- r -

RandomCombOfRingsIterator() : denoptim.graph.rings.RandomCombOfRingsIterator
Randomizer() : denoptim.utils.Randomizer
randomlyChooseOne() : denoptim.utils.Randomizer
readAllAPClasses() : denoptim.io.DenoptimIO
readAllAtomContainers() : denoptim.io.DenoptimIO
readBridgeHesFindingRules() : denoptim.io.DenoptimIO
readCandidateFromFile() : denoptim.ga.EAUtils
readCandidates() : denoptim.io.DenoptimIO
readCompatibilityMatrix() : denoptim.io.DenoptimIO
readCSDFormulae() : denoptim.io.DenoptimIO
readCuttingRules() : denoptim.io.DenoptimIO
readDENOPTIMData() : denoptim.io.DenoptimIO
readDENOPTIMGraphEditFromFile() : denoptim.io.DenoptimIO
readDENOPTIMGraphsFromFile() : denoptim.io.DenoptimIO
readDENOPTIMGraphsFromJSONFile() : denoptim.io.DenoptimIO
readDENOPTIMGraphsFromSDFile() : denoptim.io.DenoptimIO
readDENOPTIMGraphsFromTxtFile() : denoptim.io.DenoptimIO
readDENOPTIMVertexesFromJSONFile() : denoptim.io.DenoptimIO
readDENOPTIMVertexesFromSDFile() : denoptim.io.DenoptimIO
readGenerationFromSummary() : denoptim.io.DenoptimIO
readGraphFromSDFileIAC() : denoptim.io.DenoptimIO
readGraphsFromFile() : denoptim.gui.GUIGraphHandler
readInputGraphs() : denoptim.programs.grapheditor.GraphEdParameters
readKeyFileParams() : denoptim.molecularmodeling.MMBuilderUtils
readLibraryOfRCCs() : denoptim.graph.rings.RingClosuresArchive
readLightWeightCandidate() : denoptim.io.DenoptimIO
readList() : denoptim.io.DenoptimIO
readOneGeneration() : denoptim.gui.GUIInspectGARun
readParameterFile() : denoptim.programs.RunTimeParameters
readParameterLine() : denoptim.programs.RunTimeParameters
readPopulationMemberPathnames() : denoptim.io.DenoptimIO
readPopulationMembersTraces() : denoptim.io.DenoptimIO
readPopulationProps() : denoptim.io.DenoptimIO
readPSSROTOutput() : denoptim.integration.tinker.TinkerUtils
readPSSROTParams() : denoptim.integration.tinker.TinkerUtils
readRCCompatibilityMatrix() : denoptim.io.DenoptimIO
readRecentFilesMap() : denoptim.io.DenoptimIO
readSDFFile() : denoptim.io.DenoptimIO
readSDFProperties() : denoptim.io.DenoptimIO
readText() : denoptim.io.DenoptimIO
readTinkerAtomTypes() : denoptim.integration.tinker.TinkerUtils
readTinkerIC() : denoptim.integration.tinker.TinkerUtils
readTinkerXYZ() : denoptim.integration.tinker.TinkerUtils
readUID() : denoptim.ga.EAUtils
readVertexes() : denoptim.io.DenoptimIO
readYesNoTrueFalse() : denoptim.programs.RunTimeParameters
reassignSymmetricLabels() : denoptim.graph.DGraph
rebuildBranch() : denoptim.ga.GraphOperations
RecentFileItem() : denoptim.gui.MainToolBar.RecentFileItem
recordMateSelection() : denoptim.programs.denovo.GAParameters
RecreateKnownPositions() : denoptim.gui.DNPSpringLayout< V, E >.RecreateKnownPositions
recursiveCombiner() : denoptim.fragspace.FragmentSpaceUtils
registerRCV() : denoptim.fragspace.FragmentSpace
RelatedAPPair() : denoptim.graph.RelatedAPPair
remove() : denoptim.ga.Population, denoptim.ga.Population.XoverSitesAmongCandidates, denoptim.graph.APTreeMap
removeActiveTab() : denoptim.gui.MainToolBar
removeAll() : denoptim.fragmenter.DynamicCentroidCluster, denoptim.ga.Population
removeAP() : denoptim.graph.Fragment
removeAtom() : denoptim.graph.Fragment
removeAtoms() : denoptim.graph.Fragment, denoptim.gui.GUIVertexInspector
removeBond() : denoptim.graph.Fragment
removeBranchStartingAt() : denoptim.graph.DGraph
removeCandidates() : denoptim.ga.EvolutionaryAlgorithm
removeCappingGroups() : denoptim.graph.DGraph
removeCappingGroupsFromChilds() : denoptim.graph.DGraph
removeCappingGroupsOn() : denoptim.graph.DGraph
removeCard() : denoptim.gui.GUIMainPanel
removeCardActionListener() : denoptim.gui.GUICardPanel.removeCardActionListener
removeChainUpToBranching() : denoptim.graph.DGraph
removeCurrentDnGraph() : denoptim.gui.GUIGraphHandler
removeCurrentVrtx() : denoptim.gui.GUIVertexInspector
removeDummy() : denoptim.utils.DummyAtomHandler
removeDummyInHapto() : denoptim.utils.DummyAtomHandler
removeEdge() : denoptim.graph.DGraph
removeMutationType() : denoptim.graph.Vertex
removeNestedGraphViewer() : denoptim.gui.GraphVertexMolViewerPanel
removeOrphanBranchStartingAt() : denoptim.graph.DGraph
removeProjectionOfInnerAP() : denoptim.graph.Template
removeProperty() : denoptim.graph.Vertex
removeRCA() : denoptim.utils.MoleculeUtils
removeRing() : denoptim.graph.DGraph
removeSingleVertexAndWeld() : denoptim.graph.DGraph
removeSymmetryRedundance() : denoptim.graph.DGraph
removeSymmetryRedundantIds() : denoptim.graph.DGraph
removeSymmetrySet() : denoptim.graph.DGraph
removeUpdate() : denoptim.gui.ParametersForm.FieldListener
removeUsedRCA() : denoptim.utils.MoleculeUtils
removeVertex() : denoptim.graph.DGraph, denoptim.graph.Ring
removeVertexAndWeld() : denoptim.graph.DGraph
renderAsSelected() : denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken
renderdAsSelected() : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
renderForLackOfFragSpace() : denoptim.gui.ILoadFragSpace
renderForPresenceOfFragSpace() : denoptim.gui.ILoadFragSpace
renderIfMatches() : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
renderMolVieverToNeedUpdate() : denoptim.gui.GraphVertexMolViewerPanel
renderViewWithoutSelectedItems() : denoptim.gui.GUIInspectFSERun, denoptim.gui.GUIInspectGARun
renderViewWithSelectedItem() : denoptim.gui.GUIInspectFSERun, denoptim.gui.GUIInspectGARun
renumberAPs() : denoptim.gui.GraphViewerPanel
renumberGraphVertices() : denoptim.graph.DGraph
renumberVerticesGetMap() : denoptim.graph.DGraph
reorderStartingFrom() : denoptim.utils.AtomOrganizer
reorderVertexList() : denoptim.graph.DGraph
replaceHatomWithAP() : denoptim.ga.EAUtilsTest
replaceSingleSubGraph() : denoptim.graph.DGraph
replaceSubGraph() : denoptim.graph.DGraph
replaceUnusedRCVsWithCapps() : denoptim.graph.DGraph
replaceVertex() : denoptim.graph.DGraph, denoptim.graph.Ring
reportError() : denoptim.main.Main
reportForDebug() : denoptim.graph.rings.RingClosureFinder
RequestHandler() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest.RequestHandler
resetFragViewerCardDeck() : denoptim.gui.GraphVertexMolViewerPanel
resetGraphOwner() : denoptim.graph.Vertex
resetUniqueGraphCounter() : denoptim.utils.GraphUtils
resetUniqueMoleculeCounter() : denoptim.utils.GraphUtils
resetUniqueVertexCounter() : denoptim.utils.GraphUtils
resetView() : denoptim.gui.GUIInspectFSERun
resetViewInPlotByLevel() : denoptim.gui.GUIInspectFSERun
resetViewInPlotOfSortedList() : denoptim.gui.GUIInspectFSERun
restartFromCheckPoint() : denoptim.programs.combinatorial.CEBLParameters
retainAll() : denoptim.ga.Population
Ring() : denoptim.graph.Ring
RingClosingAttractor() : denoptim.graph.rings.RingClosingAttractor
RingClosingConformations() : denoptim.graph.rings.RingClosingConformations
RingClosure() : denoptim.graph.rings.RingClosure
RingClosureParameters() : denoptim.graph.rings.RingClosureParameters
RingClosuresArchive() : denoptim.graph.rings.RingClosuresArchive
RingClosureTool() : denoptim.molecularmodeling.RingClosureTool
RingSizeManager() : denoptim.graph.rings.RingSizeManager
rotatedVectorWAxisAngle() : denoptim.utils.CartesianSpaceUtils
roundValue() : denoptim.utils.MathUtils
run() : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer, denoptim.fitness.descriptors.SocketProvidedDescriptorTest.RequestHandler, denoptim.ga.EvolutionaryAlgorithm, denoptim.ga.ExternalCmdsListener, denoptim.gui.GUI, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor, denoptim.task.StaticTaskManager.ShutDownHook, denoptim.task.StreamGobbler
runExternalFitness() : denoptim.task.FitnessTask
runFitnessProvider() : denoptim.task.FitnessTask
runInternalFitness() : denoptim.task.FitnessTask
runMutation() : denoptim.programs.genetweeker.GeneOpsRunner
runProcess() : denoptim.task.ProcessHandler
runProcessInBASH() : denoptim.task.ProcessHandler
runProgram() : denoptim.programs.combinatorial.FragSpaceExplorer, denoptim.programs.denovo.GARunner, denoptim.programs.fitnessevaluator.FitnessRunner, denoptim.programs.fragmenter.Fragmenter, denoptim.programs.genetweeker.GeneOpsRunner, denoptim.programs.grapheditor.GraphEditor, denoptim.programs.graphlisthandler.GraphListsHandler, denoptim.programs.isomorphism.Isomorphism, denoptim.programs.mol2graph.Mol2Graph, denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder, denoptim.task.ProgramTask
runProgramTask() : denoptim.main.Main
RunTimeParameters() : denoptim.programs.RunTimeParameters
runXOver() : denoptim.programs.genetweeker.GeneOpsRunner