- g -

GAParameters() : denoptim.programs.denovo.GAParameters
GAParametersForm() : denoptim.gui.GAParametersForm
GARunner() : denoptim.programs.denovo.GARunner
GeneOpsRunner() : denoptim.programs.genetweeker.GeneOpsRunner
GeneOpsRunnerParameters() : denoptim.programs.genetweeker.GeneOpsRunnerParameters
generate2DCoordinates() : denoptim.utils.MoleculeUtils
GenerationChoiceDialog() : denoptim.gui.GUIInspectGARun.GenerationChoiceDialog
get() : denoptim.ga.Population.XoverSitesAmongCandidates, denoptim.graph.APTreeMap
getA() : denoptim.ga.XoverSite
getAchronimFromClass() : denoptim.gui.GUIPrepare
getActiveMapAPs() : denoptim.gui.VertexViewPanel
getAllAlternativeChainIDs() : denoptim.graph.rings.PathSubGraph
getAllAlternativesFound() : denoptim.fragspace.GraphLinkFinder
getAllAPClasses() : denoptim.graph.EmptyVertex, denoptim.graph.Vertex
getAllAPClassesAsString() : denoptim.graph.APClass
getAllAPClassesFromCPMap() : denoptim.fragspace.FragmentSpace
getAllAPMappings() : denoptim.fragspace.APMapFinder
getAllAvailableAPClasses() : denoptim.graph.Vertex
getAllBChekBoxes() : denoptim.gui.ScrollableJPupupMenu
getAllClassNamesInPackage() : denoptim.fitness.DescriptorUtils
getAllMatches() : denoptim.utils.ManySMARTSQuery
getAllowedBridgeLength() : denoptim.fragmenter.BridgeHeadFindingRule
getAllSameAs() : denoptim.graph.SymmetricAPs
getAmideFragment() : denoptim.graph.TemplateTest
getAngle() : denoptim.utils.MathUtils
getAP() : denoptim.graph.Vertex
getAPClass() : denoptim.graph.AttachmentPoint
getApClass() : denoptim.graph.rings.RingClosingAttractor
getAPClass0() : denoptim.programs.fragmenter.CuttingRule
getAPClass1() : denoptim.programs.fragmenter.CuttingRule
getAPClassesPerFragment() : denoptim.fragspace.FragmentSpace
getAPClassForFragment() : denoptim.fragspace.FragmentSpace
getAPClassOfCappingVertex() : denoptim.fragspace.FragmentSpace
getAPCountOnAtom() : denoptim.graph.Fragment
getAPDefinitionsForSDF() : denoptim.graph.AttachmentPoint
getApId() : denoptim.fragspace.IdFragmentAndAP
getApIdToLeft() : denoptim.graph.rings.ChainLink
getApIdToRight() : denoptim.graph.rings.ChainLink
getAPMappig() : denoptim.utils.GraphEdit
getAPOnLeftVertexID() : denoptim.graph.DGraph
getAPsCompatibleWithClass() : denoptim.fragspace.FragmentSpace
getAPsCompatibleWithThese() : denoptim.fragspace.FragmentSpace
getAPsFromAtom() : denoptim.graph.Fragment
getAPsFromChildren() : denoptim.graph.Vertex
getAPsNeedingMappingA() : denoptim.ga.XoverSite
getAPsNeedingMappingB() : denoptim.ga.XoverSite
getAPsSelectedInViewer() : denoptim.gui.GraphVertexMolViewerPanel
getAPsWithAPClassStartingWith() : denoptim.graph.Vertex
getApSymSetId() : denoptim.fragspace.IdFragmentAndAP
getAPTableModel() : denoptim.gui.FragmentViewPanel, denoptim.gui.IVertexAPSelection, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel, denoptim.gui.VertexViewPanel
getAPWithId() : denoptim.graph.DGraph, denoptim.graph.Vertex
getAtmIdOfRCA() : denoptim.molecularmodeling.ChemicalObjectModel
getAtmSubClass0() : denoptim.programs.fragmenter.MatchedBond
getAtmSubClass1() : denoptim.programs.fragmenter.MatchedBond
getAtom() : denoptim.graph.Fragment, denoptim.integration.tinker.TinkerBond, denoptim.integration.tinker.TinkerMolecule, denoptim.utils.ConnectedLigand
getAtomColor() : denoptim.gui.VertexAsTwoDimStructureViewPanel.AtomOrAPGenerator
getAtomCount() : denoptim.graph.Fragment
getAtomHoldingAP() : denoptim.graph.Fragment
getAtomNeighbours() : denoptim.integration.tinker.TinkerAtom
getAtomOrderingScheme() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getAtomOverlapScore() : denoptim.molecularmodeling.ChemicalObjectModel
getAtomPath() : denoptim.graph.rings.PathSubGraph
getAtomPositionNumber() : denoptim.graph.AttachmentPoint
getAtomPositionNumberInMol() : denoptim.graph.AttachmentPoint
getAtomRef() : denoptim.utils.MoleculeUtils
getAtomRefStr() : denoptim.graph.rings.PathSubGraph
getAtoms() : denoptim.integration.tinker.TinkerMolecule
getAtomsSelectedFromJMol() : denoptim.gui.FragmentViewPanel, denoptim.gui.VertexViewPanel
getAtomString() : denoptim.integration.tinker.TinkerAtom
getAtomType() : denoptim.integration.tinker.TinkerAtom
getAttachmentPoints() : denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
getAttractor() : denoptim.molecularmodeling.ChemicalObjectModel
getAttractorsList() : denoptim.molecularmodeling.ChemicalObjectModel
getAvailableAPs() : denoptim.graph.DGraph
getAvailableAPsThroughout() : denoptim.graph.DGraph
getAvailableFileName() : denoptim.files.FileUtils
getB() : denoptim.ga.XoverSite
getBaseNameOfStorageFile() : denoptim.combinatorial.CEBLUtils
getBondAdd() : denoptim.integration.tinker.TinkerMolecule
getBondCount() : denoptim.graph.Fragment
getBondDel() : denoptim.integration.tinker.TinkerMolecule
getBondingAPIndex() : denoptim.graph.DGraph
getBondOrder() : denoptim.programs.fragmenter.CuttingRule
getBondPath() : denoptim.graph.rings.PathSubGraph
getBondType() : denoptim.graph.APClass, denoptim.graph.AttachmentPoint, denoptim.graph.Edge, denoptim.graph.EdgeQuery, denoptim.graph.Ring
getBranchIdOfVertex() : denoptim.graph.DGraph
getBranchIdOfVertexAsStr() : denoptim.graph.DGraph
getBranchIdOfVertexAtPosition() : denoptim.graph.DGraph
getBridgeHeadFindingRules() : denoptim.graph.rings.RingClosureParameters
getBridgeHeadPositions() : denoptim.fragmenter.BridgeHeadFindingRule
getBuildingBlockId() : denoptim.graph.Vertex
getBuildingBlockType() : denoptim.graph.Vertex
getCandidateBBs() : denoptim.fragspace.GraphLinkFinder
getCandidateNamed() : denoptim.ga.Population
getCandidateOwner() : denoptim.graph.DGraph
getCandidatesMap() : denoptim.fragspace.FragsCombinationIterator
getCappedAPCountThroughout() : denoptim.graph.Vertex
getCappedAPs() : denoptim.graph.Vertex
getCappedAPsThroughout() : denoptim.graph.Vertex
getCappingFragment() : denoptim.fragspace.FragmentSpace
getCappingGroupsWithAPClass() : denoptim.fragspace.FragmentSpace
getCappingLibrary() : denoptim.fragspace.FragmentSpace
getCappingMap() : denoptim.fragspace.FragmentSpace
getCappingVertexWithAPClass() : denoptim.fragspace.FragmentSpace
getCarbonVertex() : denoptim.fragspace.FragmentSpaceTest
getCCFromTurningPointId() : denoptim.graph.rings.RingClosuresArchive
getCDKDescriptorEngine() : denoptim.fitness.DescriptorUtils
getCDKOrder() : denoptim.graph.Edge.BondType
getCentroid() : denoptim.fragmenter.DynamicCentroidCluster
getCH2Fragment() : denoptim.graph.TemplateTest
getChainID() : denoptim.graph.rings.PathSubGraph, denoptim.graph.rings.RingClosingConformations
getCheckPoint() : denoptim.programs.combinatorial.CEBLParameters
getCheckPointName() : denoptim.programs.combinatorial.CEBLParameters
getCheckPointStep() : denoptim.programs.combinatorial.CEBLParameters
getChemDoodleString() : denoptim.io.DenoptimIO
getChemicalRepresentation() : denoptim.graph.Candidate
getChilddren() : denoptim.graph.Vertex
getChildrenThroughout() : denoptim.graph.Vertex
getChildrenTree() : denoptim.graph.DGraph
getChildTreeLimited() : denoptim.graph.DGraph
getChildVertices() : denoptim.graph.DGraph
getChosenAlternativeLink() : denoptim.fragspace.GraphLinkFinder
getChosenAPMapping() : denoptim.fragspace.APMapFinder, denoptim.fragspace.GraphLinkFinder
getChosenFragPathname() : denoptim.fragmenter.ConformerExtractorTask
getClassName() : denoptim.fitness.DescriptorForFitness
getClassNamesToCDKDescriptors() : denoptim.fitness.DescriptorUtils
getClassNamesToDenoptimDescriptors() : denoptim.fitness.DescriptorUtils
getClosabilityConditions() : denoptim.graph.rings.RingClosure
getClosabilityEvalMode() : denoptim.graph.rings.RingClosureParameters
getClosabilityOfChain() : denoptim.graph.rings.RingClosuresArchive
getClosableChains() : denoptim.graph.DGraph
getCloserTo() : denoptim.graph.Ring
getCloserToHead() : denoptim.graph.Ring
getCloserToTail() : denoptim.graph.Ring
getClusterCentroids() : denoptim.fragmenter.FragmentClusterer
getClusterCentroidsPathname() : denoptim.fragmenter.ConformerExtractorTask
getClusterPathname() : denoptim.fragmenter.ConformerExtractorTask
getClusters() : denoptim.fragmenter.FragmentClusterer
getComments() : denoptim.graph.Candidate
getCompatibilityMatrix() : denoptim.fragspace.FragmentSpace
getCompatibilityOfPair() : denoptim.graph.rings.RingSizeManager
getCompatibleAPClasses() : denoptim.fragspace.FragmentSpace
getCompatibleCappingFragments() : denoptim.fragspace.FragmentSpace
getCompatibleCC() : denoptim.ga.GraphOperations.FragForClosabChains
getComplementaryAPClass() : denoptim.programs.fragmenter.CuttingRule
getConfirmedFormulaFileName() : denoptim.fragmenter.FragmenterTask
getConfPathExtraTolerance() : denoptim.graph.rings.RingClosureParameters
getConnectedAtoms() : denoptim.integration.tinker.TinkerMolecule
getConnectedAtomsCount() : denoptim.graph.Fragment
getConnectedAtomsList() : denoptim.graph.Fragment
getConnections() : denoptim.utils.ConnectedLigand
getConstitutionalClosabilityConds() : denoptim.graph.rings.RingClosureParameters
getConstructionWeight() : denoptim.programs.denovo.GAParameters
getContractLevel() : denoptim.graph.Template
getCrossoverWeight() : denoptim.programs.denovo.GAParameters
getCrowdedness() : denoptim.ga.EAUtils
getCrowdingFactorMiddleSigma() : denoptim.programs.denovo.GAParameters
getCrowdingFactorSteepSigma() : denoptim.programs.denovo.GAParameters
getCrowdingMultiplier() : denoptim.programs.denovo.GAParameters
getCrowdingProbability() : denoptim.ga.EAUtils
getCrowdingProbabilityForCrowdedness() : denoptim.ga.EAUtils
getCrowdingProbabilityScheme() : denoptim.programs.denovo.GAParameters
getCurrentAPs() : denoptim.graph.Fragment
getCutId() : denoptim.graph.AttachmentPoint
getCuttingRules() : denoptim.programs.fragmenter.FragmenterParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getCuttingRulesFilePathname() : denoptim.programs.fragmenter.FragmenterParameters
getData() : denoptim.integration.python.Py4JGetawayServer
getDataDirectory() : denoptim.programs.denovo.GAParameters
getDataFromJmol() : denoptim.gui.FragmentViewPanel
getDBRoot() : denoptim.programs.combinatorial.CEBLParameters
getDeepestAmongThese() : denoptim.graph.DGraph
getDefiningRegex() : denoptim.files.FileFormat
getDescription() : denoptim.logging.CounterID
getDescriptorName() : denoptim.fitness.Variable
getDescriptorNames() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
getDescriptorResultType() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
getDescriptors() : denoptim.fitness.FitnessExpressionParser, denoptim.fitness.FitnessParameters
getDictClasses() : denoptim.fitness.DescriptorForFitness
getDictDefinition() : denoptim.fitness.DescriptorForFitness
getDictionaryClass() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure, denoptim.fitness.IDenoptimDescriptor
getDictionaryDefinition() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure, denoptim.fitness.IDenoptimDescriptor
getDictionaryTitle() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure, denoptim.fitness.IDenoptimDescriptor
getDictString() : denoptim.fitness.DescriptorForFitness
getDictTitle() : denoptim.fitness.DescriptorForFitness
getDiffOfVector() : denoptim.utils.CartesianSpaceUtils
getDihedralRefPoints() : denoptim.graph.rings.PathSubGraph
getDimensions() : denoptim.utils.MoleculeUtils
getDirectionVector() : denoptim.graph.AttachmentPoint
getDistance() : denoptim.graph.Ring
getDistAngle() : denoptim.integration.tinker.TinkerAtom
getDNPVertex() : denoptim.graph.simplified.Node
getDummyInSafeDirection() : denoptim.utils.DummyAtomHandler
getEdgeAtPosition() : denoptim.graph.DGraph
getEdgeCount() : denoptim.graph.DGraph
getEdgeIDsWithLabel() : denoptim.gui.JUNGGraphSnapshot
getEdgeList() : denoptim.graph.DGraph
getEdgeQuery() : denoptim.utils.GraphEdit
getEdgesPath() : denoptim.graph.rings.PathSubGraph
getEdgesWithChild() : denoptim.graph.DGraph
getEdgesWithSrc() : denoptim.graph.DGraph
getEdgesWithTrg() : denoptim.graph.DGraph
getEdgeToParent() : denoptim.graph.Vertex
getEdgeUser() : denoptim.graph.AttachmentPoint
getEdgeUserThroughout() : denoptim.graph.AttachmentPoint
getEdgeWith() : denoptim.graph.Vertex
getEdgeWithParent() : denoptim.graph.DGraph
getElementalanalysis() : denoptim.utils.FormulaUtils
getELResolver() : denoptim.fitness.FitnessExpressionParser.CustomVariableDefiningContext, denoptim.fitness.FitnessExpressionParser.VariableDefiningContext
getEmbeddedAP() : denoptim.graph.AttachmentPoint
getEmbeddedGraphInClone() : denoptim.graph.DGraph
getEmbeddedRingsContract() : denoptim.gui.MolToGraphParametersDialog, denoptim.programs.fragmenter.FragmenterParameters
getEmbeddedVertex() : denoptim.programs.genetweeker.GeneOpsRunner
getEmbeddingPath() : denoptim.graph.DGraph
getEmbedRingsInTemplate() : denoptim.gui.MolToGraphParametersDialog
getEnglishFormattedDecimal() : denoptim.utils.GeneralUtils
getError() : denoptim.graph.Candidate, denoptim.graph.CandidateLW
getErrorMessage() : denoptim.task.Task
getErrorOutput() : denoptim.task.ProcessHandler
getException() : denoptim.task.Task
getExceptionFromSubTask() : denoptim.task.ParallelAsynchronousTaskExecutor
getExcludedMutationTypes() : denoptim.programs.denovo.GAParameters
getExistingBridgeLength() : denoptim.fragmenter.BridgeHeadFindingRule
getExitCode() : denoptim.task.ProcessHandler
getExpectedSubgraphs() : denoptim.ga.GraphOperationsTest
getExpectedTemplate() : denoptim.fragspace.FragmentSpaceTest
getExtension() : denoptim.files.FileFormat
getExternalFitnessProvider() : denoptim.fitness.FitnessParameters
getExternalFitnessProviderInterpreter() : denoptim.fitness.FitnessParameters
getFactorForSDOnStatsOfUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
getFileFormat() : denoptim.gui.GUIPrepare
getFilesCollectingIsomorphicFamilyChampions() : denoptim.fragmenter.ParallelFragmentationAlgorithm
getFirst() : denoptim.utils.ObjectPair
getFirstRefAtomId() : denoptim.integration.tinker.TinkerUtils
getFitness() : denoptim.fitness.FitnessProvider, denoptim.graph.Candidate, denoptim.graph.CandidateLW
getFitnesses() : denoptim.ga.EAUtils
getFitnessExpression() : denoptim.fitness.FitnessParameters
getFitnessProviderOutputRepresentation() : denoptim.graph.Candidate
getFlagsVector() : denoptim.utils.DummyAtomHandler
getForbiddenEndList() : denoptim.fragspace.FragmentSpace
getFormatName() : denoptim.io.SMILESListFormat
getFormulae() : denoptim.programs.fragmenter.FragmenterParameters
getFormulaeFile() : denoptim.programs.fragmenter.FragmenterParameters
getFormulaForMol() : denoptim.fragmenter.ParallelFragmentationAlgorithm
getFragAPsCompatibleWithClass() : denoptim.fragspace.FragmentSpace
getFragAPsCompatibleWithTheseAPs() : denoptim.fragspace.FragmentSpace
getFragIDs() : denoptim.ga.GraphOperations.FragForClosabChains
getFragmentForClosableChain() : denoptim.ga.GraphOperations
getFragmentLibrary() : denoptim.fragspace.FragmentSpace
getFragmentsCompatibleWithTheseAPs() : denoptim.fragspace.FragmentSpace
getFragmentsFileName() : denoptim.fragmenter.FragmenterTask
getFragmentSpace() : denoptim.fragspace.FragmentSpaceParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getFragRejectionSMARTS() : denoptim.programs.fragmenter.FragmenterParameters
getFragRetentionSMARTS() : denoptim.programs.fragmenter.FragmenterParameters
getFragsWithAPClass() : denoptim.fragspace.FragmentSpace
getFragsWithNumAps() : denoptim.fragspace.FragmentSpace
getFragType() : denoptim.graph.rings.ChainLink
getFreeAPCount() : denoptim.graph.EmptyVertex, denoptim.graph.Vertex
getFreeAPCountThroughout() : denoptim.graph.Vertex
getFreeAPList() : denoptim.graph.EmptyVertex
getFreeAPThroughout() : denoptim.graph.Vertex
getFreeAtomsFlag() : denoptim.utils.AtomOrganizer
getFreeRCVertices() : denoptim.graph.DGraph
getFrgApForSrcAp() : denoptim.ga.GraphOperations
getFunctionMapper() : denoptim.fitness.FitnessExpressionParser.CustomVariableDefiningContext, denoptim.fitness.FitnessExpressionParser.VariableDefiningContext
getFusedRings() : denoptim.ga.GraphOperationsTest
getGeneratingSource() : denoptim.graph.CandidateLW
getGeneration() : denoptim.graph.Candidate, denoptim.graph.CandidateLW
getGraph() : denoptim.graph.Candidate, denoptim.graph.rings.PathSubGraph, denoptim.molecularmodeling.ChemicalObjectModel
getGraphEditTasks() : denoptim.programs.grapheditor.GraphEdParameters
getGraphFromString() : denoptim.utils.GraphConversionTool
getGraphId() : denoptim.combinatorial.GraphBuildingTask, denoptim.graph.DGraph
getGraphIdFromStorageFile() : denoptim.combinatorial.CEBLUtils
getGraphOwner() : denoptim.graph.Vertex
getGraphStatusSnapshot() : denoptim.gui.GraphViewerPanel
getGrowthByLevelProbability() : denoptim.ga.EAUtils
getGrowthFactorMiddleSigma() : denoptim.programs.denovo.GAParameters
getGrowthFactorSteepSigma() : denoptim.programs.denovo.GAParameters
getGrowthMultiplier() : denoptim.programs.denovo.GAParameters
getGrowthProbabilityAtLevel() : denoptim.ga.EAUtils
getGrowthProbabilityScheme() : denoptim.programs.denovo.GAParameters
getHead() : denoptim.logging.HTMLLogFormatter
getHeadVertex() : denoptim.graph.Ring, denoptim.graph.rings.PathSubGraph
getHeavyAtomCount() : denoptim.utils.MoleculeUtils
getHeavyAtomsCount() : denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
getHelpString() : denoptim.main.Main
getIAtom() : denoptim.graph.rings.RingClosingAttractor
getIAtomContainer() : denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex, denoptim.molecularmodeling.ChemicalObjectModel
getICFromIAC() : denoptim.integration.tinker.TinkerUtils
getID() : denoptim.graph.AttachmentPoint
getId() : denoptim.task.Task
getIdx() : denoptim.graph.rings.ChainLink
getIdxOfClosing() : denoptim.utils.GeneralUtils
getIgnorableFragments() : denoptim.programs.fragmenter.FragmenterParameters
getImageFile() : denoptim.graph.Candidate
getImplementation() : denoptim.fitness.DescriptorForFitness, denoptim.programs.RunTimeParameters.ParametersType
getInChIKeyForMolecule() : denoptim.utils.MoleculeUtils
getIncomingAPId() : denoptim.utils.GraphEdit
getIncomingBBId() : denoptim.utils.GraphEdit
getIncomingBBType() : denoptim.utils.GraphEdit
getIncomingGraph() : denoptim.utils.GraphEdit
getIncompatibleCC() : denoptim.ga.GraphOperations.FragForClosabChains
getIndexInOwner() : denoptim.graph.AttachmentPoint
getIndexOfAP() : denoptim.graph.Vertex
getIndexOfEdgesWithChild() : denoptim.graph.DGraph
getInEdgeQuery() : denoptim.graph.VertexQuery
getInitialPopulationFile() : denoptim.programs.denovo.GAParameters
getInitMolsToFragmentFile() : denoptim.programs.denovo.GAParameters
getInitPSSROTParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getInnerAPFromOuterAP() : denoptim.graph.Template
getInnerGraph() : denoptim.graph.Template
getInpMol() : denoptim.programs.grapheditor.GraphEdParameters
getInputFile() : denoptim.programs.fitnessevaluator.FRParameters
getInputFileName() : denoptim.fragmenter.FragmenterTask
getInputGraphs() : denoptim.programs.grapheditor.GraphEdParameters
getInputMol() : denoptim.programs.mol2graph.Mol2GraphParameters
getInputMolsCount() : denoptim.programs.mol2graph.Mol2GraphParameters
getInputSDFFile() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getInstance() : denoptim.files.SingletonFileAccess, denoptim.json.DENOPTIMgson, denoptim.logging.StaticLogger, denoptim.main.CLIOptions, denoptim.task.StaticTaskManager
getInstanceFor() : denoptim.programs.RunTimeParameters
getInterfaceAPs() : denoptim.graph.DGraph
getInterfaceDir() : denoptim.programs.denovo.GAParameters
getInterVertexBonds() : denoptim.utils.RotationalSpaceUtils
getINTXYZTool() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getIsomorphicSampleSize() : denoptim.programs.fragmenter.FragmenterParameters
getIsomorphsCount() : denoptim.programs.fragmenter.FragmenterParameters
getItems() : denoptim.graph.SymmetricSetWithMode
getIteratorType() : denoptim.io.IteratingAtomContainerReader
getJGraphFragIsomorphism() : denoptim.fragmenter.ClusterableFragment, denoptim.graph.Fragment
getJGraphFromGraph() : denoptim.utils.GraphConversionTool
getJGraphKernelFromGraph() : denoptim.utils.GraphConversionTool
getJmolPositionStr() : denoptim.gui.FragmentViewPanel
getKeepDummyFlag() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getKeyFileParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getKeywordRoot() : denoptim.programs.RunTimeParameters.ParametersType
getLabel() : denoptim.graph.FragIsomorphNode, denoptim.utils.GraphUtils
getLastAtomNumber() : denoptim.integration.tinker.TinkerMolecule
getLatestSafelyCompletedGraphId() : denoptim.combinatorial.CheckPoint
getLayoutCenter() : denoptim.gui.GraphViewerPanel
getLevel() : denoptim.combinatorial.CheckPoint, denoptim.combinatorial.GraphBuildingTask, denoptim.graph.Candidate, denoptim.graph.CandidateLW, denoptim.graph.DGraph
getLinearAngleLimit() : denoptim.programs.fragmenter.FragmenterParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getLinearityLimit() : denoptim.graph.rings.RingClosureParameters
getLink() : denoptim.graph.rings.ClosableChain
getLinkedAP() : denoptim.graph.AttachmentPoint
getLinkedAPThroughout() : denoptim.graph.AttachmentPoint
getLinks() : denoptim.graph.rings.ClosableChain
getListOfConformations() : denoptim.graph.rings.RingClosingConformations
getLoadedStructure() : denoptim.gui.FragmentViewPanel, denoptim.gui.VertexViewPanel
getLocalMsg() : denoptim.graph.DGraph
getLogFileName() : denoptim.fragmenter.FragmenterTask
getLogFilePathname() : denoptim.fragmenter.ConformerExtractorTask, denoptim.fragmenter.FragmenterTask, denoptim.programs.RunTimeParameters
getLogger() : denoptim.programs.RunTimeParameters
getLowestRMSDMapping() : denoptim.fragmenter.FragmentAlignement
getMainMenu() : denoptim.gui.MainToolBar
getMapOfAPsInTable() : denoptim.gui.FragmentViewPanel, denoptim.gui.IVertexAPSelection, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
getMapOfFragsPerNumAps() : denoptim.fragspace.FragmentSpace
getMappings() : denoptim.graph.FragmentIsomorphismInspector
getMatchesOfSMARTS() : denoptim.utils.ManySMARTSQuery
getMatchingBondsAllInOne() : denoptim.fragmenter.FragmenterTools
getMaxFitness() : denoptim.ga.Population
getMaxFragHeavyAtomCount() : denoptim.programs.fragmenter.FragmenterParameters
getMaxGeneticOpAttempts() : denoptim.programs.denovo.GAParameters
getMaxHeavyAtom() : denoptim.fragspace.FragmentSpaceParameters
getMaxLevel() : denoptim.programs.combinatorial.CEBLParameters
getMaxMW() : denoptim.fragspace.FragmentSpaceParameters
getMaxNoiseUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
getMaxNumberRotatableBonds() : denoptim.graph.rings.RingClosureParameters
getMaxRcaPerType() : denoptim.graph.rings.RingClosureParameters
getMaxRingClosures() : denoptim.graph.rings.RingClosureParameters
getMaxRingsAddedByMutation() : denoptim.programs.denovo.GAParameters
getMaxRingSize() : denoptim.graph.rings.RingClosureParameters
getMaxRotatableBond() : denoptim.fragspace.FragmentSpaceParameters
getMaxTriesFactor() : denoptim.programs.denovo.GAParameters
getMaxVertexId() : denoptim.graph.DGraph
getMaxWait() : denoptim.programs.combinatorial.CEBLParameters
getMembersCompatibleWith() : denoptim.ga.Population.XoverSitesAmongCandidates
getMessage() : denoptim.utils.ManySMARTSQuery
getMessages() : denoptim.task.StreamGobbler
getMIMEType() : denoptim.io.SMILESListFormat
getMinFitness() : denoptim.ga.Population
getMinFitnessMember() : denoptim.ga.Population
getMinFitnessSD() : denoptim.programs.denovo.GAParameters
getMinFragHeavyAtomCount() : denoptim.programs.fragmenter.FragmenterParameters
getMinimumRMSD() : denoptim.fragmenter.FragmentAlignement
getMinRcaPerType() : denoptim.graph.rings.RingClosureParameters
getMinRingClosures() : denoptim.graph.rings.RingClosureParameters
getMol() : denoptim.fragmenter.FragmentClustererTest
getMolecularRepresentation() : denoptim.graph.rings.PathSubGraph
getMolecularWeight() : denoptim.utils.MoleculeUtils
getMolGrowthFactorMiddleSigma() : denoptim.programs.denovo.GAParameters
getMolGrowthFactorSteepSigma() : denoptim.programs.denovo.GAParameters
getMolGrowthMultiplier() : denoptim.programs.denovo.GAParameters
getMolGrowthProbabilityScheme() : denoptim.programs.denovo.GAParameters
getMolSizeProbability() : denoptim.ga.EAUtils
getMonitorDataHeader() : denoptim.logging.Monitor
getMonitorDataLine() : denoptim.logging.Monitor
getMonitorDumpStep() : denoptim.programs.denovo.GAParameters
getMonitorFile() : denoptim.programs.denovo.GAParameters
getMultiSiteMutationWeights() : denoptim.programs.denovo.GAParameters
getMutableSites() : denoptim.graph.DGraph
getMutationSites() : denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
getMutationTypes() : denoptim.graph.Template, denoptim.graph.Vertex
getMutationWeight() : denoptim.programs.denovo.GAParameters
getMWSlotFileNameAllFrags() : denoptim.programs.fragmenter.FragmenterParameters
getMWSlotFileNameUnqFrags() : denoptim.programs.fragmenter.FragmenterParameters
getMWSlotIdentifier() : denoptim.fragmenter.FragmenterTools
getMWSlotSize() : denoptim.programs.fragmenter.FragmenterParameters
getMWSlotToAllFragsFile() : denoptim.programs.fragmenter.FragmenterParameters
getMWSlotToUnqFragsFile() : denoptim.programs.fragmenter.FragmenterParameters
getName() : denoptim.fitness.Variable, denoptim.fragmenter.BridgeHeadFindingRule, denoptim.graph.Candidate, denoptim.graph.CandidateLW, denoptim.integration.tinker.TinkerMolecule, denoptim.molecularmodeling.ChemicalObjectModel, denoptim.programs.fragmenter.CuttingRule
getNameExtensions() : denoptim.io.SMILESListFormat
getNameLastCycleFile() : denoptim.integration.tinker.TinkerUtils
getNameOfStorageDir() : denoptim.combinatorial.CEBLUtils
getNameOfStorageFile() : denoptim.combinatorial.CEBLUtils
getNameOfStorageIndexFile() : denoptim.combinatorial.CEBLUtils
getNearestToCentroid() : denoptim.fragmenter.DynamicCentroidCluster
getNearestToClusterCentroids() : denoptim.fragmenter.FragmentClusterer
getNegatingRegex() : denoptim.files.FileFormat
getNestedTemplate() : denoptim.graph.TemplateTest
getNewRingClosures() : denoptim.molecularmodeling.ChemicalObjectModel
getNewRingClosuresQuality() : denoptim.molecularmodeling.ChemicalObjectModel
getNewToOldOrder() : denoptim.molecularmodeling.ChemicalObjectModel, denoptim.utils.AtomOrganizer
getNextIds() : denoptim.combinatorial.CheckPoint, denoptim.combinatorial.GraphBuildingTask, denoptim.fragspace.FragsCombinationIterator
getNoisyPoint() : denoptim.fragmenter.FragmentClustererTest, denoptim.utils.Randomizer
getNormalDirection() : denoptim.utils.CartesianSpaceUtils, denoptim.utils.MathUtils
getNormallyNoisyPoint() : denoptim.utils.Randomizer
getNumberOfAPs() : denoptim.graph.EmptyVertex, denoptim.graph.Vertex
getNumberOfChildren() : denoptim.programs.denovo.GAParameters
getNumberOfConformations() : denoptim.graph.rings.RingClosingConformations
getNumberOfConvergenceGenerations() : denoptim.programs.denovo.GAParameters
getNumberOfCPU() : denoptim.programs.combinatorial.CEBLParameters, denoptim.programs.denovo.GAParameters
getNumberOfGenerations() : denoptim.programs.denovo.GAParameters
getNumberOfRotatableBonds() : denoptim.utils.MoleculeUtils
getNumberOfSubTasks() : denoptim.combinatorial.GraphBuildingTask
getNumberRotatableBonds() : denoptim.molecularmodeling.ChemicalObjectModel
getNumGeneratedCombs() : denoptim.fragspace.FragsCombinationIterator
getNumMatchesOfQuery() : denoptim.utils.ManySMARTSQuery
getNumRootAPs() : denoptim.fragspace.FragsCombinationIterator
getNumTasks() : denoptim.programs.fragmenter.FragmenterParameters
getOHFragment() : denoptim.graph.TemplateTest
getOldToNewOrder() : denoptim.molecularmodeling.ChemicalObjectModel, denoptim.utils.AtomOrganizer
getOptions() : denoptim.programs.fragmenter.CuttingRule
getOrderedNodes() : denoptim.fragmenter.ClusterableFragment
getOriginal() : denoptim.graph.FragIsomorphNode
getOriginalFragment() : denoptim.fragmenter.ClusterableFragment
getOutEdgeQuery() : denoptim.graph.VertexQuery
getOuterAPFromInnerAP() : denoptim.graph.Template
getOutermostGraphOwner() : denoptim.graph.DGraph
getOutFile() : denoptim.programs.grapheditor.GraphEdParameters, denoptim.programs.graphlisthandler.GraphListsHandlerParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getOutFormat() : denoptim.programs.grapheditor.GraphEdParameters, denoptim.programs.graphlisthandler.GraphListsHandlerParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getOutputFile() : denoptim.programs.fitnessevaluator.FRParameters
getOutputSDFFile() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getOverlappingItems() : denoptim.gui.GUIInspectGARun
getOwner() : denoptim.graph.AttachmentPoint
getPaddedString() : denoptim.utils.GeneralUtils
getPairOfTestGraphs() : denoptim.ga.GraphOperationsTest
getPairOfTestGraphsB() : denoptim.ga.PopulationTest
getPairOfTestGraphsBxo() : denoptim.ga.PopulationTest
getPairOfTestGraphsBxoxo() : denoptim.ga.PopulationTest
getPanelForUnformattedInput() : denoptim.gui.ParametersForm
getParallelizationScheme() : denoptim.programs.denovo.GAParameters
getParamA11() : denoptim.graph.rings.RingClosingAttractor
getParamA12() : denoptim.graph.rings.RingClosingAttractor
getParamB11() : denoptim.graph.rings.RingClosingAttractor
getParamB12() : denoptim.graph.rings.RingClosingAttractor
getParameterFormats() : denoptim.files.FileFormat
getParameterNames() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
getParameters() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure, denoptim.programs.RunTimeParameters
getParameterType() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
getParamFile() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getParent() : denoptim.graph.DGraph, denoptim.graph.Vertex
getParentTree() : denoptim.graph.DGraph
getPathConfSearchStep() : denoptim.graph.rings.RingClosureParameters
getPathIDs() : denoptim.graph.Template, denoptim.graph.Vertex
getPathLength() : denoptim.graph.rings.PathSubGraph
getPathnameToAppendedFragments() : denoptim.fragspace.FragmentSpaceParameters
getPathnameToAppendedScaffolds() : denoptim.fragspace.FragmentSpaceParameters
getPathNameToFinalPopulationDetailsFile() : denoptim.ga.EAUtils
getPathNameToFinalPopulationFolder() : denoptim.ga.EAUtils
getPathNameToGenerationDetailsFile() : denoptim.ga.EAUtils
getPathNameToGenerationFolder() : denoptim.ga.EAUtils
getPathToFile() : denoptim.graph.CandidateLW
getPoint() : denoptim.fragmenter.ClusterableFragment, denoptim.graph.rings.RingClosure
getPoint3d() : denoptim.graph.FragIsomorphNode, denoptim.utils.MoleculeUtils
getPoints() : denoptim.fragmenter.DynamicCentroidCluster
getPolarizedRCV() : denoptim.fragspace.FragmentSpace
getPopulationFromFile() : denoptim.ga.EAUtils
getPopulationSD() : denoptim.ga.EAUtils
getPopulationSize() : denoptim.programs.denovo.GAParameters
getPort() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer
getPositionOf() : denoptim.graph.Ring
getPossibleCombinationOfRings() : denoptim.graph.rings.CyclicGraphHandler
getPrecisionLevel() : denoptim.programs.denovo.GAParameters
getPreferredNameExtension() : denoptim.io.SMILESListFormat
getPreFilteredFileName() : denoptim.fragmenter.FragmenterTask
getPreFiltrationSMARTS() : denoptim.programs.fragmenter.FragmenterParameters
getPrettyName() : denoptim.logging.CounterID
getPrintedList() : denoptim.fitness.FitnessParameters, denoptim.fragspace.FragmentSpaceParameters, denoptim.graph.rings.RingClosureParameters, denoptim.programs.combinatorial.CEBLParameters, denoptim.programs.denovo.GAParameters, denoptim.programs.fitnessevaluator.FRParameters, denoptim.programs.fragmenter.FragmenterParameters, denoptim.programs.genetweeker.GeneOpsRunnerParameters, denoptim.programs.grapheditor.GraphEdParameters, denoptim.programs.graphlisthandler.GraphListsHandlerParameters, denoptim.programs.isomorphism.IsomorphismParameters, denoptim.programs.mol2graph.Mol2GraphParameters, denoptim.programs.moldecularmodelbuilder.MMBuilderParameters, denoptim.programs.RunTimeParameters
getPriority() : denoptim.programs.fragmenter.CuttingRule
getProbability() : denoptim.ga.EAUtils
getProblem() : denoptim.utils.ManySMARTSQuery
getProgramTaskImpl() : denoptim.main.Main.RunType
getProperties() : denoptim.graph.AttachmentPoint, denoptim.graph.Vertex
getProperty() : denoptim.graph.AttachmentPoint, denoptim.graph.Vertex
getPSSROTTool() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getQueueSnapshot() : denoptim.task.StaticTaskManager
getRandomCombinationOfRings() : denoptim.graph.rings.CyclicGraphHandler
getRandomizer() : denoptim.fragspace.FragmentSpace, denoptim.programs.RunTimeParameters
getRandomPoint() : denoptim.molecularmodeling.ThreeDimTreeBuilder
getRandomSeed() : denoptim.programs.RunTimeParameters
getRandomVector() : denoptim.fragspace.FragmentSpaceTest, denoptim.ga.GraphOperationsTest
getRCACombinations() : denoptim.molecularmodeling.ChemicalObjectModel
getRCBondType() : denoptim.graph.rings.RingClosingAttractor
getRCC() : denoptim.graph.rings.PathSubGraph
getRCCLibraryFolder() : denoptim.graph.rings.RingClosureParameters
getRCCLibraryIndexFile() : denoptim.graph.rings.RingClosureParameters
getRCCompatibilityMatrix() : denoptim.fragspace.FragmentSpace
getRCCsFromArchive() : denoptim.graph.rings.RingClosuresArchive
getRCCsOfChain() : denoptim.graph.rings.RingClosuresArchive
getRCDistTolerance() : denoptim.graph.rings.RingClosureParameters
getRCDotPrTolerance() : denoptim.graph.rings.RingClosureParameters
getRCPForAP() : denoptim.fragmenter.FragmenterTools
getRCV() : denoptim.fragspace.FragmentSpaceTest
getRCVertices() : denoptim.graph.DGraph
getRCVForSrcAp() : denoptim.ga.GraphOperations
getRCVs() : denoptim.fragspace.FragmentSpace
getRCVsForAPClass() : denoptim.fragspace.FragmentSpace
getRCVsWithAPClass() : denoptim.fragspace.FragmentSpace
getReader() : denoptim.json.DENOPTIMgson
getReaderClassName() : denoptim.io.SMILESListFormat
getRejectedAPClassCombinations() : denoptim.programs.fragmenter.FragmenterParameters
getRejectedAPClasses() : denoptim.programs.fragmenter.FragmenterParameters
getRejectedElements() : denoptim.programs.fragmenter.FragmenterParameters
getRejectedFormulaLessThan() : denoptim.programs.fragmenter.FragmenterParameters
getRejectedFormulaMoreThan() : denoptim.programs.fragmenter.FragmenterParameters
getReplacementStrategy() : denoptim.programs.denovo.GAParameters
getRequiredAPs() : denoptim.graph.Template
getRequiredDataFeatures() : denoptim.io.SMILESListFormat
getRequiredRingElements() : denoptim.graph.rings.RingClosureParameters
getRestPSSROTParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getResultFile() : denoptim.fragmenter.ConformerExtractorTask, denoptim.fragmenter.FragmenterTask
getResults() : denoptim.fragmenter.ParallelConformerExtractionAlgorithm
getResultsFileName() : denoptim.fragmenter.FragmenterTask
getRingClosureQuality() : denoptim.graph.rings.RingClosure
getRingClosuresArchive() : denoptim.graph.rings.RingClosureParameters
getRingCount() : denoptim.graph.DGraph
getRings() : denoptim.graph.DGraph
getRingsInvolvingVertex() : denoptim.graph.DGraph
getRingsInvolvingVertexID() : denoptim.graph.DGraph
getRingSizeBias() : denoptim.graph.rings.RingClosureParameters
getRingUser() : denoptim.graph.rings.RingClosingAttractor
getRMSDStatsOfNoisyDistorsions() : denoptim.fragmenter.FragmentClusterer
getRNG() : denoptim.utils.Randomizer
getRootGraphs() : denoptim.programs.combinatorial.CEBLParameters
getRootId() : denoptim.combinatorial.CheckPoint, denoptim.combinatorial.GraphBuildingTask
getRotatableBonds() : denoptim.molecularmodeling.ChemicalObjectModel
getRotationalSpaceDefinition() : denoptim.utils.RotationalSpaceUtils
getRotSpaceDefFile() : denoptim.fragspace.FragmentSpaceParameters
getRSBiasedListOfCandidates() : denoptim.graph.rings.RingSizeManager
getRSInitPSSROTParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRSKeyFileParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRSRestPSSROTParams() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRule() : denoptim.graph.APClass, denoptim.programs.fragmenter.MatchedBond
getRunTypesForUser() : denoptim.main.Main.RunType
getSameAs() : denoptim.graph.SymmetricAPs
getSampleEndRegex() : denoptim.files.FileFormat
getSaveRingSystemsAsTemplatesNonScaff() : denoptim.programs.denovo.GAParameters
getSaveRingSystemsAsTemplatesScaff() : denoptim.programs.denovo.GAParameters
getSaveRingSystemsFitnessThreshold() : denoptim.programs.denovo.GAParameters
getScaffoldingPolicy() : denoptim.gui.MolToGraphParametersDialog, denoptim.programs.fragmenter.FragmenterParameters, denoptim.programs.mol2graph.Mol2GraphParameters
getScaffoldLibrary() : denoptim.fragspace.FragmentSpace
getSDFAtomNumber() : denoptim.utils.DummyAtomHandler
getSDFFile() : denoptim.graph.Candidate
getSDFFormats() : denoptim.files.FileFormat
getSecond() : denoptim.utils.ObjectPair
getSecondRefAtomId() : denoptim.integration.tinker.TinkerUtils
getSeed() : denoptim.utils.Randomizer
getSelectedAPIDs() : denoptim.gui.FragmentViewPanel, denoptim.gui.IVertexAPSelection, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel, denoptim.gui.VertexViewPanel
getSelectedAPs() : denoptim.gui.FragmentViewPanel, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
getSelectedEdges() : denoptim.gui.GraphViewerPanel
getSelectedMutableSites() : denoptim.graph.DGraph
getSelectedNodes() : denoptim.gui.GraphViewerPanel
getSelectedNodesInViewer() : denoptim.gui.GraphVertexMolViewerPanel
getSelectionStrategy() : denoptim.programs.denovo.GAParameters
getSelectionStrategyType() : denoptim.programs.denovo.GAParameters
getSelectivePressure() : denoptim.programs.denovo.GAParameters
getShortName() : denoptim.fitness.DescriptorForFitness
getSingleAPStringSDF() : denoptim.graph.AttachmentPoint
getSize() : denoptim.graph.Ring, denoptim.graph.rings.ClosableChain
getSizesOfCandidateSets() : denoptim.fragspace.FragsCombinationIterator
getSizeUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
getSMARTS() : denoptim.fragmenter.BridgeHeadFindingRule
getSMARTSAtom0() : denoptim.programs.fragmenter.CuttingRule
getSMARTSAtom1() : denoptim.programs.fragmenter.CuttingRule
getSMARTSBnd() : denoptim.programs.fragmenter.CuttingRule
getSmiles() : denoptim.graph.Candidate
getSMILESForMolecule() : denoptim.utils.MoleculeUtils
getSourceAPClass() : denoptim.graph.EdgeQuery
getSourceAPIdx() : denoptim.graph.EdgeQuery
getSourcePathName() : denoptim.integration.python.Py4JGetawayServer
getSourceVertex() : denoptim.graph.DGraph
getSourceVertexId() : denoptim.graph.EdgeQuery
getSpecification() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
getSrcAP() : denoptim.graph.Edge
getSrcAPClass() : denoptim.graph.Edge
getSrcAPID() : denoptim.graph.Edge
getSrcAPThroughout() : denoptim.graph.Edge
getSrcAtom() : denoptim.graph.rings.RingClosingAttractor
getSrcVertex() : denoptim.graph.Edge
getStackTraceAsString() : denoptim.exception.ExceptionUtils
getStandardOutput() : denoptim.task.ProcessHandler
getStringForKVLine() : denoptim.gui.ParametersForm
getStringFromTable() : denoptim.gui.ParametersForm
getStringIfNotEmpty() : denoptim.gui.ParametersForm
getStringIfSelected() : denoptim.gui.ParametersForm
getStructureFileNameBatch() : denoptim.fragmenter.ParallelFragmentationAlgorithm
getStructureFromJmolViewer() : denoptim.gui.FragmentViewPanel
getStructuresFile() : denoptim.programs.fragmenter.FragmenterParameters
getSubClass() : denoptim.graph.APClass
getSubgraphAPs() : denoptim.graph.DGraph
getSubGraphEnds() : denoptim.programs.genetweeker.GeneOpsRunner
getSummaryStatistics() : denoptim.ga.EAUtils
getSumOfVector() : denoptim.utils.CartesianSpaceUtils
getSupportedDataFeatures() : denoptim.io.SMILESListFormat
getSymbolOrLabel() : denoptim.utils.MoleculeUtils
getSymmetricAP() : denoptim.graph.EmptyVertex
getSymmetricAPs() : denoptim.graph.EmptyVertex, denoptim.graph.Vertex
getSymmetricAPSets() : denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
getSymmetricSetCount() : denoptim.graph.DGraph
getSymmetricSubGraphs() : denoptim.graph.DGraph
getSymmetryConstrain() : denoptim.fragspace.FragmentSpace
getSymmetryProbability() : denoptim.programs.denovo.GAParameters
getSymSetForVertex() : denoptim.graph.DGraph
getSymSetsIterator() : denoptim.graph.DGraph
getSymVerticesForVertex() : denoptim.graph.DGraph
getSystemRoot() : denoptim.gui.GUIFileOpener, denoptim.gui.GUIFileSaver
getTail() : denoptim.logging.HTMLLogFormatter
getTailVertex() : denoptim.graph.Ring, denoptim.graph.rings.PathSubGraph
getTargetAPClass() : denoptim.graph.EdgeQuery
getTargetAPIdx() : denoptim.graph.EdgeQuery
getTargetFragments() : denoptim.programs.fragmenter.FragmenterParameters
getTargetVertexId() : denoptim.graph.EdgeQuery
getTaskID() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getTempFile() : denoptim.gui.Utils
getTempFolder() : denoptim.files.FileUtils
getTemplateDeepTest() : denoptim.graph.TemplateTest
getTemplateJacket() : denoptim.graph.DGraph
getTestAmideTemplate() : denoptim.graph.TemplateTest
getTestCase() : denoptim.fragspace.FragmentSpaceTest
getTestTemplate() : denoptim.graph.Template
getTextForUnformattedSettings() : denoptim.gui.ParametersForm
getThirdRefAtomId() : denoptim.integration.tinker.TinkerUtils
getThreeCycle() : denoptim.ga.GraphOperationsTest
getTinkerMap() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getTinkerMolecule() : denoptim.molecularmodeling.ChemicalObjectModel
getTmpFileForCuttingRules() : denoptim.gui.CuttingRulesSelectionDialog
getTnkAtmIdOfRCA() : denoptim.molecularmodeling.ChemicalObjectModel
getTotNumbCombs() : denoptim.fragspace.FragsCombinationIterator
getTransformedClusters() : denoptim.fragmenter.FragmentClusterer
getTransformedCopy() : denoptim.fragmenter.ClusterableFragment
getTrgAP() : denoptim.graph.Edge
getTrgAPClass() : denoptim.graph.Edge
getTrgAPID() : denoptim.graph.Edge
getTrgAPThroughout() : denoptim.graph.Edge
getTrgVertex() : denoptim.graph.Edge
getTurningPointIdx() : denoptim.graph.rings.ClosableChain
getTXTFormats() : denoptim.files.FileFormat
getType() : denoptim.ga.XoverSite, denoptim.graph.rings.RingClosingAttractor, denoptim.utils.GraphEdit
getUID() : denoptim.graph.Candidate
getUid() : denoptim.graph.CandidateLW
getUIDFileIn() : denoptim.programs.denovo.GAParameters
getUIDFileName() : denoptim.programs.combinatorial.CEBLParameters
getUIDFileOut() : denoptim.programs.denovo.GAParameters
getUnfilteredMutationTypes() : denoptim.graph.Vertex
getUnique() : denoptim.graph.APClass
getUniqueAPIndex() : denoptim.graph.DGraph, denoptim.graph.Vertex
getUniqueGraphIndex() : denoptim.utils.GraphUtils
getUniqueMoleculeIndex() : denoptim.utils.GraphUtils
getUniqueTaskIndex() : denoptim.utils.TaskUtils
getUniqueVertexIndex() : denoptim.utils.GraphUtils
getUnqGraphId() : denoptim.combinatorial.CheckPoint
getUnqMolId() : denoptim.combinatorial.CheckPoint
getUnqVrtId() : denoptim.combinatorial.CheckPoint
getUsableAliphaticBridges() : denoptim.ga.EAUtils
getUsableAromaticBridges() : denoptim.ga.EAUtils
getUsedRCVertices() : denoptim.graph.DGraph
getValence() : denoptim.graph.Edge.BondType
getVariableMapper() : denoptim.fitness.FitnessExpressionParser.CustomVariableDefiningContext, denoptim.fitness.FitnessExpressionParser.VariableDefiningContext
getVariables() : denoptim.fitness.DescriptorForFitness, denoptim.fitness.FitnessExpressionParser
getVectorFromTo() : denoptim.utils.CartesianSpaceUtils
getVerbosity() : denoptim.graph.rings.RingClosureParameters, denoptim.programs.RunTimeParameters
getVersionID() : denoptim.ga.Population
getVertecesPath() : denoptim.graph.rings.PathSubGraph
getVertexAtPosition() : denoptim.graph.DGraph, denoptim.graph.Ring
getVertexBBIDQuery() : denoptim.graph.VertexQuery
getVertexBBTypeQuery() : denoptim.graph.VertexQuery
getVertexCount() : denoptim.graph.DGraph
getVertexeIDsWithLabel() : denoptim.gui.JUNGGraphSnapshot
getVertexFromLibrary() : denoptim.fragspace.FragmentSpace
getVertexId() : denoptim.fragspace.IdFragmentAndAP, denoptim.graph.Vertex, denoptim.integration.tinker.TinkerAtom
getVertexIdInPath() : denoptim.graph.rings.PathSubGraph
getVertexIDQuery() : denoptim.graph.VertexQuery
getVertexLevelQuery() : denoptim.graph.VertexQuery
getVertexList() : denoptim.graph.DGraph
getVertexMolId() : denoptim.fragspace.IdFragmentAndAP
getVertexMolType() : denoptim.fragspace.IdFragmentAndAP
getVertexPosition() : denoptim.gui.DNPSpringLayout< V, E >
getVertexQuery() : denoptim.utils.GraphEdit
getVertexToAtomIdMap() : denoptim.utils.MoleculeUtils
getVertexType() : denoptim.graph.Vertex
getVertexTypeQuery() : denoptim.graph.VertexQuery
getVertexWithId() : denoptim.graph.DGraph
getVertices() : denoptim.graph.Ring
getVerticesWithAPClass() : denoptim.fragspace.FragmentSpace
getVerticesWithAPClasses() : denoptim.fragspace.FragmentSpace
getVerticesWithAPClassStartingWith() : denoptim.fragspace.FragmentSpace
getVerticesWithAPFingerprint() : denoptim.fragspace.FragmentSpace
getVisitedGraphsFile() : denoptim.programs.denovo.GAParameters
getVrtSymSetId() : denoptim.fragspace.IdFragmentAndAP
getWaitStep() : denoptim.programs.combinatorial.CEBLParameters
getWallTime() : denoptim.programs.fitnessevaluator.FRParameters
getWholeSMARTSRule() : denoptim.programs.fragmenter.CuttingRule
getWorkDirectory() : denoptim.programs.RunTimeParameters
getWorkingDirectory() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getWriter() : denoptim.json.DENOPTIMgson
getWriterClassName() : denoptim.io.SMILESListFormat
getXoverPartners() : denoptim.ga.Population
getXoverSites() : denoptim.ga.Population
getXYZ() : denoptim.integration.tinker.TinkerAtom
getXYZIndex() : denoptim.integration.tinker.TinkerAtom
getXYZINTTool() : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
GraphBuildingTask() : denoptim.combinatorial.GraphBuildingTask
GraphEdit() : denoptim.utils.GraphEdit
GraphEditor() : denoptim.programs.grapheditor.GraphEditor
GraphEdParameters() : denoptim.programs.grapheditor.GraphEdParameters
GraphLinkFinder() : denoptim.fragspace.GraphLinkFinder
GraphListsHandler() : denoptim.programs.graphlisthandler.GraphListsHandler
GraphListsHandlerParameters() : denoptim.programs.graphlisthandler.GraphListsHandlerParameters
graphNeedsCappingGroups() : denoptim.graph.DGraph
GraphOptsPopup() : denoptim.gui.GraphViewerPanel.GraphOptsPopup
GraphSpinnerChangeEvent() : denoptim.gui.GUIGraphHandler.GraphSpinnerChangeEvent
GraphVertexMolViewerPanel() : denoptim.gui.GraphVertexMolViewerPanel
GraphViewerPanel() : denoptim.gui.GraphViewerPanel
groupAndClassifyFragments() : denoptim.fragspace.FragmentSpace
GUI() : denoptim.gui.GUI
GUIAPClassDefinitionDialog() : denoptim.gui.GUIAPClassDefinitionDialog
GUICardPanel() : denoptim.gui.GUICardPanel
GUICompatibilityMatrixTab() : denoptim.gui.GUICompatibilityMatrixTab
GUIEmptyVertexMaker() : denoptim.gui.GUIEmptyVertexMaker
GUIGraphHandler() : denoptim.gui.GUIGraphHandler
GUIInspectFSERun() : denoptim.gui.GUIInspectFSERun
GUIInspectGARun() : denoptim.gui.GUIInspectGARun
GUIMainPanel() : denoptim.gui.GUIMainPanel
GUIModalDialog() : denoptim.gui.GUIModalDialog
GUIPreferencesDialog() : denoptim.gui.GUIPreferencesDialog
GUIPrepare() : denoptim.gui.GUIPrepare
GUIPrepareFitnessRunner() : denoptim.gui.GUIPrepareFitnessRunner
GUIPrepareFSERun() : denoptim.gui.GUIPrepareFSERun
GUIPrepareGARun() : denoptim.gui.GUIPrepareGARun
GUITextReader() : denoptim.gui.GUITextReader
GUIVertexInspector() : denoptim.gui.GUIVertexInspector
GUIVertexSelector() : denoptim.gui.GUIVertexSelector