDataFeatures() - Method in class ambit2.core.io.PDFWriter

getSupportedDataFeatures() - Method in class ambit2.core.io.XLSFileFormat

getSupportedExtDescriptions() - Method in class ambit2.core.io.FileState

getSupportedExtensions() - Method in class ambit2.core.io.FileState

getTemplate() - Method in class ambit2.core.data.experiment.Study

getTemplateName() - Method in class ambit2.core.data.experiment.Study

getTestInstances() - Method in class ambit2.core.data.model.ModelWrapper

getTextDelimiter() - Method in class ambit2.core.io.DelimitedFileFormat

getTimeout() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

getTimeProperty() - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator

getTitle(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getTrainingInstances() - Method in class ambit2.core.data.model.ModelWrapper

getType() - Method in class ambit2.core.data.experiment.TemplateField

getType() - Method in class ambit2.core.groups.ContainerGroup

getType() - Method in class ambit2.core.processors.structure.key.CASKey

getType() - Method in class ambit2.core.processors.structure.key.DSSToxCID

getType() - Method in class ambit2.core.processors.structure.key.DSSToxRID

getType() - Method in class ambit2.core.processors.structure.key.EINECSKey

getType() - Method in class ambit2.core.processors.structure.key.EmptyKey

getType() - Method in class ambit2.core.processors.structure.key.InchiKey

getType() - Method in class ambit2.core.processors.structure.key.InchiPropertyKey

getType() - Method in interface ambit2.core.processors.structure.key.IStructureKey

getType() - Method in class ambit2.core.processors.structure.key.PropertyKey

getType() - Method in class ambit2.core.processors.structure.key.PubchemCID

getType() - Method in class ambit2.core.processors.structure.key.SmilesKey

getUnits() - Method in class ambit2.core.data.experiment.TemplateField

getValue(String) - Static method in class ambit2.core.io.SGroupMDL2000Helper

Extracts first 6 chars, replaces spaces with underscore '_' and calls SGROUP_LINE.valueof method.

getVolume(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

getWriter() - Method in class ambit2.core.io.FileOutputState

getWriter(OutputStream, String) - Static method in class ambit2.core.io.FileOutputState

getWriter() - Method in interface ambit2.core.io.IOutputState

getWriterClassName() - Method in class ambit2.core.io.DelimitedFileFormat

getWriterClassName() - Method in class ambit2.core.io.XLSFileFormat

getYear(HSSFRow) - Method in class ambit2.core.io.bcf.EurasBCFReader

groundTruth - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

GroupException - Exception in ambit2.core.groups

GroupException(String) - Constructor for exception ambit2.core.groups.GroupException

GroupException(String, Exception) - Constructor for exception ambit2.core.groups.GroupException

GroupNotFoundException - Exception in ambit2.core.groups

GroupNotFoundException(String) - Constructor for exception ambit2.core.groups.GroupNotFoundException

H

hAdder - Variable in class ambit2.core.processors.structure.FingerprintGenerator

has2DCoordinates(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor

has3DCoordinates(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor

hashCode - Variable in class ambit2.core.io.FileState

hasHydrogens(IAtomContainer) - Static method in class ambit2.core.processors.structure.StructureTypeProcessor

hasNext() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator

hasNext() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper

hasNext() - Method in class ambit2.core.io.IteratingDelimitedFileReader

hasNext() - Method in class ambit2.core.io.IteratingFileReader

hasNext() - Method in class ambit2.core.io.IteratingFolderReader

hasNext() - Method in class ambit2.core.io.IteratingXLSReader

hasNext() - Method in class ambit2.core.io.MyIteratingMDLReader

Returns true if another IMolecule can be read.

hasNext() - Method in class ambit2.core.io.RandomAccessReader

hasNext() - Method in class ambit2.core.io.RawIteratingReader

hasNext() - Method in class ambit2.core.io.RawIteratingWrapper

hasPrevious() - Method in class ambit2.core.io.RandomAccessReader

header - Variable in class ambit2.core.io.FilesWithHeaderWriter

header - Variable in class ambit2.core.io.FileWithHeaderWriter

headerOptions - Variable in class ambit2.core.io.RandomAccessReader

highestSupportedChemObject() - Method in class ambit2.core.io.DelimitedFileWriter

highestSupportedChemObject() - Method in class ambit2.core.io.FileWithHeaderWriter

HIN_INDEX - Static variable in class ambit2.core.io.FileInputState

HIN_INDEX - Static variable in class ambit2.core.io.FileOutputState

HTML_INDEX - Static variable in class ambit2.core.io.FileOutputState

HydrogenAdderProcessor - Class in ambit2.core.processors.structure

HydrogenAdderProcessor() - Constructor for class ambit2.core.processors.structure.HydrogenAdderProcessor

hydrogens - Variable in class ambit2.core.processors.structure.FingerprintGenerator

I

ICHI_INDEX - Static variable in class ambit2.core.io.FileInputState

id - Variable in class ambit2.core.data.experiment.Study

id - Variable in class ambit2.core.data.experiment.StudyTemplate

id - Variable in class ambit2.core.data.experiment.TemplateField

id - Variable in class ambit2.core.data.model.ModelWrapper

IExpandable - Interface in ambit2.core.groups

IFiltered<T> - Interface in ambit2.core.groups

IInputState - Interface in ambit2.core.io

Status of the input reader.

imageSize - Variable in class ambit2.core.io.CompoundImageTools

imageTools - Variable in class ambit2.core.io.PDFWriter

INCHI - Static variable in class ambit2.core.config.AmbitCONSTANTS

Inchi

inchi - Variable in class ambit2.core.processors.structure.key.InchiKey

INCHI_INDEX - Static variable in class ambit2.core.io.FileInputState

InchiKey - Class in ambit2.core.processors.structure.key

Returns inchi

InchiKey() - Constructor for class ambit2.core.processors.structure.key.InchiKey

InchiProcessor - Class in ambit2.core.processors.structure

InchiProcessor() - Constructor for class ambit2.core.processors.structure.InchiProcessor

InchiPropertyKey - Class in ambit2.core.processors.structure.key

InchiPropertyKey() - Constructor for class ambit2.core.processors.structure.key.InchiPropertyKey

inchitag - Static variable in class ambit2.core.processors.structure.key.InchiPropertyKey

index - Static variable in class ambit2.core.data.EINECS

index - Variable in class ambit2.core.io.IteratingFolderReader

index - Variable in class ambit2.core.io.RandomAccessReader

indexCreated - Variable in class ambit2.core.io.RandomAccessReader

indexOf(Object) - Method in class ambit2.core.groups.FilteredList

indexVersion - Variable in class ambit2.core.io.RandomAccessReader

init() - Method in class ambit2.core.data.experiment.DefaultTemplate

init() - Method in class ambit2.core.data.experiment.DSSToxCarcinogenicityTemplate

init() - Method in class ambit2.core.data.experiment.DSSToxERBindingTemplate

init() - Method in class ambit2.core.data.experiment.DSSToxLC50Template

init() - Method in class ambit2.core.data.experiment.LLNATemplate

init() - Method in class ambit2.core.groups.SuppleAtomContainer

initialize() - Method in class ambit2.core.external.ShellSDFoutput

initialize() - Method in class ambit2.core.smiles.OpenBabelShell

input - Variable in class ambit2.core.io.IteratingXLSReader

instances - Variable in class ambit2.core.data.model.ModelWrapper

IntArrayResult - Class in ambit2.core.data

Array of integers implementing IDescriptorResult.

IntArrayResult() - Constructor for class ambit2.core.data.IntArrayResult

InteractiveIteratingMDLReader - Class in ambit2.core.io

A descendant of IteratingMDLReader able to ask for type of each SDF property

InteractiveIteratingMDLReader(Reader, IChemObjectBuilder) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader

InteractiveIteratingMDLReader(InputStream, IChemObjectBuilder) - Constructor for class ambit2.core.io.InteractiveIteratingMDLReader

IOutputState - Interface in ambit2.core.io

Status of the output writer.

IRawReader<T> - Interface in ambit2.core.io

isAddEexplicitHydrogens() - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor

isEmpty() - Method in class ambit2.core.groups.FilteredList

isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingMOLReader

isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingReader

isEndOfRecord(String) - Method in class ambit2.core.io.RawIteratingSDFReader

isExpanded(IBond) - Method in class ambit2.core.groups.AbstractGroup

isExpanded() - Method in interface ambit2.core.groups.IExpandable

isExpanded() - Method in class ambit2.core.groups.MultipleGroup

isExpanded(IBond) - Method in class ambit2.core.groups.SuperAtom

isExpanded() - Method in class ambit2.core.groups.SuperAtom

isFiltered() - Method in class ambit2.core.groups.FilteredList

isFiltered(T) - Method in class ambit2.core.groups.FilteredList

isFiltered(T) - Method in interface ambit2.core.groups.IFiltered

isFiltered() - Method in interface ambit2.core.groups.IFiltered

isFiltered(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

isFiltered(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

isFiltered() - Method in class ambit2.core.groups.SuppleAtomContainer

ISGroup - Interface in ambit2.core.groups

isGroupVisible(IChemObject) - Static method in class ambit2.core.groups.AbstractGroup

isHeaderEmpty() - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

isHydrogens() - Method in class ambit2.core.processors.structure.FingerprintGenerator

isIndexCreated() - Method in class ambit2.core.io.RandomAccessReader

isInterrupted() - Method in class ambit2.core.smiles.DeduceBondSystemTool

isNumeric() - Method in class ambit2.core.data.experiment.TemplateField

isOK(IMolecule) - Method in class ambit2.core.smiles.DeduceBondSystemTool

isoTester - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

isReadOutput() - Method in class ambit2.core.external.ShellSDFoutput

isRecordEnd(String) - Method in class ambit2.core.io.RandomAccessReader

isRecordEnd(String) - Method in class ambit2.core.io.RandomAccessSDFReader

isResult - Variable in class ambit2.core.data.experiment.TemplateField

isResult() - Method in class ambit2.core.data.experiment.TemplateField

isSgroupLine(String) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

IStructureKey<Target,Result> - Interface in ambit2.core.processors.structure.key

isValid(String) - Static method in class ambit2.core.data.EINECS

200-002-3 200-006-5 EINECS:abc-def-g
g=(a+2b+3c+4d+5e+6f)mod11

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.CASKey

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.DSSToxCID

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.DSSToxRID

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.EINECSKey

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.InchiPropertyKey

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PropertyKey

isValid(Object, Object) - Method in class ambit2.core.processors.structure.key.PubchemCID

isVisible(T) - Method in class ambit2.core.groups.FilteredList

isVisible(T) - Method in interface ambit2.core.groups.IFiltered

isVisible(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

isXMLBased() - Method in class ambit2.core.io.DelimitedFileFormat

isXMLBased() - Method in class ambit2.core.io.XLSFileFormat

IteratingChemObjectReaderWrapper - Class in ambit2.core.io

A wrapper for DefaultChemObjectReader.

IteratingChemObjectReaderWrapper(DefaultChemObjectReader) - Constructor for class ambit2.core.io.IteratingChemObjectReaderWrapper

IteratingDelimitedFileReader - Class in ambit2.core.io

Iterating reader for delimited files.

IteratingDelimitedFileReader(Reader) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader

IteratingDelimitedFileReader(Reader, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader

IteratingDelimitedFileReader(InputStream) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader

IteratingDelimitedFileReader(InputStream, DelimitedFileFormat) - Constructor for class ambit2.core.io.IteratingDelimitedFileReader

IteratingFileReader - Class in ambit2.core.io

A wrapper for all file readers.

IteratingFileReader(File) - Constructor for class ambit2.core.io.IteratingFileReader

IteratingFileReader(File, IChemFormat) - Constructor for class ambit2.core.io.IteratingFileReader

IteratingFilesWithHeaderReader - Class in ambit2.core.io

IteratingFilesWithHeaderReader() - Constructor for class ambit2.core.io.IteratingFilesWithHeaderReader

IteratingFolderReader<T,ItemReader extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader> - Class in ambit2.core.io

IteratingFolderReader(File[]) - Constructor for class ambit2.core.io.IteratingFolderReader

IteratingMolFolderReader - Class in ambit2.core.io

IteratingMolFolderReader() - Constructor for class ambit2.core.io.IteratingMolFolderReader

IteratingMolFolderReader(File[]) - Constructor for class ambit2.core.io.IteratingMolFolderReader

IteratingXLSReader - Class in ambit2.core.io

Reads XLS files.

IteratingXLSReader(InputStream, int) - Constructor for class ambit2.core.io.IteratingXLSReader

iterator() - Method in class ambit2.core.groups.AbstractGroup.SelfIterable

iterator() - Method in class ambit2.core.groups.FilteredList

iterator - Variable in class ambit2.core.io.IteratingXLSReader

J

JPG_INDEX - Static variable in class ambit2.core.io.FileOutputState

K

key - Variable in class ambit2.core.processors.structure.key.CASKey

key - Variable in class ambit2.core.processors.structure.key.InchiKey

key - Variable in class ambit2.core.processors.structure.key.PropertyKey

key - Variable in class ambit2.core.processors.structure.key.SmilesKey

L

last() - Method in class ambit2.core.io.RandomAccessReader

lastIndexOf(Object) - Method in class ambit2.core.groups.FilteredList

lastModified - Variable in class ambit2.core.io.FileState

length() - Method in class ambit2.core.data.ArrayResult

length() - Method in class ambit2.core.data.StringDescriptorResultType

length - Variable in class ambit2.core.io.FileState

level - Variable in class ambit2.core.io.SimpleIOListener

libFiles - Static variable in class ambit2.core.smiles.OpenBabelShell

listIterator() - Method in class ambit2.core.groups.FilteredList

listIterator(int) - Method in class ambit2.core.groups.FilteredList

LLNATemplate - Class in ambit2.core.data.experiment

Template for LLNA data.

LLNATemplate(String) - Constructor for class ambit2.core.data.experiment.LLNATemplate

load(InputStream) - Method in class ambit2.core.data.experiment.StudyTemplate

load(Reader) - Method in class ambit2.core.data.experiment.StudyTemplate

loadIndex(File) - Method in class ambit2.core.io.RandomAccessReader

logger - Static variable in class ambit2.core.io.FilesWithHeaderWriter

logger - Static variable in class ambit2.core.io.FileWithHeaderWriter

logger - Static variable in class ambit2.core.io.IteratingFilesWithHeaderReader

logger - Static variable in class ambit2.core.io.RandomAccessReader

logger - Static variable in class ambit2.core.io.RawIteratingReader

logger - Static variable in class ambit2.core.processors.structure.FingerprintGenerator

lonePairs - Variable in class ambit2.core.groups.SuppleAtomContainer

lonePairs() - Method in class ambit2.core.groups.SuppleAtomContainer

M

mainsubscript - Static variable in class ambit2.core.groups.ComponentGroup

makeIndex() - Method in class ambit2.core.io.RandomAccessReader

match() - Method in class ambit2.core.io.FileState

match(File) - Method in class ambit2.core.io.FileState

matches(int, String) - Method in class ambit2.core.io.DelimitedFileFormat

matches(int, String) - Method in class ambit2.core.io.XLSFileFormat

maxCyclicBonds - Static variable in class ambit2.core.config.AmbitCONSTANTS

max cyclic bonds for skipping huge compounds

maxHAtoms - Static variable in class ambit2.core.config.AmbitCONSTANTS

max H atoms for skipping huge compounds

maxHeavyAtoms - Static variable in class ambit2.core.config.AmbitCONSTANTS

max heavy atoms for skipping huge compounds

MDLReader - Class in ambit2.core.io

Reads a molecule from the original MDL MOL or SDF file {cdk.cite DAL92}.

MDLReader() - Constructor for class ambit2.core.io.MDLReader

MDLReader(InputStream) - Constructor for class ambit2.core.io.MDLReader

Contructs a new MDLReader that can read Molecule from a given InputStream.

MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLReader

MDLReader(Reader) - Constructor for class ambit2.core.io.MDLReader

Contructs a new MDLReader that can read Molecule from a given Reader.

MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLReader

MDLV2000ReaderExtended - Class in ambit2.core.io

Supports SGroups.

MDLV2000ReaderExtended() - Constructor for class ambit2.core.io.MDLV2000ReaderExtended

MDLV2000ReaderExtended(InputStream) - Constructor for class ambit2.core.io.MDLV2000ReaderExtended

Contructs a new MDLReader that can read Molecule from a given InputStream.

MDLV2000ReaderExtended(InputStream, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLV2000ReaderExtended

MDLV2000ReaderExtended(Reader) - Constructor for class ambit2.core.io.MDLV2000ReaderExtended

Contructs a new MDLReader that can read Molecule from a given Reader.

MDLV2000ReaderExtended(Reader, IChemObjectReader.Mode) - Constructor for class ambit2.core.io.MDLV2000ReaderExtended

MDLWriter - Class in ambit2.core.io

Copied here from CDK source tree in order to handle the aromatic bond issue (this code writes 4 as aromatic bond code); until a proper fix is available.

MDLWriter(Writer) - Constructor for class ambit2.core.io.MDLWriter

Contructs a new MDLWriter that can write an array of Molecules to a Writer.

MDLWriter(OutputStream) - Constructor for class ambit2.core.io.MDLWriter

Contructs a new MDLWriter that can write an array of Molecules to a given OutputStream.

MDLWriter() - Constructor for class ambit2.core.io.MDLWriter

mediaType - Variable in class ambit2.core.processors.AbstractRepresentationConvertor

ModelWrapper<T,TrainingInstances extends T,TestInstances extends T,Content> - Class in ambit2.core.data.model

Encapsulated a Model, defined by Template predictors, Template dependent variables and instances.

ModelWrapper() - Constructor for class ambit2.core.data.model.ModelWrapper

MOL_INDEX - Static variable in class ambit2.core.io.FileInputState

MOL_INDEX - Static variable in class ambit2.core.io.FileOutputState

MoleculeReader - Class in ambit2.core.processors.structure

MoleculeReader() - Constructor for class ambit2.core.processors.structure.MoleculeReader

MoleculeTools - Class in ambit2.core.data

Various structure processing.

MoleculeTools() - Constructor for class ambit2.core.data.MoleculeTools

MoleculeWriter - Class in ambit2.core.processors.structure

MoleculeWriter() - Constructor for class ambit2.core.processors.structure.MoleculeWriter

MolPropertiesIOSetting - Class in ambit2.core.io

An IOSetting descendant to provide means for transforming property names.

MolPropertiesIOSetting(String, int, String, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting

MolPropertiesIOSetting(ArrayList, int, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting

MolPropertiesIOSetting(Map, int, String) - Constructor for class ambit2.core.io.MolPropertiesIOSetting

MOLWEIGHT - Static variable in class ambit2.core.config.AmbitCONSTANTS

Molecular weight

MonomerGroup - Class in ambit2.core.groups

MonomerGroup(String, int) - Constructor for class ambit2.core.groups.MonomerGroup

MRV_MULTICENTER - Static variable in class ambit2.core.groups.DataGroup

MSG_CANTCREATEFILE - Static variable in class ambit2.core.io.FileState

MSG_EMPTYFILE - Static variable in class ambit2.core.config.Resources

Empty file

MSG_ERRORONOPEN - Static variable in class ambit2.core.config.Resources

error on file open

MSG_ERRORONSAVE - Static variable in class ambit2.core.config.Resources

Error on file save

MSG_ERRORSAVE - Static variable in class ambit2.core.io.FileState

msg_exit - Static variable in class ambit2.core.config.Resources

Exit

MSG_FILEDONOTEXISTS - Static variable in class ambit2.core.io.FileState

msg_notallowed - Static variable in class ambit2.core.config.Resources

not allowed

MSG_OPEN - Static variable in class ambit2.core.io.FileState

MSG_OPENSUCCESS - Static variable in class ambit2.core.config.Resources

successful file open

MSG_SAVESUCCESS - Static variable in class ambit2.core.config.Resources

Successful file save

MSG_UNSUPPORTEDFORMAT - Static variable in class ambit2.core.config.Resources

unsupported format

MSG_UNSUPPORTEDFORMAT - Static variable in class ambit2.core.io.FileState

multicenter - Variable in class ambit2.core.groups.DataGroup

MultiNewlineFilterReader - Class in ambit2.core.io

MultiNewlineFilterReader(Reader) - Constructor for class ambit2.core.io.MultiNewlineFilterReader

MultipleGroup - Class in ambit2.core.groups

MultipleGroup(String, int) - Constructor for class ambit2.core.groups.MultipleGroup

multiplier - Variable in class ambit2.core.groups.MultipleGroup

MyIteratingMDLReader - Class in ambit2.core.io

Copied here (with corrections)until Bug 1758372 in CDK is fixed.

MyIteratingMDLReader(Reader, IChemObjectBuilder) - Constructor for class ambit2.core.io.MyIteratingMDLReader

Contructs a new MyIteratingMDLReader that can read Molecule from a given Reader.

MyIteratingMDLReader(InputStream, IChemObjectBuilder) - Constructor for class ambit2.core.io.MyIteratingMDLReader

Contructs a new MyIteratingMDLReader that can read Molecule from a given InputStream.

N

name - Variable in class ambit2.core.data.experiment.Study

name - Variable in class ambit2.core.data.experiment.StudyTemplate

name - Variable in class ambit2.core.data.experiment.TemplateField

name - Variable in class ambit2.core.data.model.ModelWrapper

NAMES - Static variable in class ambit2.core.config.AmbitCONSTANTS

Chemical name

next() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator

next() - Method in class ambit2.core.io.InteractiveIteratingMDLReader

next() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper

next() - Method in class ambit2.core.io.IteratingDelimitedFileReader

next() - Method in class ambit2.core.io.IteratingFileReader

next() - Method in class ambit2.core.io.IteratingFolderReader

next() - Method in class ambit2.core.io.IteratingMolFolderReader

next() - Method in class ambit2.core.io.IteratingXLSReader

next() - Method in class ambit2.core.io.MyIteratingMDLReader

Returns the next IMolecule.

next() - Method in class ambit2.core.io.RandomAccessReader

next() - Method in class ambit2.core.io.RawIteratingFolderReader

next() - Method in class ambit2.core.io.RawIteratingMOLReader

next() - Method in class ambit2.core.io.RawIteratingReader

next() - Method in class ambit2.core.io.RawIteratingSDFReader

next() - Method in class ambit2.core.io.RawIteratingWrapper

nextIndex() - Method in class ambit2.core.io.RandomAccessReader

nextRecord() - Method in interface ambit2.core.io.IRawReader

nextRecord() - Method in class ambit2.core.io.RawIteratingFolderReader

nextRecord() - Method in class ambit2.core.io.RawIteratingMOLReader

nextRecord() - Method in class ambit2.core.io.RawIteratingReader

nextRecord() - Method in class ambit2.core.io.RawIteratingSDFReader

nextRecord() - Method in class ambit2.core.io.RawIteratingWrapper

number - Variable in class ambit2.core.groups.AbstractGroup

number - Variable in class ambit2.core.groups.MultipleGroup

numberOfHeaderLines - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader

numeric - Variable in class ambit2.core.data.experiment.TemplateField

O

offset - Variable in class ambit2.core.io.FileState

onStopEvent() - Method in class ambit2.core.io.SimpleIOListener

OpenBabelShell - Class in ambit2.core.smiles

OpenBabelShell() - Constructor for class ambit2.core.smiles.OpenBabelShell

order - Variable in class ambit2.core.groups.ComponentGroup

out - Variable in class ambit2.core.io.XLSFileWriter

output - Variable in class ambit2.core.processors.ProcessorFileExport

P

paint(Renderer2D, IMoleculeSet, boolean, Graphics2D, IAtomContainer) - Method in class ambit2.core.io.CompoundImageTools

paint(Renderer2D, IMoleculeSet, boolean, Graphics2D, IAtomContainer, Dimension) - Static method in class ambit2.core.io.CompoundImageTools

TODO sort molecules, in order to display the largest part first

PairwiseSimilarity - Static variable in class ambit2.core.config.AmbitCONSTANTS

Pairwise similarity

parentAtoms - Variable in class ambit2.core.groups.MultipleGroup

parentBonds - Variable in class ambit2.core.groups.MultipleGroup

parse(String) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

parseByPosition(String, int[]) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

parseList(String, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

parseList(String, int, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

parseOutput(String, INPUT) - Method in class ambit2.core.external.ShellSDFoutput

parsePairs(String, int) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

parser - Variable in class ambit2.core.io.CompoundImageTools

parser - Variable in class ambit2.core.smiles.SmilesParserWrapper

parseSmiles(String) - Method in class ambit2.core.smiles.SmilesParserWrapper

PDB_INDEX - Static variable in class ambit2.core.io.FileInputState

PDB_INDEX - Static variable in class ambit2.core.io.FileOutputState

PDF_INDEX - Static variable in class ambit2.core.io.FileOutputState

pdfDoc - Variable in class ambit2.core.io.PDFWriter

PDFWriter - Class in ambit2.core.io

Exporting set of structures as PDF file.

PDFWriter(OutputStream) - Constructor for class ambit2.core.io.PDFWriter

pdfWriter - Variable in class ambit2.core.io.PDFWriter

PNG_INDEX - Static variable in class ambit2.core.io.FileOutputState

PREDICTED - Static variable in class ambit2.core.config.AmbitCONSTANTS

Predicted data record

predictors - Variable in class ambit2.core.data.model.ModelWrapper

prepareInput(String, String) - Method in class ambit2.core.smiles.OpenBabelShell

previous() - Method in class ambit2.core.io.RandomAccessReader

previousIndex() - Method in class ambit2.core.io.RandomAccessReader

printCoordinates(Renderer2DModel) - Static method in class ambit2.core.io.CompoundImageTools

process(IAtomContainer) - Method in class ambit2.core.data.distances.AtomDistanceProcessor

process(Content) - Method in class ambit2.core.processors.AbstractRepresentationConvertor

process(Content) - Method in class ambit2.core.processors.ProcessorFileExport

process(IMolecule) - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

process(IStructureRecord) - Method in class ambit2.core.processors.structure.AbstractPropertyGenerator

process(IAtomContainer) - Method in class ambit2.core.processors.structure.AtomConfigurator

process(IAtomContainer) - Method in class ambit2.core.processors.structure.CloneProcessor

process(IAtomContainer) - Method in class ambit2.core.processors.structure.FingerprintGenerator

process(IAtomContainer) - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor

process(IAtomContainer) - Method in class ambit2.core.processors.structure.InchiProcessor

process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.CASKey

process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.DSSToxCID

process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.DSSToxRID

process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.EmptyKey

process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.InchiKey

process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PropertyKey

process(IStructureRecord) - Method in class ambit2.core.processors.structure.key.PubchemCID

process(IAtomContainer) - Method in class ambit2.core.processors.structure.key.SmilesKey

process(IStructureRecord) - Method in class ambit2.core.processors.structure.MoleculeReader

process(IAtomContainer) - Method in class ambit2.core.processors.structure.MoleculeWriter

process(IAtomContainer) - Method in class ambit2.core.processors.structure.StructureTypeProcessor

processHeader() - Method in class ambit2.core.io.bcf.EurasBCFReader

processHeader(BufferedReader) - Method in class ambit2.core.io.IteratingDelimitedFileReader

processHeader() - Method in class ambit2.core.io.IteratingXLSReader

processHeader(HSSFRow) - Method in class ambit2.core.io.IteratingXLSReader

processIOSettingQuestion(IOSetting) - Method in class ambit2.core.io.SimpleIOListener

ProcessorFileExport<Content> - Class in ambit2.core.processors

TODO merge with representation convertor make use of http://jmimemagic.sourceforge.net/maven-reports.html for mime recognition

ProcessorFileExport() - Constructor for class ambit2.core.processors.ProcessorFileExport

ProcessorFileExport(FileOutputState) - Constructor for class ambit2.core.processors.ProcessorFileExport

processRow(IAtomContainer) - Method in class ambit2.core.io.bcf.EurasBCFReader

processRow(IAtomContainer) - Method in class ambit2.core.io.IteratingXLSReader

properties - Variable in class ambit2.core.io.MolPropertiesIOSetting

properties - Variable in class ambit2.core.io.SimpleIOListener

propertyChange(PropertyChangeEvent) - Method in class ambit2.core.smiles.SmilesParserWrapper

PropertyKey<Result> - Class in ambit2.core.processors.structure.key

PropertyKey() - Constructor for class ambit2.core.processors.structure.key.PropertyKey

PropertyKey(Property) - Constructor for class ambit2.core.processors.structure.key.PropertyKey

PubchemCID - Class in ambit2.core.processors.structure.key

returns pubchem cid given the structure properties

PubchemCID() - Constructor for class ambit2.core.processors.structure.key.PubchemCID

Q

QSARPOINT - Static variable in class ambit2.core.config.AmbitCONSTANTS

QSAR point

qualityVerifier - Variable in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

query - Variable in class ambit2.core.data.experiment.StudyTemplate

R

r - Variable in class ambit2.core.io.RawIteratingMOLReader

r - Variable in class ambit2.core.io.RawIteratingSDFReader

r - Variable in class ambit2.core.io.RawIteratingWrapper

raFile - Variable in class ambit2.core.io.RandomAccessReader

RandomAccessReader - Class in ambit2.core.io

Random access to text files of compounds.

RandomAccessReader(File, IChemObjectBuilder) - Constructor for class ambit2.core.io.RandomAccessReader

RandomAccessReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class ambit2.core.io.RandomAccessReader

RandomAccessSDFReader - Class in ambit2.core.io

Random access of SDF file.

RandomAccessSDFReader(File, IChemObjectBuilder) - Constructor for class ambit2.core.io.RandomAccessSDFReader

RandomAccessSDFReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class ambit2.core.io.RandomAccessSDFReader

RawIteratingFolderReader - Class in ambit2.core.io

RawIteratingFolderReader(File[]) - Constructor for class ambit2.core.io.RawIteratingFolderReader

RawIteratingMOLReader - Class in ambit2.core.io

RawIteratingMOLReader(Reader) - Constructor for class ambit2.core.io.RawIteratingMOLReader

RawIteratingReader<T> - Class in ambit2.core.io

RawIteratingReader(Reader) - Constructor for class ambit2.core.io.RawIteratingReader

RawIteratingSDFReader - Class in ambit2.core.io

RawIteratingSDFReader(Reader) - Constructor for class ambit2.core.io.RawIteratingSDFReader

RawIteratingWrapper<R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader> - Class in ambit2.core.io

RawIteratingWrapper(R) - Constructor for class ambit2.core.io.RawIteratingWrapper

read(IChemObject) - Method in class ambit2.core.io.DelimitedFileReader

read(IChemObject) - Method in class ambit2.core.io.MDLReader

Takes an object which subclasses IChemObject, e.g.

read(IChemObject) - Method in class ambit2.core.io.MDLV2000ReaderExtended

Takes an object which subclasses IChemObject, e.g.

read(char[], int, int) - Method in class ambit2.core.io.MultiNewlineFilterReader

read(char[], int, int) - Method in class ambit2.core.io.RandomAccessReader

readCMLMolecule(String) - Static method in class ambit2.core.data.MoleculeTools

readCMLMolecule(Reader) - Static method in class ambit2.core.data.MoleculeTools

readContent(String, int) - Method in class ambit2.core.io.RandomAccessReader

readContent(String, int) - Method in class ambit2.core.io.RandomAccessSDFReader

reader - Variable in class ambit2.core.io.IteratingFileReader

reader - Variable in class ambit2.core.io.IteratingFolderReader

reader - Variable in class ambit2.core.io.RawIteratingWrapper

reader - Variable in class ambit2.core.processors.batch.DefaultInputState

reader - Variable in class ambit2.core.processors.structure.AbstractPropertyGenerator

ReaderFactoryExtended - Class in ambit2.core.io

ReaderFactoryExtended() - Constructor for class ambit2.core.io.ReaderFactoryExtended

readMolfile(Reader) - Static method in class ambit2.core.data.MoleculeTools

readMolfile(String) - Static method in class ambit2.core.data.MoleculeTools

readOutput - Variable in class ambit2.core.external.ShellSDFoutput

readRecord(int) - Method in class ambit2.core.io.RandomAccessReader

readReferences() - Method in class ambit2.core.io.bcf.EurasBCFReader

record - Variable in class ambit2.core.io.IteratingChemObjectReaderWrapper

recordBuffer - Variable in class ambit2.core.io.RawIteratingReader

records - Variable in class ambit2.core.io.RandomAccessReader

reference - Variable in class ambit2.core.io.RawIteratingReader

reference - Variable in class ambit2.core.io.RawIteratingWrapper

references - Variable in class ambit2.core.io.bcf.EurasBCFReader

remove() - Method in class ambit2.core.groups.AbstractGroup.EmptyIterator

remove(Object) - Method in class ambit2.core.groups.FilteredList

remove(int) - Method in class ambit2.core.groups.FilteredList

remove(IAtomContainer) - Method in class ambit2.core.groups.SuppleAtomContainer

remove() - Method in class ambit2.core.io.IteratingDelimitedFileReader

remove() - Method in class ambit2.core.io.IteratingFileReader

remove() - Method in class ambit2.core.io.MyIteratingMDLReader

remove() - Method in class ambit2.core.io.RawIteratingWrapper

removeAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList

removeAllBonds() - Method in class ambit2.core.groups.SuppleAtomContainer

removeAllElectronContainers() - Method in class ambit2.core.groups.SuppleAtomContainer

removeAllElements() - Method in class ambit2.core.groups.SuppleAtomContainer

removeAtom(int) - Method in class ambit2.core.groups.SuppleAtomContainer

removeAtom(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

removeAtomAndConnectedElectronContainers(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

removeBond(int) - Method in class ambit2.core.groups.SuppleAtomContainer

removeBond(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

removeBond(IAtom, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.IteratingFileReader

removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RandomAccessReader

removeChemObjectIOListener(IChemObjectIOListener) - Method in class ambit2.core.io.RawIteratingWrapper

removeElectronContainer(int) - Method in class ambit2.core.groups.SuppleAtomContainer

removeElectronContainer(IElectronContainer) - Method in class ambit2.core.groups.SuppleAtomContainer

removeFromFilter(int) - Method in class ambit2.core.groups.FilteredList

removeFromFilter(T) - Method in class ambit2.core.groups.FilteredList

removeFromFilter(T) - Method in interface ambit2.core.groups.IFiltered

removeFromFilter(IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

removeFromFilter(IBond) - Method in class ambit2.core.groups.SuppleAtomContainer

removeLonePair(int) - Method in class ambit2.core.groups.SuppleAtomContainer

removeLonePair(ILonePair) - Method in class ambit2.core.groups.SuppleAtomContainer

removeSingleElectron(int) - Method in class ambit2.core.groups.SuppleAtomContainer

removeSingleElectron(ISingleElectron) - Method in class ambit2.core.groups.SuppleAtomContainer

reporter - Variable in class ambit2.core.processors.AbstractRepresentationConvertor

resize(long[][], int) - Method in class ambit2.core.io.RandomAccessReader

resourceBundle - Static variable in class ambit2.core.config.Resources

Resources - Class in ambit2.core.config

Localisation resources (singleton)

responseType - Variable in class ambit2.core.io.FileState

responseType - Variable in class ambit2.core.processors.batch.DefaultIOState

result - Static variable in class ambit2.core.data.experiment.DefaultTemplate

retainAll(Collection<?>) - Method in class ambit2.core.groups.FilteredList

RTF_INDEX - Static variable in class ambit2.core.io.FileOutputState

run() - Method in class ambit2.core.io.RandomAccessReader

S

save(OutputStream) - Method in class ambit2.core.data.experiment.StudyTemplate

save(Writer) - Method in class ambit2.core.data.experiment.StudyTemplate

save(OutputStream) - Method in class ambit2.core.data.experiment.TemplateField

save(Writer) - Method in class ambit2.core.data.experiment.TemplateField

saveIndex(File) - Method in class ambit2.core.io.RandomAccessReader

SDF_INDEX - Static variable in class ambit2.core.io.FileInputState

SDF_INDEX - Static variable in class ambit2.core.io.FileOutputState

SDFBrokenLineTerminationConverter - Class in ambit2.core.io

SDFBrokenLineTerminationConverter() - Constructor for class ambit2.core.io.SDFBrokenLineTerminationConverter

sdFields - Variable in class ambit2.core.io.MDLWriter

selectProperties(IOSetting) - Method in class ambit2.core.io.SimpleIOListener

set(int, T) - Method in class ambit2.core.data.ArrayResult

set(int, T) - Method in class ambit2.core.groups.FilteredList

set(Object) - Method in class ambit2.core.io.RandomAccessReader

setAddEexplicitHydrogens(boolean) - Method in class ambit2.core.processors.structure.HydrogenAdderProcessor

setAtom(int, IAtom) - Method in class ambit2.core.groups.SuppleAtomContainer

setAtoms(IAtom[]) - Method in class ambit2.core.groups.SuppleAtomContainer

setBackground(Color) - Method in class ambit2.core.io.CompoundImageTools

setBonds(IBond[]) - Method in class ambit2.core.groups.SuppleAtomContainer

setBorderColor(Color) - Method in class ambit2.core.io.CompoundImageTools

Creates gradient border of this color.

setBorderWidth(int) - Method in class ambit2.core.io.CompoundImageTools

setChemObjectReader(IChemObjectReader) - Method in class ambit2.core.io.RandomAccessReader

setComponents(List<ISGroup>) - Method in class ambit2.core.groups.ContainerGroup

setContent(Content) - Method in class ambit2.core.data.model.ModelWrapper

setCurrentRecord(long) - Method in class ambit2.core.io.FileState

setCurrentRecord(long) - Method in class ambit2.core.processors.batch.DefaultIOState

setDefaultImage(BufferedImage) - Method in class ambit2.core.io.CompoundImageTools

setDependent(Template) - Method in class ambit2.core.data.model.ModelWrapper

setExpanded(boolean) - Method in interface ambit2.core.groups.IExpandable

setExpanded(boolean) - Method in class ambit2.core.groups.MultipleGroup

setExpanded(boolean) - Method in class ambit2.core.groups.SuperAtom

setFieldFormat(String) - Method in class ambit2.core.groups.DataGroup

setFieldType(String) - Method in class ambit2.core.groups.DataGroup

setFile(File) - Method in class ambit2.core.io.FileState

setFilename(String) - Method in class ambit2.core.io.FileState

setFiles(File[]) - Method in class ambit2.core.io.IteratingFolderReader

setFiltered(boolean) - Method in class ambit2.core.groups.FilteredList

setFiltered(boolean) - Method in interface ambit2.core.groups.IFiltered

setFiltered(boolean) - Method in class ambit2.core.groups.SuppleAtomContainer

setGroundTruth(IMolecule) - Method in class ambit2.core.processors.quality.ChemicalStructureQualityCheck

setGroupVisible(IChemObject, boolean) - Static method in class ambit2.core.groups.AbstractGroup

setHashCode(int) - Method in class ambit2.core.io.FileState

setHeader(Map) - Method in class ambit2.core.io.FilesWithHeaderWriter

Creates header from Hashtable keys Used for default header - created from properties of the first molecule written

setHeader(ArrayList) - Method in class ambit2.core.io.FilesWithHeaderWriter

setHeader(ArrayList) - Method in class ambit2.core.io.FileWithHeaderWriter

setHeader(Map) - Method in class ambit2.core.io.FileWithHeaderWriter

Creates header from Hashtable keys Used for default header - created from properties of the first molecule written

setHeaderColumn(int, String) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

setHydrogens(boolean) - Method in class ambit2.core.processors.structure.FingerprintGenerator

setId(int) - Method in class ambit2.core.data.experiment.Study

setId(int) - Method in class ambit2.core.data.experiment.StudyTemplate

setId(int) - Method in class ambit2.core.data.experiment.TemplateField

setId(int) - Method in class ambit2.core.data.model.ModelWrapper

setImageSize(Dimension) - Method in class ambit2.core.io.CompoundImageTools

setIndexCreated(boolean) - Method in class ambit2.core.io.RandomAccessReader

setInterrupted(boolean) - Method in class ambit2.core.smiles.DeduceBondSystemTool

setKey(Object) - Method in class ambit2.core.processors.structure.key.InchiKey

setKey(Property) - Method in class ambit2.core.processors.structure.key.PropertyKey

setKey(Object) - Method in class ambit2.core.processors.structure.key.SmilesKey

setLastModified(long) - Method in class ambit2.core.io.FileState

setLength(long) - Method in class ambit2.core.io.FileState

setMediaType(Media) - Method in class ambit2.core.processors.AbstractRepresentationConvertor

setMulticenter(IAtom) - Method in class ambit2.core.groups.DataGroup

setMultiplier(int) - Method in class ambit2.core.groups.MultipleGroup

setName(String) - Method in class ambit2.core.data.experiment.Study

setName(String) - Method in class ambit2.core.data.experiment.StudyTemplate

setName(String) - Method in class ambit2.core.data.experiment.TemplateField

setName(String) - Method in class ambit2.core.data.model.ModelWrapper

setName(String) - Method in class ambit2.core.groups.DataGroup

setNumber(int) - Method in class ambit2.core.groups.AbstractGroup

setNumber(int) - Method in interface ambit2.core.groups.ISGroup

setNumberOfHeaderLines(int) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

setNumeric(boolean) - Method in class ambit2.core.data.experiment.TemplateField

setOffset(long) - Method in class ambit2.core.io.FileState

setOrder(Integer) - Method in class ambit2.core.groups.ComponentGroup

setOutput(FileOutputState) - Method in class ambit2.core.processors.ProcessorFileExport

setParser(SmilesParserWrapper.SMILES_PARSER) - Method in class ambit2.core.smiles.SmilesParserWrapper

setPredictors(Template) - Method in class ambit2.core.data.model.ModelWrapper

setProperties(Profile) - Method in class ambit2.core.io.SimpleIOListener

setQueryOperator(String) - Method in class ambit2.core.groups.DataGroup

setQueryType(String) - Method in class ambit2.core.groups.DataGroup

setReader(Reader) - Method in class ambit2.core.io.DelimitedFileReader

setReader(InputStream) - Method in class ambit2.core.io.DelimitedFileReader

setReader(InputStream) - Method in class ambit2.core.io.FilteredMDLReader

setReader(Reader) - Method in class ambit2.core.io.FilteredMDLReader

setReader(Reader) - Method in class ambit2.core.io.MDLReader

setReader(InputStream) - Method in class ambit2.core.io.MDLReader

setReader(Reader) - Method in class ambit2.core.io.MDLV2000ReaderExtended

setReader(InputStream) - Method in class ambit2.core.io.MDLV2000ReaderExtended

setReadOutput(boolean) - Method in class ambit2.core.external.ShellSDFoutput

setReference(LiteratureEntry) - Method in class ambit2.core.io.RawIteratingReader

setReference(LiteratureEntry) - Method in class ambit2.core.io.RawIteratingWrapper

setReporter(ItemReporter) - Method in class ambit2.core.processors.AbstractRepresentationConvertor

setResponseType(String) - Method in class ambit2.core.io.FileState

setResponseType(String) - Method in class ambit2.core.processors.batch.DefaultIOState

setResult(boolean) - Method in class ambit2.core.data.experiment.TemplateField

setSdFields(Map) - Method in class ambit2.core.io.MDLWriter

Here you can set a map which will be used to build sd fields in the file.

setSimple(boolean) - Method in class ambit2.core.data.experiment.AquireTemplate

setSource(String) - Method in class ambit2.core.data.experiment.StudyTemplate

setStudyResults(Hashtable) - Method in class ambit2.core.data.experiment.Study

setSubscript(String) - Method in class ambit2.core.groups.AbstractGroup

setSubscript(String) - Method in interface ambit2.core.groups.ISGroup

text of Sgroup subscript.

setSubscript(String) - Method in class ambit2.core.groups.SuperAtom

setSupportedExtDescriptions(String[]) - Method in class ambit2.core.io.FileState

setSupportedExtensions(String[]) - Method in class ambit2.core.io.FileState

setTemplate(Template) - Method in class ambit2.core.data.experiment.Study

setTemplateName(String) - Method in class ambit2.core.data.experiment.Study

setTestInstances(TestInstances) - Method in class ambit2.core.data.model.ModelWrapper

setTimeout(long) - Method in class ambit2.core.io.IteratingFilesWithHeaderReader

setTrainingInstances(TrainingInstances) - Method in class ambit2.core.data.model.ModelWrapper

setType(ContainerGroup.SGROUP_MIXTURE) - Method in class ambit2.core.groups.ContainerGroup

setUnits(String) - Method in class ambit2.core.data.experiment.TemplateField

setWriter(OutputStream) - Method in class ambit2.core.io.DelimitedFileWriter

setWriter(Writer) - Method in class ambit2.core.io.DelimitedFileWriter

setWriter(Writer) - Method in class ambit2.core.io.MDLWriter

setWriter(OutputStream) - Method in class ambit2.core.io.MDLWriter

setWriter(Writer) - Method in class ambit2.core.io.PDFWriter

setWriter(OutputStream) - Method in class ambit2.core.io.PDFWriter

setWriter(Writer) - Method in class ambit2.core.io.XLSFileWriter

setWriter(OutputStream) - Method in class ambit2.core.io.XLSFileWriter

sg - Variable in class ambit2.core.io.DelimitedFileWriter

sg - Variable in class ambit2.core.io.FileWithHeaderWriter

SGROUP_CONNECTIVITY - Static variable in interface ambit2.core.groups.ISGroup

SGROUP_VISIBLE - Static variable in interface ambit2.core.groups.ISGroup

SGroupMDL2000Helper - Class in ambit2.core.io

Helper for MDL SGroups

SGroupMDL2000Helper() - Constructor for class ambit2.core.io.SGroupMDL2000Helper

SGroupMDL2000Helper.SGROUP_CONNECTIVITY - Enum in ambit2.core.io

SGroupMDL2000Helper.SGROUP_LINE - Enum in ambit2.core.io

SGroupMDL2000Helper.SGROUP_POLYMER_TYPE - Enum in ambit2.core.io

SGroupMDL2000Helper.SGROUP_TYPE - Enum in ambit2.core.io

sheet - Variable in class ambit2.core.io.IteratingXLSReader

sheet - Variable in class ambit2.core.io.XLSFileWriter

ShellSDFoutput<INPUT> - Class in ambit2.core.external

ShellSDFoutput() - Constructor for class ambit2.core.external.ShellSDFoutput

SHOW_AROMATICITY - Static variable in class ambit2.core.config.Resources

show aromaticity

simple - Variable in class ambit2.core.data.experiment.AquireTemplate

SimpleIOListener - Class in ambit2.core.io

SimpleIOListener(int) - Constructor for class ambit2.core.io.SimpleIOListener

singleElectrons - Variable in class ambit2.core.groups.SuppleAtomContainer

Internal array of single electrons.

singleElectrons() - Method in class ambit2.core.groups.SuppleAtomContainer

size() - Method in class ambit2.core.data.ArrayResult

size - Variable in class ambit2.core.groups.FilteredList

size() - Method in class ambit2.core.groups.FilteredList

size() - Method in class ambit2.core.io.RandomAccessReader

SMARTS_UNDEFINED - Static variable in class ambit2.core.config.Resources

Undefined smarts

SMARTSQuery - Static variable in class ambit2.core.config.AmbitCONSTANTS

SMARTS Query

SMI_INDEX - Static variable in class ambit2.core.io.FileInputState

SMI_INDEX - Static variable in class ambit2.core.io.FileOutputState

SMILES - Static variable in class ambit2.core.config.AmbitCONSTANTS

SMILES

smilesIndex - Variable in class ambit2.core.io.FilesWithHeaderWriter

smilesIndex - Variable in class ambit2.core.io.FileWithHeaderWriter

smilesIndex - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader

SmilesKey - Class in ambit2.core.processors.structure.key

Returns smiles, given the structure

SmilesKey() - Constructor for class ambit2.core.processors.structure.key.SmilesKey

SMILESPARSER - Static variable in class ambit2.core.config.Resources

Openbabel or CDK smiles parser

SmilesParserWrapper - Class in ambit2.core.smiles

SmilesParserWrapper() - Constructor for class ambit2.core.smiles.SmilesParserWrapper

SmilesParserWrapper(SmilesParserWrapper.SMILES_PARSER) - Constructor for class ambit2.core.smiles.SmilesParserWrapper

SmilesParserWrapper.SMILES_PARSER - Enum in ambit2.core.smiles

source - Variable in class ambit2.core.data.experiment.StudyTemplate

sp - Static variable in class ambit2.core.data.MoleculeTools

sp - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader

species - Static variable in class ambit2.core.data.experiment.DefaultTemplate

species_sex - Static variable in class ambit2.core.data.experiment.DefaultTemplate

species_strain - Static variable in class ambit2.core.data.experiment.DefaultTemplate

stateChanged(IChemObjectChangeEvent) - Method in class ambit2.core.groups.SuppleAtomContainer

StringDescriptorResultType - Class in ambit2.core.data

StringDescriptorResultType(String) - Constructor for class ambit2.core.data.StringDescriptorResultType

StructuralKey - Static variable in class ambit2.core.config.AmbitCONSTANTS

StructuralKey_STATUS - Static variable in class ambit2.core.config.AmbitCONSTANTS

StructuralKey_TIME - Static variable in class ambit2.core.config.AmbitCONSTANTS

StructureRepeatingUnit - Class in ambit2.core.groups

StructureRepeatingUnit(String, int) - Constructor for class ambit2.core.groups.StructureRepeatingUnit

STRUCTURETYPE - Static variable in class ambit2.core.config.AmbitCONSTANTS

Structure tyoe

StructureTypeProcessor - Class in ambit2.core.processors.structure

StructureTypeProcessor() - Constructor for class ambit2.core.processors.structure.StructureTypeProcessor

Study - Class in ambit2.core.data.experiment

A single study, defined by its template Template and conditions.

Study() - Constructor for class ambit2.core.data.experiment.Study

Study(String, Template) - Constructor for class ambit2.core.data.experiment.Study

Study(String, int, Template) - Constructor for class ambit2.core.data.experiment.Study

StudyList - Class in ambit2.core.data.experiment

A list of Study

StudyList() - Constructor for class ambit2.core.data.experiment.StudyList

studyResults - Variable in class ambit2.core.data.experiment.Study

StudyTemplate - Class in ambit2.core.data.experiment

Study templates are introduced in order to provide generic framework for storing experimental data results, without predefined fieldnames, which may not be relevant to all endpoints (e.g.

StudyTemplate(String) - Constructor for class ambit2.core.data.experiment.StudyTemplate

style - Variable in class ambit2.core.io.XLSFileWriter

subList(int, int) - Method in class ambit2.core.groups.FilteredList

SUBSTANCETYPE - Static variable in class ambit2.core.config.AmbitCONSTANTS

Substance type

substanceType - Static variable in class ambit2.core.data.MoleculeTools

substTypeInorganic - Static variable in class ambit2.core.data.MoleculeTools

substTypeMetallic - Static variable in class ambit2.core.data.MoleculeTools

substTypeMixture - Static variable in class ambit2.core.data.MoleculeTools

substTypeOrganic - Static variable in class ambit2.core.data.MoleculeTools

SuperAtom - Class in ambit2.core.groups

SuperAtom(String, int) - Constructor for class ambit2.core.groups.SuperAtom

SuppleAtomContainer - Class in ambit2.core.groups

SuppleAtomContainer() - Constructor for class ambit2.core.groups.SuppleAtomContainer

supportedExtensions - Variable in class ambit2.core.io.FileState

SVG_INDEX - Static variable in class ambit2.core.io.FileOutputState

T

table - Variable in class ambit2.core.io.PDFWriter

Tanimoto - Static variable in class ambit2.core.config.AmbitCONSTANTS

Ttanimoto coefficient

template - Variable in class ambit2.core.data.experiment.Study

TemplateField - Class in ambit2.core.data.experiment

A StudyTemplate field.

TemplateField() - Constructor for class ambit2.core.data.experiment.TemplateField

TemplateField(String) - Constructor for class ambit2.core.data.experiment.TemplateField

TemplateField(String, String, boolean, boolean) - Constructor for class ambit2.core.data.experiment.TemplateField

Creates a templte field

TemplateField(String, int) - Constructor for class ambit2.core.data.experiment.TemplateField

testInstances - Variable in class ambit2.core.data.model.ModelWrapper

textDelimiter - Variable in class ambit2.core.io.DelimitedFileFormat

timeout - Variable in class ambit2.core.io.IteratingFilesWithHeaderReader

toArray() - Method in class ambit2.core.groups.FilteredList

toArray(T[]) - Method in class ambit2.core.groups.FilteredList

toString() - Method in class ambit2.core.data.ArrayResult

toString() - Method in class ambit2.core.data.experiment.Study

toString() - Method in class ambit2.core.data.experiment.StudyTemplate

toString() - Method in class ambit2.core.data.StringDescriptorResultType

toString() - Method in class ambit2.core.io.DelimitedFileReader

toString() - Method in class ambit2.core.io.DelimitedFileWriter

toString() - Method in class ambit2.core.io.FileState

toString() - Method in class ambit2.core.io.InteractiveIteratingMDLReader

toString() - Method in class ambit2.core.io.IteratingChemObjectReaderWrapper

toString() - Method in class ambit2.core.io.IteratingDelimitedFileReader

toString() - Method in class ambit2.core.io.IteratingFileReader

toString() - Method in class ambit2.core.io.IteratingFolderReader

toString() - Method in class ambit2.core.io.IteratingXLSReader

toString() - Method in class ambit2.core.io.MolPropertiesIOSetting

toString() - Method in class ambit2.core.io.RandomAccessReader

toString() - Method in class ambit2.core.io.XLSFileWriter

toString() - Method in class ambit2.core.processors.structure.FingerprintGenerator

toString() - Method in class ambit2.core.processors.structure.key.PropertyKey

toString() - Method in class ambit2.core.smiles.OpenBabelShell

transform(String) - Method in class ambit2.core.smiles.OpenBabelShell

TXT_INDEX - Static variable in class ambit2.core.io.FileInputState

TXT_INDEX - Static variable in class ambit2.core.io.FileOutputState

type - Variable in class ambit2.core.groups.ContainerGroup

U

UNIQUE_SMILES - Static variable in class ambit2.core.config.AmbitCONSTANTS

Unique SMILES

UNIQUE_SMILES_TIME - Static variable in class ambit2.core.config.AmbitCONSTANTS

Time to generate an unique smiles

units - Static variable in class ambit2.core.data.experiment.DefaultTemplate

units - Variable in class ambit2.core.data.experiment.TemplateField

UnsupportedGroupOperation - Exception in ambit2.core.groups

UnsupportedGroupOperation(String) - Constructor for exception ambit2.core.groups.UnsupportedGroupOperation

UnsupportedGroupOperation(String, Exception) - Constructor for exception ambit2.core.groups.UnsupportedGroupOperation

updateSGroups(String, SuppleAtomContainer, Hashtable<Integer, ISGroup>) - Method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

V

value - Variable in class ambit2.core.data.StringDescriptorResultType

valueOf(String) - Static method in enum ambit2.core.config.AmbitCONSTANTS.STRUC_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.groups.ContainerGroup.SGROUP_MIXTURE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.groups.DataGroup.DGROUP_DISPLAY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.groups.DataGroup.SGROUP_FIELD

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_CONNECTIVITY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_POLYMER_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER

Returns the enum constant of this type with the specified name.

values() - Static method in enum ambit2.core.config.AmbitCONSTANTS.STRUC_TYPE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.groups.ContainerGroup.SGROUP_MIXTURE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.groups.DataGroup.DGROUP_DISPLAY

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.groups.DataGroup.SGROUP_FIELD

Returns an array containing the constants of this enum type, in the order they're declared.

values - Variable in class ambit2.core.io.IteratingDelimitedFileReader

values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_CONNECTIVITY

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_POLYMER_TYPE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.io.SGroupMDL2000Helper.SGROUP_TYPE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER

Returns an array containing the constants of this enum type, in the order they're declared.

version - Static variable in class ambit2.core.config.AmbitCONSTANTS

Version

W

w - Static variable in class ambit2.core.data.EINECS

workbook - Variable in class ambit2.core.io.IteratingXLSReader

workbook - Variable in class ambit2.core.io.XLSFileWriter

wrapper - Static variable in class ambit2.core.smiles.SmilesParserWrapper

write(IChemObject) - Method in class ambit2.core.io.DelimitedFileWriter

write(IChemObject) - Method in class ambit2.core.io.FileWithHeaderWriter

write(IChemObject) - Method in class ambit2.core.io.MDLWriter

Writes a IChemObject to the MDL molfile formated output.

write(IChemObject) - Method in class ambit2.core.io.PDFWriter

write(Document, Content) - Method in class ambit2.core.processors.ProcessorFileExport

writeHeader() - Method in class ambit2.core.io.DelimitedFileWriter

writeHeader() - Method in class ambit2.core.io.FilesWithHeaderWriter

writeHeader() - Method in class ambit2.core.io.FileWithHeaderWriter

writeHeader() - Method in class ambit2.core.io.PDFWriter

writeHeader() - Method in class ambit2.core.io.XLSFileWriter

writeHTML(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport

writeMolecule(IMolecule) - Method in class ambit2.core.io.DelimitedFileWriter

writeMolecule(IMolecule) - Method in class ambit2.core.io.FileWithHeaderWriter

writeMolecule(IMolecule) - Method in class ambit2.core.io.MDLWriter

Writes a Molecule to an OutputStream in MDL sdf format.

writeMolecule(IMolecule) - Method in class ambit2.core.io.PDFWriter

writeMolecule(IMolecule) - Method in class ambit2.core.io.XLSFileWriter

writePDF(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport

writer - Variable in class ambit2.core.io.DelimitedFileWriter

writer - Variable in class ambit2.core.io.RawIteratingWrapper

writeRTF(Document, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport

writeSDF(Content, OutputStream) - Method in class ambit2.core.processors.ProcessorFileExport

writeSetOfMolecules(IMoleculeSet) - Method in class ambit2.core.io.DelimitedFileWriter

writeSetOfMolecules(IMoleculeSet) - Method in class ambit2.core.io.FileWithHeaderWriter

writeSetOfMolecules(IMoleculeSet) - Method in class ambit2.core.io.PDFWriter

writingStarted - Variable in class ambit2.core.io.FilesWithHeaderWriter

writingStarted - Variable in class ambit2.core.io.FileWithHeaderWriter

writingStarted - Variable in class ambit2.core.io.XLSFileWriter

X

XLS_INDEX - Static variable in class ambit2.core.io.FileInputState

XLS_INDEX - Static variable in class ambit2.core.io.FileOutputState

XLSFileFormat - Class in ambit2.core.io

Microsoft Excel XLS file format.

XLSFileFormat() - Constructor for class ambit2.core.io.XLSFileFormat

XLSFileWriter - Class in ambit2.core.io

XLSFileWriter(OutputStream) - Constructor for class ambit2.core.io.XLSFileWriter

XYZ_INDEX - Static variable in class ambit2.core.io.FileOutputState

_

_FPLength - Static variable in class ambit2.core.data.MoleculeTools

A B C D E F G H I J K L M N O P Q R S T U V W X _