Here is a list of all class members with links to the classes they belong to:

- 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
sample : denoptim.fragmenter.ConformerExtractorTask
satisfiesOptions() : denoptim.programs.fragmenter.CuttingRule
satisfiesRuleOptions : denoptim.programs.fragmenter.MatchedBond
saturateRingClosingAttractor() : denoptim.molecularmodeling.RingClosureTool
saveClustersOfConformerToFile : denoptim.programs.fragmenter.FragmenterParameters
savePopFile() : denoptim.programs.denovo.GAParameters
saveResults() : denoptim.gui.CuttingRulesSelectionDialog, denoptim.gui.MolToGraphParametersDialog
saveRingSystemsAsTemplatesNonScaff : denoptim.programs.denovo.GAParameters
saveRingSystemsAsTemplatesScaffolds : denoptim.programs.denovo.GAParameters
saveRingSystemsFitnessThreshold : denoptim.programs.denovo.GAParameters
saveUnsavedChanges() : denoptim.gui.GUIGraphHandler, denoptim.gui.GUIVertexInspector
sb : denoptim.task.StreamGobbler
SCAF : denoptim.gui.GraphViewerPanel.JVertexType
SCAFFOLD : denoptim.graph.Vertex.BBType
scaffoldingPolicy : denoptim.programs.fragmenter.FragmenterParameters
scaffoldLib : denoptim.fragspace.FragmentSpace
scaffoldLibFile : denoptim.fragspace.FragmentSpaceParameters
scalar() : denoptim.utils.MathUtils
scale() : denoptim.utils.MathUtils
scaling : denoptim.gui.GraphViewerPanel
scheme : denoptim.utils.AtomOrganizer
ScrollableJPupupMenu() : denoptim.gui.ScrollableJPupupMenu
scrollerSize : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
scrollPanel : denoptim.gui.GUIGraphHandler.ConfigTemplateDialog
scrollPanelCPMap : denoptim.gui.CompatibilityMatrixForm
scs : denoptim.ga.EvolutionaryAlgorithm
sdfFile : denoptim.graph.Candidate
SDG : denoptim.utils.MoleculeUtils
searchAPClass() : denoptim.gui.CompatibilityMatrixForm
searchRingFusionSites() : denoptim.ga.EAUtils
SEED : denoptim.graph.TemplateTest
seed : denoptim.programs.denovo.GAParameters, denoptim.utils.ConnectedLigand
selectBasedOnFitness() : denoptim.ga.EAUtils
SELECTEDBACKGROUND : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine, denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken
selectFragmentsFromClosableChains() : denoptim.graph.rings.RingClosureParameters
selectFragsFromCC : denoptim.graph.rings.RingClosureParameters
selectivePressure : denoptim.programs.denovo.GAParameters
selectNonScaffoldNonCapVertex() : denoptim.ga.EAUtils
sendToFitnessProvider() : denoptim.combinatorial.GraphBuildingTask
SEP : denoptim.fitness.FitnessExpressionParserTest, denoptim.fitness.FitnessProviderTest, denoptim.fragmenter.ParallelFragmentationAlgorithmTest, denoptim.fragspace.FragmentSpaceTest, denoptim.ga.EAUtilsTest, denoptim.graph.TemplateTest, denoptim.io.DenoptimIOTest, denoptim.main.MainTest, denoptim.programs.denovo.GAParametersTest, denoptim.task.Task, denoptim.utils.SizeControlledSetTest
SEPARATORAPPROPAAP : denoptim.constants.DENOPTIMConstants
SEPARATORAPPROPAPS : denoptim.constants.DENOPTIMConstants
SEPARATORAPPROPATMS : denoptim.constants.DENOPTIMConstants
SEPARATORAPPROPSCL : denoptim.constants.DENOPTIMConstants
SEPARATORAPPROPXYZ : denoptim.constants.DENOPTIMConstants
serFileAlreadyUsed() : denoptim.combinatorial.CheckPoint
serFromChkRestart : denoptim.combinatorial.CombinatorialExplorerByLayer
SERGFILENAMEEXT : denoptim.constants.DENOPTIMConstants
SERGFILENAMEROOT : denoptim.constants.DENOPTIMConstants
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
serialVersionUID : denoptim.exception.DENOPTIMException, denoptim.files.UndetectedFileFormatException, denoptim.ga.Population, denoptim.graph.APMapping, denoptim.graph.APTreeMap, denoptim.graph.rings.RingClosingConformations, denoptim.graph.SymmetricAPs, denoptim.graph.SymmetricSet< T >, denoptim.graph.SymmetricVertexes, denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine, denoptim.gui.CompatibilityMatrixForm, denoptim.gui.CuttingRulesSelectionDialog.MyJSVGCanvas, denoptim.gui.CuttingRulesSelectionDialog, denoptim.gui.FitnessParametersForm, denoptim.gui.FragmentViewPanel, denoptim.gui.FSEParametersForm, denoptim.gui.FSParametersForm, denoptim.gui.FSParamsDialog, denoptim.gui.GAParametersForm, denoptim.gui.GraphVertexMolViewerPanel, denoptim.gui.GraphViewerPanel, denoptim.gui.GUIAPClassDefinitionDialog, denoptim.gui.GUICardPanel, denoptim.gui.GUICompatibilityMatrixTab, denoptim.gui.GUIEmptyVertexMaker, denoptim.gui.GUIGraphHandler, denoptim.gui.GUIInspectFSERun, denoptim.gui.GUIInspectGARun, denoptim.gui.GUIMainPanel, denoptim.gui.GUIModalDialog, denoptim.gui.GUIPreferencesDialog, denoptim.gui.GUIPrepare, denoptim.gui.GUIPrepareFitnessRunner.InputForm, denoptim.gui.GUIPrepareFitnessRunner, denoptim.gui.GUIPrepareFSERun, denoptim.gui.GUIPrepareGARun, denoptim.gui.GUITextReader, denoptim.gui.GUIVertexInspector, denoptim.gui.GUIVertexSelector, denoptim.gui.HomePanel, denoptim.gui.JmolPanel, denoptim.gui.MainToolBar, denoptim.gui.MoleculeViewPanel, denoptim.gui.MolToGraphParametersDialog, denoptim.gui.ParametersForm, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel, denoptim.gui.VertexViewPanel, denoptim.integration.tinker.TinkerException, denoptim.logging.Monitor, denoptim.main.CLIOptions
server : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer, denoptim.fitness.descriptors.SocketProvidedDescriptorTest, denoptim.integration.python.Py4JGetawayServer
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
settings : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.fragmenter.ConformerExtractorTask, denoptim.fragmenter.FragmentClusterer, denoptim.fragmenter.FragmenterTask, denoptim.fragmenter.ParallelConformerExtractionAlgorithm, denoptim.fragmenter.ParallelFragmentationAlgorithm, denoptim.fragspace.FragmentSpace, denoptim.fragspace.FragsCombinationIterator, denoptim.ga.EvolutionaryAlgorithm, denoptim.ga.Population, denoptim.graph.rings.CyclicGraphHandler, denoptim.graph.rings.RandomCombOfRingsIterator, denoptim.graph.rings.RingClosure, denoptim.graph.rings.RingClosuresArchive, denoptim.graph.rings.RingSizeManager, denoptim.molecularmodeling.MultiMolecularModelBuilder, denoptim.molecularmodeling.RingClosureTool, denoptim.programs.fitnessevaluator.FPRunner, denoptim.programs.genetweeker.GeneOpsRunner
setTinkerTypes() : denoptim.integration.tinker.TinkerUtils, denoptim.molecularmodeling.RingClosureTool
setTurningPoint() : denoptim.graph.rings.ClosableChain
setUID() : denoptim.graph.Candidate
SETUNFORMATTEDINPUTTXTCOLOR : denoptim.gui.ParametersForm
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
sfa : denoptim.files.SingletonFileAccess
shareAPs() : denoptim.ga.EAUtils
shareBond() : denoptim.graph.rings.CyclicGraphHandler.ClosableConf
shortName : denoptim.fitness.DescriptorForFitness
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
showLegenInEvolutionPlot : denoptim.gui.GUIPreferences
showLegenInMonitorPlot : denoptim.gui.GUIPreferences
showMenu() : denoptim.gui.ScrollableJPupupMenu
showPopup() : denoptim.gui.MoleculeViewPanel
showPromptIfEmpty() : denoptim.gui.ParametersForm
showUnknownKeyWarning() : denoptim.gui.ParametersForm
shutdown() : denoptim.integration.python.Py4JGetawayServer
sibling : denoptim.ga.OffspringEvaluationTask
SIGMA : denoptim.gui.GAParametersForm.ProbabilityFuncitonShape
SINGLE : denoptim.graph.Edge.BondType
SingletonFileAccess() : denoptim.files.SingletonFileAccess
size() : denoptim.utils.SizeControlledSet
SizeControlledSet() : denoptim.utils.SizeControlledSet
sizeUnimodalPop : denoptim.programs.fragmenter.FragmenterParameters
skewness() : denoptim.utils.StatUtils
smarts : denoptim.fitness.Variable, denoptim.fragmenter.BridgeHeadFindingRule
smartsAtm0 : denoptim.programs.fragmenter.CuttingRule
smartsAtm1 : denoptim.programs.fragmenter.CuttingRule
smartsBnd : denoptim.programs.fragmenter.CuttingRule
SMARTSVisualizationButton() : denoptim.gui.CuttingRulesSelectionDialog.SMARTSVisualizationButton
SMGEN : denoptim.utils.MoleculeUtils
smiles : denoptim.graph.Candidate
SMILESTAG : denoptim.constants.DENOPTIMConstants
smiTo3dResolver : denoptim.gui.GUIPreferences
socket : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.RequestHandler
SocketProvidedDescriptor() : denoptim.fitness.descriptors.SocketProvidedDescriptor
solution : denoptim.integration.tinker.TinkerException
sorted : denoptim.gui.GUIInspectFSERun
sortOrderDecreasing : denoptim.programs.denovo.GAParameters
sp : denoptim.fitness.FitnessExpressionParserTest, denoptim.fitness.FitnessProviderTest
splitInputForThreads() : denoptim.fragmenter.ParallelFragmentationAlgorithm
spnPar12 : denoptim.gui.GAParametersForm
spnPar13 : denoptim.gui.GAParametersForm
spnPar14 : denoptim.gui.GAParametersForm
spnParCrowd2 : denoptim.gui.GAParametersForm
spnParCrowd3 : denoptim.gui.GAParametersForm
spnParCrowd4 : denoptim.gui.GAParametersForm
spnParMolSz2 : denoptim.gui.GAParametersForm
spnParMolSz3 : denoptim.gui.GAParametersForm
spnParMolSz4 : denoptim.gui.GAParametersForm
spnRingSysTmpl : denoptim.gui.GAParametersForm
src : denoptim.graph.rings.RingClosingAttractor
srcAP : denoptim.graph.Edge
srcAPC : denoptim.graph.EdgeQuery, denoptim.gui.GraphViewerPanel.JEdge
srcAPClass : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine, denoptim.gui.CompatibilityMatrixForm.TrgRemovalListener
srcAPID : denoptim.graph.EdgeQuery, denoptim.gui.GraphViewerPanel.JEdge
srcClassName : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
srcClassNameScroller : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
srcFolder : denoptim.gui.GUIInspectGARun
srcVertexId : denoptim.graph.EdgeQuery
standardOutput : denoptim.task.ProcessHandler
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
stopped : denoptim.ga.EvolutionaryAlgorithm
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
STOREDVID : denoptim.constants.DENOPTIMConstants
storeEntry() : denoptim.graph.rings.RingClosuresArchive
storeGraphOfLevel() : denoptim.combinatorial.CEBLUtils
storePairsSymmetricRelations() : denoptim.ga.EAUtils
storeValues() : denoptim.gui.GUIPreferencesDialog
StreamGobbler() : denoptim.task.StreamGobbler
strFieldSize : denoptim.gui.CuttingRulesSelectionDialog, denoptim.gui.GUIAPClassDefinitionDialog, denoptim.gui.GUIPreferencesDialog, denoptim.gui.ParametersForm
strokes : denoptim.gui.GUIInspectGARun
structures : denoptim.fragmenter.ParallelFragmentationAlgorithm
structuresFile : denoptim.programs.fragmenter.FragmenterParameters
strXoverSelectionMode : denoptim.programs.denovo.GAParameters
subClass : denoptim.graph.APClass
SUBGRAPH : denoptim.utils.CrossoverType
subGraphA : denoptim.ga.XoverSite
subGraphB : denoptim.ga.XoverSite
submit() : denoptim.task.StaticTaskManager
submitAndWait() : denoptim.task.StaticTaskManager
submitFitnessTask() : denoptim.programs.combinatorial.CEBLParameters
submitSyncParallelBatch() : denoptim.ga.EvolutionaryAlgorithm
submitTask() : denoptim.task.ParallelAsynchronousTaskExecutor
submitted : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.ga.EvolutionaryAlgorithm, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor
submittedAndFutures : denoptim.combinatorial.CombinatorialExplorerByLayer
substituteLink() : denoptim.ga.GraphOperations
substructuressmarts : denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
subtaskHasException() : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.task.ParallelAsynchronousTaskExecutor
subToFutureMap : denoptim.task.StaticTaskManager
subtract() : denoptim.utils.MathUtils
subtractDoneTask() : denoptim.task.StaticTaskManager
subtractDoneTasks() : denoptim.task.StaticTaskManager
sum() : denoptim.utils.MathUtils, denoptim.utils.StatUtils
switchbleByVertexType : denoptim.gui.VertexViewPanel
switchTo2DViewer() : denoptim.gui.VertexViewPanel
switchToEmptyCard() : denoptim.gui.VertexViewPanel
switchToGraphNodeViewer() : denoptim.gui.VertexViewPanel
switchToMolecularViewer() : denoptim.gui.VertexViewPanel
SYM_ID : denoptim.graph.DGraph
symItems : denoptim.graph.SymmetricSetWithMode
symmConstraints : denoptim.fragspace.FragmentSpace
symmConstraintsMap : denoptim.fragspace.FragmentSpaceParameters
SymmetricAPs() : denoptim.graph.SymmetricAPs
SymmetricSetWithMode() : denoptim.graph.SymmetricSetWithMode
symmetricSubProbability : denoptim.programs.denovo.GAParameters
SymmetricVertexes() : denoptim.graph.SymmetricVertexes
symmetry : denoptim.programs.grapheditor.GraphEdParameters
symmetryConstraints : denoptim.fragspace.FragmentSpaceParameters
symmetryFlag() : denoptim.programs.grapheditor.GraphEdParameters
symVertices : denoptim.graph.DGraph
sz : denoptim.graph.rings.RingSizeManager
szB : denoptim.gui.GraphViewerPanel.VertexShapePaintTransformer
szM : denoptim.gui.GraphViewerPanel.VertexShapePaintTransformer
szS : denoptim.gui.GraphViewerPanel.VertexShapePaintTransformer
szTolTip : denoptim.gui.GUIGraphHandler.ConfigTemplateDialog.TemplateConfiguration