- r -

randomizer : denoptim.molecularmodeling.ThreeDimTreeBuilder
randomPosition : denoptim.gui.DNPSpringLayout< V, E >.RecreateKnownPositions
rbtLevelGrowth : denoptim.gui.GAParametersForm
rbtMolSzGrowth : denoptim.gui.GAParametersForm
RC_PARAMS : denoptim.programs.RunTimeParameters.ParametersType
RCAAPCLASSSET : denoptim.graph.rings.RingClosingAttractor
RCAAPCMAP : denoptim.graph.rings.RingClosingAttractor
RCACLASSMINUS : denoptim.graph.APClass
RCACLASSNEUTRAL : denoptim.graph.APClass
RCACLASSPLUS : denoptim.graph.APClass
RCALABELPERAPCLASS : denoptim.graph.rings.RingClosingAttractor
RCAPROPAPCTORCA : denoptim.constants.DENOPTIMConstants
RCAPROPCHORDBNDTYP : denoptim.constants.DENOPTIMConstants
RCAPROPRINGUSER : denoptim.constants.DENOPTIMConstants
rcArchive : denoptim.graph.rings.RingClosureParameters
RCATYPEMAP : denoptim.graph.rings.RingClosingAttractor
rcbEvoChartLegend : denoptim.gui.GUIPreferencesDialog
rcbIsRCV : denoptim.gui.GUIEmptyVertexMaker
rcbMntChartLegend : denoptim.gui.GUIPreferencesDialog
rcc : denoptim.graph.rings.PathSubGraph
rccFolder : denoptim.graph.rings.RingClosureParameters
rccIndex : denoptim.graph.rings.RingClosureParameters
rcCompatMap : denoptim.fragspace.FragmentSpace
rcCompMatrixFile : denoptim.fragspace.FragmentSpaceParameters
rccsPerChainId : denoptim.graph.rings.RingClosuresArchive
rceMode : denoptim.graph.rings.RingClosureParameters
rcMaxDot : denoptim.graph.rings.RingClosureParameters
rcTolDist : denoptim.graph.rings.RingClosureParameters
RCV : denoptim.gui.GraphViewerPanel.JVertexType
rcvs : denoptim.fragspace.FragmentSpace
rdb3dTrees : denoptim.gui.FitnessParametersForm
rdbAddH : denoptim.gui.GAParametersForm
rdbEmbTmpl : denoptim.gui.MolToGraphParametersDialog
rdbFieldChange : denoptim.gui.ParametersForm
rdbIntOrExt : denoptim.gui.FitnessParametersForm
rdbPar10 : denoptim.gui.FSParametersForm
rdbPar12 : denoptim.gui.FSParametersForm
rdbPar24 : denoptim.gui.FSParametersForm
rdbPar28 : denoptim.gui.FSParametersForm
rdbPar5 : denoptim.gui.GAParametersForm
rdbPar5a : denoptim.gui.GAParametersForm
rdbPreFitnessUIDCheck : denoptim.gui.FitnessParametersForm
rdbRingTmplsFrags : denoptim.gui.GAParametersForm
rdbRingTmplsScaff : denoptim.gui.GAParametersForm
rdbSrcOrNew : denoptim.gui.FitnessParametersForm, denoptim.gui.FSEParametersForm, denoptim.gui.FSParametersForm, denoptim.gui.GAParametersForm
rdbUseCustom : denoptim.gui.CuttingRulesSelectionDialog
rdbUseDefault : denoptim.gui.CuttingRulesSelectionDialog
reader : denoptim.json.DENOPTIMgson
reason : denoptim.graph.EdgeTest, denoptim.graph.VertexTest
recCount : denoptim.graph.rings.CyclicGraphHandler
RECENTFILESLIST : denoptim.constants.DENOPTIMConstants
recNum : denoptim.utils.DummyAtomHandler
recordMateSelection : denoptim.programs.denovo.GAParameters
referenceFingerprint : denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
referenceX : denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel
referenceY : denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel
refToThis : denoptim.gui.CuttingRulesSelectionDialog.SMARTSVisualizationButton
REFTOVERTEXKERNEL : denoptim.graph.simplified.Node
rejectedAPClassCombinations : denoptim.programs.fragmenter.FragmenterParameters
rejectedAPClasses : denoptim.programs.fragmenter.FragmenterParameters
rejectedDescriptors : denoptim.fitness.DescriptorUtils
rejectedElements : denoptim.programs.fragmenter.FragmenterParameters
REMOVETRGAPC : denoptim.gui.CompatibilityMatrixForm
renderer : denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel
REPLACECHILD : denoptim.utils.GraphEdit.EditTask
replacementStrategy : denoptim.programs.denovo.GAParameters
replaceWorstPopMember : denoptim.ga.OffspringEvaluationTask
reportTimeoutIncidents : denoptim.graph.FragmentIsomorphismInspector
reqElInRings : denoptim.graph.rings.RingClosureParameters
requireCompleteRingclosure : denoptim.graph.rings.RingClosureParameters
requiredAPs : denoptim.graph.Template
resolver : denoptim.fitness.FitnessExpressionParser.CustomVariableDefiningContext, denoptim.fitness.FitnessExpressionParser.VariableDefiningContext
restartFromChkPt : denoptim.combinatorial.CombinatorialExplorerByLayer
result : denoptim.gui.GUIModalDialog, denoptim.task.FitnessTask
resultId : denoptim.fitness.DescriptorForFitness
results : denoptim.fragmenter.ConformerExtractorTask, denoptim.fragmenter.FragmenterTask, denoptim.io.IteratingAtomContainerReader, denoptim.task.ParallelAsynchronousTaskExecutor
revChainID : denoptim.graph.rings.PathSubGraph
rightDownPanel : denoptim.gui.GUIInspectGARun
rightPanel : denoptim.gui.GUIInspectFSERun, denoptim.gui.GUIInspectGARun
rightUpPanel : denoptim.gui.GUIInspectGARun
RING : denoptim.graph.GraphPattern
ringClosabCondAsSMARTS : denoptim.graph.rings.RingClosureParameters
ringSizeBias : denoptim.graph.rings.RingClosureParameters, denoptim.graph.rings.RingSizeManager
ringUser : denoptim.graph.rings.RingClosingAttractor
rndSeed : denoptim.utils.Randomizer
rng : denoptim.fragmenter.FragmentClustererTest, denoptim.fragspace.FragmentSpaceTest, denoptim.ga.GraphOperationsTest, denoptim.graph.TemplateTest, denoptim.programs.RunTimeParameters
rootGraph : denoptim.fragspace.FragsCombinationIterator
rootGraphs : denoptim.programs.combinatorial.CEBLParameters
rootGraphsFile : denoptim.programs.combinatorial.CEBLParameters
rootId : denoptim.combinatorial.CheckPoint, denoptim.combinatorial.GraphBuildingTask
rotatableBnds : denoptim.molecularmodeling.ChemicalObjectModel
rotBndsFile : denoptim.fragspace.FragmentSpaceParameters
rsKeyFile : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
rsKeyFileParams : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
rsPssrotFile : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
rsPssrotParams_Init : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
rsPssrotParams_Rest : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
RULAPC1 : denoptim.fragspace.FragmentSpaceTest
RULAPC2 : denoptim.fragspace.FragmentSpaceTest
RULAPC3 : denoptim.fragspace.FragmentSpaceTest
RULAPC4 : denoptim.fragspace.FragmentSpaceTest
RULAPC5 : denoptim.fragspace.FragmentSpaceTest
RULAPC6 : denoptim.fragspace.FragmentSpaceTest
RULAPCC1 : denoptim.fragspace.FragmentSpaceTest
RULAPCC2 : denoptim.fragspace.FragmentSpaceTest
RULAPCS : denoptim.fragspace.FragmentSpaceTest
rule : denoptim.graph.APClass, denoptim.programs.fragmenter.MatchedBond
ruleName : denoptim.fragmenter.BridgeHeadFindingRule, denoptim.programs.fragmenter.CuttingRule
run : denoptim.main.CLIOptions
runFitnessTask : denoptim.programs.combinatorial.CEBLParameters
runner : denoptim.programs.fitnessevaluator.FitnessRunner
RUNTIME : denoptim.utils.GeneralUtils
runType : denoptim.main.Behavior