- s -

sameAs() : denoptim.graph.AttachmentPoint, denoptim.graph.DGraph, denoptim.graph.Edge, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.SymmetricAPs, denoptim.graph.Template, denoptim.graph.Vertex
sameAsRings() : denoptim.graph.DGraph
sameFragAndAp() : denoptim.fragspace.IdFragmentAndAP
sameVertexFeatures() : denoptim.graph.Vertex
satisfiesOptions() : denoptim.programs.fragmenter.CuttingRule
satisfiesRuleOptions() : denoptim.programs.fragmenter.MatchedBond
saturateRingClosingAttractor() : denoptim.molecularmodeling.RingClosureTool
savePopFile() : denoptim.programs.denovo.GAParameters
saveResults() : denoptim.gui.CuttingRulesSelectionDialog, denoptim.gui.MolToGraphParametersDialog
saveUnsavedChanges() : denoptim.gui.GUIGraphHandler, denoptim.gui.GUIVertexInspector
scalar() : denoptim.utils.MathUtils
scale() : denoptim.utils.MathUtils
ScrollableJPupupMenu() : denoptim.gui.ScrollableJPupupMenu
searchAPClass() : denoptim.gui.CompatibilityMatrixForm
searchRingFusionSites() : denoptim.ga.EAUtils
selectBasedOnFitness() : denoptim.ga.EAUtils
selectFragmentsFromClosableChains() : denoptim.graph.rings.RingClosureParameters
selectNonScaffoldNonCapVertex() : denoptim.ga.EAUtils
sendToFitnessProvider() : denoptim.combinatorial.GraphBuildingTask
serFileAlreadyUsed() : denoptim.combinatorial.CheckPoint
serialize() : denoptim.graph.APTreeMap.APMapSerializer, denoptim.graph.DGraph.DENOPTIMGraphSerializer, denoptim.graph.Edge.DENOPTIMEdgeSerializer, denoptim.graph.Ring.DENOPTIMRingSerializer, denoptim.graph.SymmetricAPs.SymmetricAPsSerializer, denoptim.graph.SymmetricVertexes.SymmetricVertexesSerializer, denoptim.json.IAtomContainerSerializer
serializeCheckPoint() : denoptim.combinatorial.CEBLUtils
serializeRCCs() : denoptim.graph.rings.RingClosureParameters
set() : denoptim.ga.Population
set3DCoordinates() : denoptim.integration.tinker.TinkerMolecule
setActive() : denoptim.gui.FragmentViewPanel.PausableTableModelListener, denoptim.gui.VertexAsGraphViewPanel.PausableTableModelListener, denoptim.gui.VertexAsTwoDimStructureViewPanel.PausableTableModelListener
setAddExplicitH() : denoptim.programs.fragmenter.FragmenterParameters
setAlignBBsIn3D() : denoptim.molecularmodeling.ThreeDimTreeBuilder
setAP() : denoptim.utils.GraphEdit
setAPClass() : denoptim.graph.AttachmentPoint
setAPclassBasedApproach() : denoptim.fragspace.FragmentSpace
setAsRCV() : denoptim.graph.Vertex
setAtomNeighbours() : denoptim.integration.tinker.TinkerAtom
setAtomPositionNumber() : denoptim.graph.AttachmentPoint
setAtomPositionNumberInMol() : denoptim.graph.AttachmentPoint
setAtoms() : denoptim.integration.tinker.TinkerMolecule
setAtomString() : denoptim.integration.tinker.TinkerAtom
setAtomType() : denoptim.integration.tinker.TinkerAtom
setBondPairs() : denoptim.integration.tinker.TinkerMolecule
setBondType() : denoptim.graph.APClass, denoptim.graph.Ring
setBuildingBlockId() : denoptim.graph.Vertex
setBuildingBlockType() : denoptim.graph.Vertex
setCandidateClosableChains() : denoptim.graph.DGraph
setCandidateOwner() : denoptim.graph.DGraph
setCappingLibrary() : denoptim.fragspace.FragmentSpace
setCappingMap() : denoptim.fragspace.FragmentSpace
setCheckFormula() : denoptim.programs.fragmenter.FragmenterParameters
setChemicalRepresentation() : denoptim.graph.Candidate
setComments() : denoptim.graph.Candidate
setCompatibilityMatrix() : denoptim.fragspace.FragmentSpace
setConstitutionalClosabilityConds() : denoptim.graph.rings.RingClosureParameters
setContractLevel() : denoptim.graph.Template
setCoordsVector() : denoptim.fragmenter.ClusterableFragment
setCutId() : denoptim.graph.AttachmentPoint
setCuttingRules() : denoptim.programs.fragmenter.FragmenterParameters
setCuttingRulesFilePathname() : denoptim.programs.fragmenter.FragmenterParameters
setDBRoot() : denoptim.programs.combinatorial.CEBLParameters
setDescriptorName() : denoptim.fitness.Variable
setDescriptorParameters() : denoptim.fitness.Variable
setDirectionVector() : denoptim.graph.AttachmentPoint
setDistAngle() : denoptim.integration.tinker.TinkerAtom
setEdgeList() : denoptim.graph.DGraph
setEdgeQuery() : denoptim.utils.GraphEdit
setEmbeddedRingsContract() : denoptim.programs.fragmenter.FragmenterParameters
setEmbedRingsInTemplate() : denoptim.programs.fragmenter.FragmenterParameters
setEnabled() : denoptim.gui.GUIGraphHandler.GraphSpinnerChangeEvent, denoptim.gui.GUIVertexInspector.VrtxSpinnerChangeEvent
setError() : denoptim.graph.Candidate, denoptim.graph.CandidateLW
setFactorForSDOnStatsOfUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
setFirst() : denoptim.utils.ObjectPair
setFitness() : denoptim.graph.Candidate, denoptim.graph.CandidateLW
setForbiddenEndList() : denoptim.fragspace.FragmentSpace
setFormulaeFile() : denoptim.programs.fragmenter.FragmenterParameters
setFragmentLibrary() : denoptim.fragspace.FragmentSpace
setFragmentSpace() : denoptim.fragspace.FragmentSpaceParameters
setFragRejectionSMARTS() : denoptim.programs.fragmenter.FragmenterParameters
setFragRetentionSMARTS() : denoptim.programs.fragmenter.FragmenterParameters
setGeneratingSource() : denoptim.graph.CandidateLW
setGeneration() : denoptim.graph.Candidate, denoptim.graph.CandidateLW
setGraph() : denoptim.graph.Candidate
setGraphId() : denoptim.graph.DGraph
setGraphOwner() : denoptim.graph.Vertex
setIAtom() : denoptim.graph.rings.RingClosingAttractor
setIAtomContainer() : denoptim.graph.Template
setID() : denoptim.graph.AttachmentPoint
setImageFile() : denoptim.graph.Candidate
setIncomingGraph() : denoptim.utils.GraphEdit
setInitialLocations() : denoptim.gui.DNPSpringLayout< V, E >
setInnerGraph() : denoptim.graph.Template
setIsomorphicSampleSize() : denoptim.programs.fragmenter.FragmenterParameters
setJmolViewer() : denoptim.gui.FragmentViewPanel, denoptim.gui.MoleculeViewPanel
setLevel() : denoptim.combinatorial.CheckPoint, denoptim.graph.Candidate, denoptim.graph.CandidateLW
setLinearAngleLimit() : denoptim.programs.fragmenter.FragmenterParameters
setLinkToProgressBar() : denoptim.task.StaticTaskManager
setLocalMsg() : denoptim.graph.DGraph
setLogFilePathname() : denoptim.programs.RunTimeParameters
setLogger() : denoptim.programs.RunTimeParameters
setMaxFragHeavyAtomCount() : denoptim.programs.fragmenter.FragmenterParameters
setMaxNoiseUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
setMinFragHeavyAtomCount() : denoptim.programs.fragmenter.FragmenterParameters
setMouseMode() : denoptim.gui.GraphVertexMolViewerPanel, denoptim.gui.GraphViewerPanel
setMutationTypes() : denoptim.graph.Vertex
setMWSlotSize() : denoptim.programs.fragmenter.FragmenterParameters
setMWSlotToAllFragsFile() : denoptim.programs.fragmenter.FragmenterParameters
setName() : denoptim.graph.Candidate, denoptim.integration.tinker.TinkerMolecule
setNaturalNodeOrder() : denoptim.fragmenter.ClusterableFragment
setNextIds() : denoptim.combinatorial.CheckPoint, denoptim.combinatorial.GraphBuildingTask
setNotify() : denoptim.task.Task
setNumTasks() : denoptim.programs.fragmenter.FragmenterParameters
setOrderOfNodes() : denoptim.fragmenter.ClusterableFragment
setOwner() : denoptim.graph.AttachmentPoint
setParameters() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure, denoptim.programs.RunTimeParameters
setPopulationSize() : denoptim.programs.denovo.GAParameters
setPreDefinedAPClass() : denoptim.gui.GUIAPClassDefinitionDialog
setProperties() : denoptim.graph.Vertex
setProperty() : denoptim.graph.AttachmentPoint, denoptim.graph.Vertex
setRandomizer() : denoptim.programs.RunTimeParameters
setRCC() : denoptim.graph.rings.PathSubGraph
setRCCompatibilityMatrix() : denoptim.fragspace.FragmentSpace
setReferenceToRunningEAlgorithm() : denoptim.ga.ExternalCmdsListener
setRefToMainPanel() : denoptim.gui.MainToolBar
setRefToMasterGUI() : denoptim.gui.MainToolBar
setRejectedAPClassCombinations() : denoptim.programs.fragmenter.FragmenterParameters
setRejectedAPClasses() : denoptim.programs.fragmenter.FragmenterParameters
setRejectedElements() : denoptim.programs.fragmenter.FragmenterParameters
setRejectedFormulaLessThan() : denoptim.programs.fragmenter.FragmenterParameters
setRejectedFormulaMoreThan() : denoptim.programs.fragmenter.FragmenterParameters
setRejectWeirdIsotopes() : denoptim.programs.fragmenter.FragmenterParameters
setRequireApSelection() : denoptim.gui.GUIVertexSelector
setRings() : denoptim.graph.DGraph
setRingSizeBias() : denoptim.graph.rings.RingClosureParameters
setRootId() : denoptim.combinatorial.CheckPoint
setRule() : denoptim.graph.APClass
setSafelyCompletedGraphId() : denoptim.combinatorial.CheckPoint
setSaveClustersOfConformerToFile() : denoptim.programs.fragmenter.FragmenterParameters
setScaffold() : denoptim.graph.DGraph
setScaffoldingPolicy() : denoptim.programs.fragmenter.FragmenterParameters
setScaffoldLibrary() : denoptim.fragspace.FragmentSpace
setScheme() : denoptim.utils.AtomOrganizer
setSDFFile() : denoptim.graph.Candidate
setSecond() : denoptim.utils.ObjectPair
setSeed() : denoptim.utils.Randomizer
setServer() : denoptim.integration.python.Py4JGetawayServer
setSizeUnimodalPop() : denoptim.programs.fragmenter.FragmenterParameters
setSMARTS() : denoptim.fitness.Variable
setSmiles() : denoptim.graph.Candidate
setSourceTitle() : denoptim.gui.GUITextReader
setStartingPoint() : denoptim.fragspace.FragsCombinationIterator
setStructuresFile() : denoptim.programs.fragmenter.FragmenterParameters
setSubClass() : denoptim.graph.APClass
setSwitchable() : denoptim.gui.VertexViewPanel
setSymmConstraints() : denoptim.fragspace.FragmentSpace
setSymmetricAP() : denoptim.graph.EmptyVertex
setSymmetricAPSets() : denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
setSymmetricVertexSets() : denoptim.graph.DGraph
setTemplateJacket() : denoptim.graph.DGraph
setTinkerTypes() : denoptim.integration.tinker.TinkerUtils, denoptim.molecularmodeling.RingClosureTool
setTurningPoint() : denoptim.graph.rings.ClosableChain
setUID() : denoptim.graph.Candidate
setUniquefyingProperty() : denoptim.graph.Vertex
setUnqGraphId() : denoptim.combinatorial.CheckPoint
setUnqMolId() : denoptim.combinatorial.CheckPoint
setUnqVrtId() : denoptim.combinatorial.CheckPoint
setUnsavedChanges() : denoptim.gui.IParametersForm, denoptim.gui.ParametersForm
setUp() : denoptim.fitness.descriptors.TanimotoMolSimilarityTest, denoptim.fitness.FitnessExpressionParserTest, denoptim.fitness.FitnessProviderTest
setUpClass() : denoptim.ga.GraphOperationsTest, denoptim.graph.EdgeTest
setupRings() : denoptim.ga.EAUtils
setUpServer() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest
setUseCentroidsAsRepresentativeConformer() : denoptim.programs.fragmenter.FragmenterParameters
setUsed() : denoptim.graph.rings.RingClosingAttractor
setUser() : denoptim.graph.AttachmentPoint
setVariables() : denoptim.fitness.DescriptorForFitness
setVerbosity() : denoptim.programs.RunTimeParameters, denoptim.task.Task
setVertexAsDone() : denoptim.graph.rings.RingSizeManager
setVertexCounterValue() : denoptim.ga.EAUtils
setVertexId() : denoptim.graph.Vertex, denoptim.integration.tinker.TinkerAtom
setVertexList() : denoptim.graph.DGraph
setVertexQuery() : denoptim.utils.GraphEdit
setVertexSpecificEditableAPTable() : denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
setVisibilityAccordingToFitnessProviderSelection() : denoptim.gui.FitnessParametersForm
setVrtSymSetId() : denoptim.fragspace.IdFragmentAndAP
setWorkDirectory() : denoptim.programs.RunTimeParameters
setWorkingDirectory() : denoptim.programs.denovo.GAParameters
setWorkingIn3D() : denoptim.programs.fragmenter.FragmenterParameters
setWorkSpace() : denoptim.task.Task
setXYZ() : denoptim.integration.tinker.TinkerAtom
setXYZIndex() : denoptim.integration.tinker.TinkerAtom
setZeroImplicitHydrogensToAllAtoms() : denoptim.utils.MoleculeUtils
shareAPs() : denoptim.ga.EAUtils
shareBond() : denoptim.graph.rings.CyclicGraphHandler.ClosableConf
shouldSkipClass() : denoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategy, denoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategyNoAPMap
shouldSkipField() : denoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategy, denoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategyNoAPMap
showDialog() : denoptim.gui.GUIModalDialog
showHideLabelsListener() : denoptim.gui.GUIGraphHandler.showHideLabelsListener
showMenu() : denoptim.gui.ScrollableJPupupMenu
showPopup() : denoptim.gui.MoleculeViewPanel
showPromptIfEmpty() : denoptim.gui.ParametersForm
showUnknownKeyWarning() : denoptim.gui.ParametersForm
shutdown() : denoptim.integration.python.Py4JGetawayServer
SingletonFileAccess() : denoptim.files.SingletonFileAccess
size() : denoptim.utils.SizeControlledSet
SizeControlledSet() : denoptim.utils.SizeControlledSet
skewness() : denoptim.utils.StatUtils
SMARTSVisualizationButton() : denoptim.gui.CuttingRulesSelectionDialog.SMARTSVisualizationButton
SocketProvidedDescriptor() : denoptim.fitness.descriptors.SocketProvidedDescriptor
splitInputForThreads() : denoptim.fragmenter.ParallelFragmentationAlgorithm
startConsoleLogger() : denoptim.programs.RunTimeParameters
startGraphFromFragSpaceOrCreationOfEmptyVertex() : denoptim.gui.GUIGraphHandler
startNewGraphFromScaffold() : denoptim.combinatorial.CombinatorialExplorerByLayer
startProgramSpecificLogger() : denoptim.programs.RunTimeParameters
startRandomizer() : denoptim.programs.RunTimeParameters
startServer() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer
stateChanged() : denoptim.gui.GUIGraphHandler.GraphSpinnerChangeEvent, denoptim.gui.GUIVertexInspector.VrtxSpinnerChangeEvent, denoptim.gui.GUIVertexSelector.VrtxSpinnerChangeEvent, denoptim.gui.ParametersForm.RdbFieldChange
StaticLogger() : denoptim.logging.StaticLogger
StaticTaskManager() : denoptim.task.StaticTaskManager
stddev() : denoptim.utils.StatUtils
step() : denoptim.gui.DNPSpringLayout< V, E >
stop() : denoptim.task.StaticTaskManager, denoptim.task.TasksBatchManager
stopAll() : denoptim.task.StaticTaskManager
stopExternalCmdListener() : denoptim.programs.denovo.GARunner
stopLogger() : denoptim.task.ProgramTask
stopProcess() : denoptim.task.ProcessHandler
stopRun() : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.ga.EvolutionaryAlgorithm, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor
stopServer() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer
stopTask() : denoptim.task.Task
storeAllGraphsOfLevel() : denoptim.combinatorial.CEBLUtils
storeCurrentVertexIDs() : denoptim.graph.DGraph
storeEntry() : denoptim.graph.rings.RingClosuresArchive
storeGraphOfLevel() : denoptim.combinatorial.CEBLUtils
storePairsSymmetricRelations() : denoptim.ga.EAUtils
storeValues() : denoptim.gui.GUIPreferencesDialog
StreamGobbler() : denoptim.task.StreamGobbler
submit() : denoptim.task.StaticTaskManager
submitAndWait() : denoptim.task.StaticTaskManager
submitFitnessTask() : denoptim.programs.combinatorial.CEBLParameters
submitSyncParallelBatch() : denoptim.ga.EvolutionaryAlgorithm
submitTask() : denoptim.task.ParallelAsynchronousTaskExecutor
substituteLink() : denoptim.ga.GraphOperations
subtaskHasException() : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.task.ParallelAsynchronousTaskExecutor
subtract() : denoptim.utils.MathUtils
subtractDoneTask() : denoptim.task.StaticTaskManager
subtractDoneTasks() : denoptim.task.StaticTaskManager
sum() : denoptim.utils.MathUtils, denoptim.utils.StatUtils
switchTo2DViewer() : denoptim.gui.VertexViewPanel
switchToEmptyCard() : denoptim.gui.VertexViewPanel
switchToGraphNodeViewer() : denoptim.gui.VertexViewPanel
switchToMolecularViewer() : denoptim.gui.VertexViewPanel
SymmetricAPs() : denoptim.graph.SymmetricAPs
SymmetricSetWithMode() : denoptim.graph.SymmetricSetWithMode
SymmetricVertexes() : denoptim.graph.SymmetricVertexes
symmetryConstraints() : denoptim.fragspace.FragmentSpaceParameters
symmetryFlag() : denoptim.programs.grapheditor.GraphEdParameters