- c -

calcDate() : denoptim.logging.HTMLLogFormatter
calculate() : denoptim.fitness.descriptors.SocketProvidedDescriptor, denoptim.fitness.descriptors.TanimotoMolSimilarity, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure
calculateAngle() : denoptim.utils.MathUtils
calculateCentroid() : denoptim.utils.MoleculeUtils
calculateCompatibilityOfAllRCAPairs() : denoptim.graph.rings.RingSizeManager
calculateDescriptors() : denoptim.graph.rings.RingClosure
call() : denoptim.combinatorial.GraphBuildingTask, denoptim.fragmenter.ConformerExtractorTask, denoptim.fragmenter.FragmenterTask, denoptim.ga.OffspringEvaluationTask, denoptim.programs.fitnessevaluator.FitnessEvaluationTask, denoptim.task.ProgramTask
canBeUsedForRingFusion() : denoptim.ga.EAUtils
canCoexistWith() : denoptim.graph.rings.CyclicGraphHandler.ClosableConf
Candidate() : denoptim.graph.Candidate
CandidateLW() : denoptim.graph.CandidateLW
canWriteAndReadTo() : denoptim.files.FileUtils
CEBLParameters() : denoptim.programs.combinatorial.CEBLParameters
centerGraphLayout() : denoptim.gui.GraphViewerPanel
centroidOf() : denoptim.utils.MathUtils
ChainLink() : denoptim.graph.rings.ChainLink
changeBy() : denoptim.logging.Monitor
changedUpdate() : denoptim.gui.ParametersForm.FieldListener
changeSignOfVertexID() : denoptim.graph.DGraph
checkAndAddXoverSites() : denoptim.ga.GraphOperations
checkAvailNT() : denoptim.graph.AttachmentPointTest
checkChelatesGraph() : denoptim.graph.rings.CyclicGraphHandler
checkClosabilityOfInterdependentPaths() : denoptim.graph.rings.CyclicGraphHandler
checkConsistency() : denoptim.graph.DGraph
checkElementalAnalysisAgainstFormula() : denoptim.fragmenter.FragmenterTools
checkExists() : denoptim.files.FileUtils
checkForException() : denoptim.ga.EvolutionaryAlgorithm
checkGetEdgeUserThroughput() : denoptim.graph.AttachmentPointTest
checkIdentityOfEmbeddedAP() : denoptim.graph.AttachmentPointTest
checkInput() : denoptim.gui.GUIPreferencesDialog
checkInterdependentChains() : denoptim.graph.rings.RingClosureParameters
checkOtherParameters() : denoptim.programs.RunTimeParameters
checkParameters() : denoptim.fitness.FitnessParameters, denoptim.fragspace.FragmentSpaceParameters, denoptim.graph.rings.RingClosureParameters, denoptim.programs.combinatorial.CEBLParameters, denoptim.programs.denovo.GAParameters, denoptim.programs.fitnessevaluator.FRParameters, denoptim.programs.fragmenter.FragmenterParameters, denoptim.programs.genetweeker.GeneOpsRunnerParameters, denoptim.programs.grapheditor.GraphEdParameters, denoptim.programs.graphlisthandler.GraphListsHandlerParameters, denoptim.programs.isomorphism.IsomorphismParameters, denoptim.programs.mol2graph.Mol2GraphParameters, denoptim.programs.moldecularmodelbuilder.MMBuilderParameters, denoptim.programs.RunTimeParameters
CheckPoint() : denoptim.combinatorial.CheckPoint
checkPreFitnessUID() : denoptim.fitness.FitnessParameters
ChemicalObjectModel() : denoptim.molecularmodeling.ChemicalObjectModel
chooseGenerationMethod() : denoptim.ga.EAUtils
chooseNumberOfSitesToMutate() : denoptim.ga.EAUtils
choseAmongPossiblyOverlapping() : denoptim.gui.GUIInspectFSERun, denoptim.gui.GUIInspectGARun
choseOrCreateNewAPClass() : denoptim.gui.GUIVertexInspector
classifyFragment() : denoptim.fragspace.FragmentSpace
cleanup() : denoptim.combinatorial.CombinatorialExplorerByLayer, denoptim.graph.Candidate, denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Vertex, denoptim.gui.GraphViewerPanel, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor
cleanupAsync() : denoptim.ga.EvolutionaryAlgorithm
cleanupCompleted() : denoptim.ga.EvolutionaryAlgorithm, denoptim.programs.fitnessevaluator.FPRunner, denoptim.task.ParallelAsynchronousTaskExecutor
clear() : denoptim.ga.Population
clearAll() : denoptim.fragspace.FragmentSpace, denoptim.gui.FragmentViewPanel, denoptim.gui.MoleculeViewPanel, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
clearAPTable() : denoptim.gui.FragmentViewPanel, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
clearCurrentSystem() : denoptim.gui.GraphVertexMolViewerPanel, denoptim.gui.GUIGraphHandler, denoptim.gui.GUIVertexInspector, denoptim.gui.GUIVertexSelector, denoptim.gui.VertexViewPanel
cleardataTable() : denoptim.gui.MoleculeViewPanel
clearIAtomContainer() : denoptim.graph.Template
clearMatches() : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
clearMolecularViewer() : denoptim.gui.FragmentViewPanel, denoptim.gui.GraphVertexMolViewerPanel, denoptim.gui.MoleculeViewPanel, denoptim.gui.VertexViewPanel
clearPanel() : denoptim.gui.VertexAsTwoDimStructureViewPanel
clearSearchMatches() : denoptim.gui.CompatibilityMatrixForm
clearUnformattedTxtArea() : denoptim.gui.ParametersForm
clearVertexViewer() : denoptim.gui.GraphVertexMolViewerPanel
CLIOptions() : denoptim.main.CLIOptions
clone() : denoptim.fragmenter.ClusterableFragment, denoptim.ga.Population, denoptim.ga.Population.XoverSitesAmongCandidates, denoptim.ga.XoverSite, denoptim.graph.APClass, denoptim.graph.APMapping, denoptim.graph.AttachmentPoint, denoptim.graph.Candidate, denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.rings.ChainLink, denoptim.graph.rings.ClosableChain, denoptim.graph.Template, denoptim.graph.Vertex, denoptim.integration.tinker.TinkerMolecule, denoptim.logging.StaticLogger
cloneAllButImpl() : denoptim.fitness.DescriptorForFitness
ClosableChain() : denoptim.graph.rings.ClosableChain
ClosableConf() : denoptim.graph.rings.CyclicGraphHandler.ClosableConf
close() : denoptim.gui.GUIModalDialog, denoptim.io.IteratingAtomContainerReader
closeEnough() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest, denoptim.fitness.descriptors.TanimotoMolSimilarityTest, denoptim.fitness.FitnessProviderTest
closeIfAllSaved() : denoptim.gui.GUI
closeRings() : denoptim.molecularmodeling.RingClosureTool
closeServer() : denoptim.fitness.descriptors.SocketProvidedDescriptorTest
closeWatcher() : denoptim.ga.ExternalCmdsListener
cluster() : denoptim.fragmenter.FragmentClusterer
ClusterableFragment() : denoptim.fragmenter.ClusterableFragment
collectClusterableFragmentsFromFile() : denoptim.fragmenter.ConformerExtractorTask
collectFragAndAPsCompatibleWithSelectedAPs() : denoptim.gui.GUIGraphHandler
CombinatorialExplorerByLayer() : denoptim.combinatorial.CombinatorialExplorerByLayer
combineCompatPathSubGraphs() : denoptim.graph.rings.CyclicGraphHandler
combineRelatedAPPair() : denoptim.ga.EAUtils
combineRelatedAPPairUtil() : denoptim.ga.EAUtils
compare() : denoptim.graph.AttachmentPointComparator, denoptim.graph.simplified.Node, denoptim.graph.simplified.NodeConnection, denoptim.graph.simplified.UndirectedEdge, denoptim.gui.GUIInspectGARun.PlottedCandidatesComparator, denoptim.molecularmodeling.RingClosureTool.RingClosedMolComparator, denoptim.utils.ConnectedLigandComparator
compareAsUndirected() : denoptim.graph.Edge
compareFormulaAndElementalAnalysis() : denoptim.utils.FormulaUtils
compareGraphNodes() : denoptim.graph.DGraph
comparePropertiesTo() : denoptim.graph.AttachmentPoint
compareSitesLists() : denoptim.ga.PopulationTest
compareSizeOfSites() : denoptim.ga.PopulationTest
compareTo() : denoptim.graph.APClass, denoptim.graph.AttachmentPoint, denoptim.graph.Candidate
CompatibilityMatrixForm() : denoptim.gui.CompatibilityMatrixForm
CompatibilityRuleLine() : denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine
CompatRulesHeader() : denoptim.gui.CompatibilityMatrixForm.CompatRulesHeader
compute() : denoptim.fragmenter.FragmentClusterer.DistanceAsRMSD
computeCrossProduct() : denoptim.utils.MathUtils
computeDihedralAngle() : denoptim.utils.MathUtils
computeDotProduct() : denoptim.utils.MathUtils
ConfigTemplateDialog() : denoptim.gui.GUIGraphHandler.ConfigTemplateDialog
ConformerExtractorTask() : denoptim.fragmenter.ConformerExtractorTask
ConnectedLigand() : denoptim.utils.ConnectedLigand
connectedTo() : denoptim.graph.Vertex
contains() : denoptim.ga.Population.XoverSitesAmongCandidates, denoptim.graph.Ring, denoptim.utils.SizeControlledSet
containsAllKeys() : denoptim.graph.APMapping
containsAllValues() : denoptim.graph.APMapping
containsAtoms() : denoptim.graph.DGraph, denoptim.graph.EmptyVertex, denoptim.graph.Fragment, denoptim.graph.Template, denoptim.graph.Vertex
containsChain() : denoptim.graph.rings.RingClosuresArchive
containsID() : denoptim.graph.Ring
containsMolecule() : denoptim.ga.EAUtils
containsOrEmbedsVertex() : denoptim.graph.DGraph
containsParameters() : denoptim.programs.RunTimeParameters
containsVertex() : denoptim.graph.DGraph
containsVertexID() : denoptim.graph.DGraph
convertAtomToAP() : denoptim.gui.GUIVertexInspector
convertDnGraphToGSGraph() : denoptim.gui.GraphViewerPanel
convertGraphTo3DAtomContainer() : denoptim.molecularmodeling.ThreeDimTreeBuilder
convertIACToVertex() : denoptim.graph.Vertex
convertProbabilityScheme() : denoptim.programs.denovo.GAParameters
convertRingsToRCACombinations() : denoptim.molecularmodeling.ChemicalObjectModel
convertSimpleToString() : denoptim.utils.FormulaUtilsTest
convertSymmetricLabelsToSymmetricSets() : denoptim.graph.DGraph
convertToCoordsVector() : denoptim.fragmenter.ClusterableFragment
convertToPointArray() : denoptim.fragmenter.ClusterableFragment
convertToString() : denoptim.utils.FormulaUtilsTest
copyStringBasedProperties() : denoptim.graph.Vertex
countAtomsOfElement() : denoptim.utils.MoleculeUtils
countLinesInFile() : denoptim.files.FileUtils
countLinesWKeywordInFile() : denoptim.molecularmodeling.MMBuilderUtils
countPredefinedNeighbours() : denoptim.integration.tinker.TinkerUtils
countSubTasks() : denoptim.combinatorial.CombinatorialExplorerByLayer
coupleMutationAndCrossover() : denoptim.programs.denovo.GAParameters
createAndSubmitTasks() : denoptim.fragmenter.ParallelConformerExtractionAlgorithm, denoptim.fragmenter.ParallelFragmentationAlgorithm, denoptim.task.ParallelAsynchronousTaskExecutor
createCrowdProbChart() : denoptim.gui.GAParametersForm
createCrowdProbDataset() : denoptim.gui.GAParametersForm
createCrowdProbGraph() : denoptim.gui.GAParametersForm
createDirectory() : denoptim.files.FileUtils
createEmptyVertexAndPlaceItInGraph() : denoptim.gui.GUIGraphHandler
createFolderForGeneration() : denoptim.ga.EAUtils
createLvlProbChart() : denoptim.gui.GAParametersForm
createLvlProbDataset() : denoptim.gui.GAParametersForm
createLvlProbGraph() : denoptim.gui.GAParametersForm
createMap() : denoptim.constants.DENOPTIMConstants
createMirror() : denoptim.ga.XoverSite
createMolSizeProbDataset() : denoptim.gui.GAParametersForm
createMolSzProbChart() : denoptim.gui.GAParametersForm
createMolSzProbGraph() : denoptim.gui.GAParametersForm
createWorkingDirectory() : denoptim.programs.combinatorial.CEBLParameters, denoptim.programs.denovo.GAParameters, denoptim.programs.fragmenter.FragmenterParameters
createZipFile() : denoptim.files.FileUtils
CuttingRule() : denoptim.programs.fragmenter.CuttingRule
CuttingRulesSelectionDialog() : denoptim.gui.CuttingRulesSelectionDialog
CyclicGraphHandler() : denoptim.graph.rings.CyclicGraphHandler