- s -

sample : denoptim.fragmenter.ConformerExtractorTask
satisfiesRuleOptions : denoptim.programs.fragmenter.MatchedBond
saveClustersOfConformerToFile : denoptim.programs.fragmenter.FragmenterParameters
saveRingSystemsAsTemplatesNonScaff : denoptim.programs.denovo.GAParameters
saveRingSystemsAsTemplatesScaffolds : denoptim.programs.denovo.GAParameters
saveRingSystemsFitnessThreshold : denoptim.programs.denovo.GAParameters
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
scaling : denoptim.gui.GraphViewerPanel
scheme : denoptim.utils.AtomOrganizer
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
SEED : denoptim.graph.TemplateTest
seed : denoptim.programs.denovo.GAParameters, denoptim.utils.ConnectedLigand
SELECTEDBACKGROUND : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine, denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken
selectFragsFromCC : denoptim.graph.rings.RingClosureParameters
selectivePressure : denoptim.programs.denovo.GAParameters
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
serFromChkRestart : denoptim.combinatorial.CombinatorialExplorerByLayer
SERGFILENAMEEXT : denoptim.constants.DENOPTIMConstants
SERGFILENAMEROOT : denoptim.constants.DENOPTIMConstants
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
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
SETUNFORMATTEDINPUTTXTCOLOR : denoptim.gui.ParametersForm
sfa : denoptim.files.SingletonFileAccess
shortName : denoptim.fitness.DescriptorForFitness
showLegenInEvolutionPlot : denoptim.gui.GUIPreferences
showLegenInMonitorPlot : denoptim.gui.GUIPreferences
sibling : denoptim.ga.OffspringEvaluationTask
SIGMA : denoptim.gui.GAParametersForm.ProbabilityFuncitonShape
SINGLE : denoptim.graph.Edge.BondType
sizeUnimodalPop : denoptim.programs.fragmenter.FragmenterParameters
smarts : denoptim.fitness.Variable, denoptim.fragmenter.BridgeHeadFindingRule
smartsAtm0 : denoptim.programs.fragmenter.CuttingRule
smartsAtm1 : denoptim.programs.fragmenter.CuttingRule
smartsBnd : denoptim.programs.fragmenter.CuttingRule
SMGEN : denoptim.utils.MoleculeUtils
smiles : denoptim.graph.Candidate
SMILESTAG : denoptim.constants.DENOPTIMConstants
smiTo3dResolver : denoptim.gui.GUIPreferences
socket : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.RequestHandler
solution : denoptim.integration.tinker.TinkerException
sorted : denoptim.gui.GUIInspectFSERun
sortOrderDecreasing : denoptim.programs.denovo.GAParameters
sp : denoptim.fitness.FitnessExpressionParserTest, denoptim.fitness.FitnessProviderTest
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
stopped : denoptim.ga.EvolutionaryAlgorithm
STOREDVID : denoptim.constants.DENOPTIMConstants
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
submitted : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.ga.EvolutionaryAlgorithm, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor
submittedAndFutures : denoptim.combinatorial.CombinatorialExplorerByLayer
substructuressmarts : denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
subToFutureMap : denoptim.task.StaticTaskManager
switchbleByVertexType : denoptim.gui.VertexViewPanel
SYM_ID : denoptim.graph.DGraph
symItems : denoptim.graph.SymmetricSetWithMode
symmConstraints : denoptim.fragspace.FragmentSpace
symmConstraintsMap : denoptim.fragspace.FragmentSpaceParameters
symmetricSubProbability : denoptim.programs.denovo.GAParameters
symmetry : denoptim.programs.grapheditor.GraphEdParameters
symmetryConstraints : denoptim.fragspace.FragmentSpaceParameters
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