- t -

tableChanged() : denoptim.gui.FragmentViewPanel.PausableTableModelListener, denoptim.gui.ParametersForm.TabFieldChange, denoptim.gui.VertexAsGraphViewPanel.PausableTableModelListener, denoptim.gui.VertexAsTwoDimStructureViewPanel.PausableTableModelListener
TanimotoMolSimilarity() : denoptim.fitness.descriptors.TanimotoMolSimilarity
TanimotoMolSimilarityBySubstructure() : denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
TargetAPClassToken() : denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken
Task() : denoptim.task.Task
TasksBatchManager() : denoptim.task.TasksBatchManager
Template() : denoptim.graph.Template
TemplateConfiguration() : denoptim.gui.GUIGraphHandler.ConfigTemplateDialog.TemplateConfiguration
terminate() : denoptim.main.Main
tesGetNoisyPoint() : denoptim.utils.RandomizerTest
test() : denoptim.utils.SizeControlledSetTest
testAddAP_after_setInnerGraph_throwsException() : denoptim.graph.TemplateTest
testAddFusedRings() : denoptim.ga.GraphOperationsTest
testAddRing() : denoptim.ga.GraphOperationsTest
testAPMapFinder() : denoptim.fragspace.APMapFinderTest
testAPMapFinder_ConstrainAll() : denoptim.fragspace.APMapFinderTest
testAPMapFinder_Constrained() : denoptim.fragspace.APMapFinderTest
testAppendToJSON() : denoptim.io.DenoptimIOTest
testAtLeastSameNumberOfAPs() : denoptim.graph.TemplateTest
testAvailableThrougout() : denoptim.graph.AttachmentPointTest
testAvoidRedundantXOver() : denoptim.ga.EAUtilsTest
testBuildByXOver_Embedded_FixedStructure() : denoptim.ga.EAUtilsTest
testBuildByXOver_Embedded_Free() : denoptim.ga.EAUtilsTest
testBuildByXOver_Embedded_FreeBackwards() : denoptim.ga.EAUtilsTest
testBuildByXOver_SubGraph() : denoptim.ga.EAUtilsTest
testBuildGraphFromTemplateScaffold() : denoptim.ga.EAUtilsTest
testCalculateCentroid() : denoptim.utils.MoleculeUtilsTest
testCandidateGenerationMethod() : denoptim.ga.EAUtilsTest
testCandidateGenerationMethodReproducibility() : denoptim.ga.EAUtilsTest
TestCase() : denoptim.fragspace.FragmentSpaceTest.TestCase
testChooseNumberOfSitesToMutate() : denoptim.ga.EAUtilsTest
testClone() : denoptim.ga.PopulationTest, denoptim.graph.AttachmentPointTest, denoptim.graph.DGraphTest, denoptim.graph.FragmentTest, denoptim.graph.TemplateTest, denoptim.graph.VertexTest
testCluster() : denoptim.fragmenter.FragmentClustererTest
testCluster2() : denoptim.fragmenter.FragmentClustererTest
testCompareFormulaAndElementalAnalysis() : denoptim.utils.FormulaUtilsTest
testCompareTo() : denoptim.graph.APClassTest
testConfigureDescriptorsList() : denoptim.fitness.FitnessProviderTest
testConnectionDeconnectionLoop() : denoptim.graph.EdgeTest
testConstructor() : denoptim.graph.APClassTest
testConstructorsAndSDFString() : denoptim.graph.AttachmentPointTest
testConstructorsAndSDFStringNoDirVec() : denoptim.graph.AttachmentPointTest
testConversionTo3dTree() : denoptim.molecularmodeling.ThreeDimTreeBuilderTest
testConversionToIAC() : denoptim.graph.FragmentTest
testConvertSymmetricLabelsToSymmetricSets() : denoptim.graph.DGraphTest
testCrowdingProbability() : denoptim.ga.EAUtilsTest
testDefineProgramBehavior() : denoptim.main.MainTest
testDetectFileFormat() : denoptim.io.DenoptimIOTest
testDetectSymVertexSets() : denoptim.graph.DGraphTest
testDistanceAsRMSD() : denoptim.fragmenter.FragmentClustererTest
testEmbedPatternsInTemplates() : denoptim.graph.DGraphTest
testEquals() : denoptim.graph.APClassTest, denoptim.graph.RelatedAPPairTest, denoptim.graph.SymmetricSetWithModeTest
testEvaluateConstitutionalClosability() : denoptim.graph.rings.PathClosabilityToolsTest, denoptim.graph.rings.RandomCombOfRingIteratorTest
testEvaluateRCVPair() : denoptim.graph.rings.RingSizeManagerTest
testExploreConnectivity() : denoptim.fragmenter.FragmenterToolsTest
testExploreHapticity() : denoptim.fragmenter.FragmenterToolsTest
testExtendGraph() : denoptim.ga.GraphOperationsTest
testExtractClusterableFragments() : denoptim.fragmenter.ConformerExtractorTaskTest
testExtractPattern_fusedRings() : denoptim.ga.GraphOperationsTest
testExtractPattern_returnsEmptyListIfNoRings() : denoptim.ga.GraphOperationsTest
testExtractPattern_singleRingSystem() : denoptim.ga.GraphOperationsTest
testExtractSubgraph() : denoptim.graph.DGraphTest
testExtractSubgraphFromCollection() : denoptim.graph.DGraphTest
testFilterFragment() : denoptim.fragmenter.FragmenterToolsTest
testFindCDKDescriptors() : denoptim.fitness.DescriptorUtilsTest
testFindDemoptimDescriptors() : denoptim.fitness.DescriptorUtilsTest
testFindMappingCompatibileAPs() : denoptim.fragspace.APMapFinderTest
testFindVertex() : denoptim.graph.DGraphTest
testFromToJSON() : denoptim.graph.DGraphTest
testFromToJSON_minimal() : denoptim.graph.VertexTest
testFromToJSON_withSymmetricAPs() : denoptim.graph.VertexTest
testFusedRingAddedToFragmentLibrary() : denoptim.fragspace.FragmentSpaceTest
testFusedRingAddedToScaffoldLibrary() : denoptim.fragspace.FragmentSpaceTest
testFusedRingOnlyAddedOnce() : denoptim.fragspace.FragmentSpaceTest
testFusionSiteDetection_ImposeSymmetry() : denoptim.ga.EAUtilsTest
testGetAPsWithAPClassStartingWith() : denoptim.graph.VertexTest
testGetAttachmentPoints_returnsAPsWithTemplateAsOwner() : denoptim.graph.TemplateTest
testGetAttachmentPoints_returnsCorrectNumberOfAPs() : denoptim.graph.TemplateTest
testGetAvailableAPs_returnsListOfAvailableAPs() : denoptim.graph.DGraphTest
testGetCentroid() : denoptim.fragmenter.DynamicCentroidClusterTest
testGetChildrenTree() : denoptim.graph.DGraphTest
testGetChildrenTreeWithBranchIdentifier() : denoptim.graph.DGraphTest
testGetCloserVertex() : denoptim.graph.RingTest
testGetConstantFitness() : denoptim.fitness.FitnessProviderTest
testGetDistance() : denoptim.graph.RingTest
testGetEdbeUserThrougout() : denoptim.graph.AttachmentPointTest
testGetEdgesWithSrcOrTrg() : denoptim.graph.DGraphTest
testGetEmbeddedAP() : denoptim.graph.AttachmentPointTest
testGetEmbeddedGraphInClone() : denoptim.graph.DGraphTest
testGetEmbeddingPath() : denoptim.graph.DGraphTest
testGetFitness() : denoptim.fitness.FitnessProviderTest
testGetFitnessWithCustomDescriptors() : denoptim.fitness.FitnessProviderTest
testGetFitnessWithParametrizedDescriptors() : denoptim.fitness.FitnessProviderTest
testGetFragAPsCompatibleWithClass() : denoptim.fragspace.FragmentSpaceTest
testGetFragAPsCompatibleWithTheseAPs() : denoptim.fragspace.FragmentSpaceTest
testGetFragmentsCompatibleWithTheseAPs() : denoptim.fragspace.FragmentSpaceTest
testGetFragsWithAPClass() : denoptim.fragspace.FragmentSpaceTest
testGetFragsWithAPClassStartingWith() : denoptim.fragspace.FragmentSpaceTest
testGetIAtomContainer() : denoptim.graph.TemplateTest
testGetIAtomContainer_DeepVertex() : denoptim.graph.TemplateTest
testGetInterfaceAPs() : denoptim.graph.DGraphTest
testGetJGraphKernelFromGraph() : denoptim.utils.GraphConversionToolTest
testGetLevel() : denoptim.graph.DGraphTest
testGetLinkedAP() : denoptim.graph.AttachmentPointTest
testGetMatchingBonds() : denoptim.fragmenter.FragmenterToolsTest
testGetMinimumRMSD() : denoptim.fragmenter.FragmentAlignementTest
testGetMinMax() : denoptim.ga.PopulationTest
testGetMutationSites() : denoptim.graph.DGraphTest, denoptim.graph.VertexTest
testGetMWSlotIdentifier() : denoptim.fragmenter.FragmenterToolsTest
testGetNearestToCentroid() : denoptim.fragmenter.DynamicCentroidClusterTest
testGetPoint3d() : denoptim.utils.MoleculeUtilsTest
testGetRCVsForAPClass() : denoptim.fragspace.FragmentSpaceTest
testGetRCVsWithAPClass() : denoptim.fragspace.FragmentSpaceTest
testGetRMSDStatsOfNoisyDistorsions() : denoptim.fragmenter.FragmentClustererTest
testGetSameAsThis() : denoptim.graph.SymmetricAPsTest
testGetSourceVertex() : denoptim.graph.DGraphTest
testGetSubgraphAPs() : denoptim.graph.DGraphTest
testGetSymmetricSubGraphs() : denoptim.graph.DGraphTest
testGetTransformedCopy() : denoptim.fragmenter.ClusterableFragmentTest
testGetUsableAliphaticBridges() : denoptim.ga.EAUtilsTest
testGetUsableAromaticBridges() : denoptim.ga.EAUtilsTest
testGetVerticesWithAPClass() : denoptim.fragspace.FragmentSpaceTest
testGetVerticesWithAPClasses() : denoptim.fragspace.FragmentSpaceTest
testGetVerticesWithAPFingerprint() : denoptim.fragspace.FragmentSpaceTest
testGraphIsomorphism() : denoptim.graph.DGraphTest
testHandlingAPsAsObjOrProperty() : denoptim.graph.FragmentTest
testHasConnectedSrcAtom() : denoptim.graph.AttachmentPointTest
testHashCode() : denoptim.graph.SymmetricSetWithModeTest
testHasSameSrcAtom() : denoptim.graph.AttachmentPointTest
testIAtomContainerToJSONAndBack() : denoptim.json.DENOPTIMgsonTest
testInterpretationOfKeywords() : denoptim.programs.denovo.GAParametersTest
testIOCuttingRules() : denoptim.io.DenoptimIOTest
testIOEmptyVertex() : denoptim.io.DenoptimIOTest
testIOMolFragment() : denoptim.io.DenoptimIOTest
testIOTemplate() : denoptim.io.DenoptimIOTest
testIsConnectedToAromaticBridge() : denoptim.graph.VertexTest
testIsInPercentile() : denoptim.ga.PopulationTest
testIsIsostructuralTo() : denoptim.graph.DGraphTest
testIsomorphicInLinear() : denoptim.graph.FragmentTest
testIsomorphicTo() : denoptim.graph.FragmentTest
testIsomorphismExists() : denoptim.graph.FragmentIsomorphismInspectorTest
testIsSrcInUser() : denoptim.graph.AttachmentPointTest
testIsValidAPRuleString() : denoptim.graph.APClassTest
testIsValidAPSubCLassString() : denoptim.graph.APClassTest
testLinkFromEdge() : denoptim.fragspace.GraphLinkFinderTest
testLinkFromEdgeNoMatch() : denoptim.fragspace.GraphLinkFinderTest
testLinkFromEdgeOneMatch() : denoptim.fragspace.GraphLinkFinderTest
testLinkFromVertex() : denoptim.fragspace.GraphLinkFinderTest
testListContains() : denoptim.graph.APClassTest
testLocateCompatibleXOverPoints() : denoptim.ga.GraphOperationsTest
testLogging() : denoptim.programs.denovo.GAParametersTest
testMakeGraphFromFragmentationOfMol() : denoptim.ga.EAUtilsTest
testMakeGraphFromFragmentationOfMol_cappingGroups() : denoptim.ga.EAUtilsTest
testMakeGraphFromFragmentationOfMol_linearities() : denoptim.ga.EAUtilsTest
testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy() : denoptim.ga.EAUtilsTest
testMakeGraphFromFragmentationOfMol_symmetry() : denoptim.ga.EAUtilsTest
testMakeGraphFromFragmentationOfMol_Symmetry() : denoptim.ga.EAUtilsTest
testMakePathSubGraph() : denoptim.graph.rings.PathSubGraphTest
testMatches() : denoptim.io.SMILESListFormatTest
testMolecularFragmentSerialization() : denoptim.json.DENOPTIMgsonTest
testNaNFitness() : denoptim.fitness.FitnessProviderTest
testNestedTemplateCloning() : denoptim.graph.TemplateTest
testParseFormula() : denoptim.utils.FormulaUtilsTest
testParsingOfCSDFormula() : denoptim.utils.FormulaUtilsTest
testParsingofSdfAPString() : denoptim.graph.AttachmentPointTest
testPerformSUS() : denoptim.ga.SeelctionHelperTest
testPopulationVersion() : denoptim.ga.PopulationTest
testProcessExpressions() : denoptim.fitness.FitnessExpressionParserTest
testProjectToClonedGraphs() : denoptim.ga.XoverSiteTest
testRandomizerReproducibility() : denoptim.utils.RandomizerTest
testRandomlyChooseOne() : denoptim.utils.RandomizerTest
testReadAllAPClasses() : denoptim.io.DenoptimIOTest
testReadAllAtomContainersFromCIF() : denoptim.io.DenoptimIOTest
testReadCSDFormulae() : denoptim.io.DenoptimIOTest
testReadCuttingRulsedDefault() : denoptim.io.DenoptimIOTest
testReadGenerationFromSummary() : denoptim.io.DenoptimIOTest
testReadLightWeightCandidate() : denoptim.io.DenoptimIOTest
testRemoveCapping() : denoptim.graph.DGraphTest
testRemoveUnusedRCVs() : denoptim.graph.DGraphTest
testRemoveVertex() : denoptim.graph.DGraphTest
testReplaceSubGraph() : denoptim.graph.DGraphTest
testReplaceSubGraph_inTemplate() : denoptim.graph.DGraphTest
testReplaceVertex() : denoptim.graph.DGraphTest
testReplaceVertex_inRing() : denoptim.graph.DGraphTest
testSameAPClass() : denoptim.graph.TemplateTest
testSameAs() : denoptim.graph.AttachmentPointTest, denoptim.graph.SymmetricAPsTest
testSameAs_DiffAPClass() : denoptim.graph.AttachmentPointTest
testSameAs_DiffAPNum() : denoptim.graph.VertexTest
testSameAs_DiffBndTyp() : denoptim.graph.EdgeTest
testSameAs_DiffRings() : denoptim.graph.DGraphTest
testSameAs_DiffSrcAtm() : denoptim.graph.AttachmentPointTest
testSameAs_DiffSymmSet() : denoptim.graph.DGraphTest
testSameAs_DiffVertex() : denoptim.graph.DGraphTest
testSameAs_DisorderRings() : denoptim.graph.DGraphTest
testSameAs_Equal() : denoptim.graph.DGraphTest, denoptim.graph.EdgeTest, denoptim.graph.VertexTest
testSameAs_SameRings() : denoptim.graph.DGraphTest
testSameAs_SameSymmSet() : denoptim.graph.DGraphTest
testSearchForApPairsSuitableToRingFusion() : denoptim.ga.EAUtilsTest
testSelectNonScaffoldNonCapVertex() : denoptim.ga.EAUtilsTest
testSerializeDeserializeDENOPTIMGraphs() : denoptim.io.DenoptimIOTest
testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs() : denoptim.graph.TemplateTest
testSetNaturalNodeOrder() : denoptim.fragmenter.ClusterableFragmentTest
testSocketProvidedDescriptor() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest
testSortAPs() : denoptim.graph.AttachmentPointTest
testSplitInputForThreads() : denoptim.fragmenter.ParallelFragmentationAlgorithmTest
testSymmetricSetLabels() : denoptim.graph.DGraphTest
testSymmetry() : denoptim.fragspace.FragmentSpaceTest
testTanimotoMolSimilarity() : denoptim.fitness.descriptors.TanimotoMolSimilarityTest
testTemplateSerialization() : denoptim.json.DENOPTIMgsonTest
testTermination() : denoptim.gui.DNPSpringLayout< V, E >
testTimeout() : denoptim.graph.FragmentIsomorphismInspectorTest
testUndirectedComparison() : denoptim.graph.EdgeTest, denoptim.graph.RingTest, denoptim.graph.UndirectedEdgeRelationTest
testUnionOfSets() : denoptim.utils.GenUtilsTest
testUseWholeMolGeometryForExtractedTemplates() : denoptim.fragspace.FragmentSpaceTest
testXOverCompatibility() : denoptim.ga.PopulationTest
testYesNoTrueFalseKeyword() : denoptim.programs.denovo.GAParametersTest
ThreeDimTreeBuilder() : denoptim.molecularmodeling.ThreeDimTreeBuilder
TinkerAtom() : denoptim.integration.tinker.TinkerAtom
TinkerBond() : denoptim.integration.tinker.TinkerBond
TinkerException() : denoptim.integration.tinker.TinkerException
TinkerMolecule() : denoptim.integration.tinker.TinkerMolecule
toIAtom() : denoptim.json.LWAtom
toIntMappig() : denoptim.graph.APMapping
toJson() : denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template
toOldInt() : denoptim.graph.Vertex.BBType
torsion() : denoptim.utils.MathUtils
toSDFString() : denoptim.graph.APClass
toString() : denoptim.combinatorial.CheckPoint, denoptim.fitness.DescriptorForFitness, denoptim.fitness.Variable, denoptim.fragspace.IdFragmentAndAP, denoptim.ga.XoverSite, denoptim.graph.APClass, denoptim.graph.APMapping, denoptim.graph.AttachmentPoint, denoptim.graph.Candidate, denoptim.graph.DGraph, denoptim.graph.Edge, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.RelatedAPPair, denoptim.graph.Ring, denoptim.graph.rings.ChainLink, denoptim.graph.rings.ClosableChain, denoptim.graph.rings.CyclicGraphHandler.ClosableConf, denoptim.graph.rings.PathSubGraph, denoptim.graph.rings.RingClosingAttractor, denoptim.graph.rings.RingClosingConformations, denoptim.graph.rings.RingClosure, denoptim.graph.simplified.Node, denoptim.graph.simplified.UndirectedEdge, denoptim.graph.SymmetricAPs, denoptim.graph.SymmetricVertexes, denoptim.graph.Vertex, denoptim.integration.tinker.TinkerAtom, denoptim.programs.fragmenter.CuttingRule, denoptim.task.Task, denoptim.utils.ConnectedLigand, denoptim.utils.ObjectPair
toStringNoId() : denoptim.graph.AttachmentPoint
translateOrigin() : denoptim.utils.CartesianSpaceUtils
TrgRemovalListener() : denoptim.gui.CompatibilityMatrixForm.TrgRemovalListener
trim() : denoptim.ga.Population
TwoDimStructurePanel() : denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel