A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | X

B: Vertex.BBType (denoptim.graph); Behavior (denoptim.main); Edge.BondType (denoptim.graph); BridgeHeadFindingRule (denoptim.fragmenter); ButtonsBar (denoptim.gui)

C: Candidate (denoptim.graph); CandidateLW (denoptim.graph); EAUtils.CandidateSource (denoptim.ga); CartesianSpaceUtils (denoptim.utils); CEBLParameters (denoptim.programs.combinatorial); CEBLUtils (denoptim.combinatorial); ChainLink (denoptim.graph.rings); CheckPoint (denoptim.combinatorial); ChemicalObjectModel (denoptim.molecularmodeling); CLIOptions (denoptim.main); ClosableChain (denoptim.graph.rings); CyclicGraphHandler.ClosableConf (denoptim.graph.rings); ClusterableFragment (denoptim.fragmenter); ClusterableFragmentTest (denoptim.fragmenter); ParametersForm.CmbFieldChange (denoptim.gui); CombinatorialExplorerByLayer (denoptim.combinatorial); CompatibilityMatrixForm (denoptim.gui); CompatibilityMatrixForm.CompatibilityRuleLine (denoptim.gui); CompatibilityMatrixForm.CompatRulesHeader (denoptim.gui); GUIGraphHandler.ConfigTemplateDialog (denoptim.gui); ConformationalSearchPSSROT (denoptim.integration.tinker); ConformerExtractorTask (denoptim.fragmenter); ConformerExtractorTaskTest (denoptim.fragmenter); ConnectedLigand (denoptim.utils); ConnectedLigandComparator (denoptim.utils); Template.ContractLevel (denoptim.graph); CounterID (denoptim.logging); CrossoverType (denoptim.utils); FitnessExpressionParser.CustomVariableDefiningContext (denoptim.fitness); CuttingRule (denoptim.programs.fragmenter); CuttingRulesSelectionDialog (denoptim.gui); CyclicGraphHandler (denoptim.graph.rings)

D: FileFormat.DataKind (denoptim.files); DENOPTIMConstants (denoptim.constants); Edge.DENOPTIMEdgeSerializer (denoptim.graph); DENOPTIMException (denoptim.exception); DENOPTIMgson.DENOPTIMExclusionStrategy (denoptim.json); DENOPTIMgson.DENOPTIMExclusionStrategyNoAPMap (denoptim.json); DGraph.DENOPTIMGraphDeserializer (denoptim.graph); DGraph.DENOPTIMGraphSerializer (denoptim.graph); DENOPTIMgson (denoptim.json); DENOPTIMgsonTest (denoptim.json); DenoptimIO (denoptim.io); DenoptimIOTest (denoptim.io); Ring.DENOPTIMRingSerializer (denoptim.graph); Vertex.DENOPTIMVertexDeserializer (denoptim.graph); DescriptorForFitness (denoptim.fitness); FitnessParametersForm.DescriptorTreeNode (denoptim.gui); DescriptorUtils (denoptim.fitness); DescriptorUtilsTest (denoptim.fitness); DGraph (denoptim.graph); DGraphTest (denoptim.graph); FragmentClusterer.DistanceAsRMSD (denoptim.fragmenter); DNPSpringLayout (denoptim.gui); DummyAtomHandler (denoptim.utils); DynamicCentroidCluster (denoptim.fragmenter); DynamicCentroidClusterTest (denoptim.fragmenter)

F: ParametersForm.FieldListener (denoptim.gui); FileAndFormat (denoptim.files); FileFormat (denoptim.files); FileUtils (denoptim.files); FitnessEvaluationTask (denoptim.programs.fitnessevaluator); FitnessExpressionParser (denoptim.fitness); FitnessExpressionParserTest (denoptim.fitness); FitnessParameters (denoptim.fitness); FitnessParametersForm (denoptim.gui); FitnessProvider (denoptim.fitness); FitnessProviderTest (denoptim.fitness); FitnessRunner (denoptim.programs.fitnessevaluator); FitnessTask (denoptim.task); FormulaUtils (denoptim.utils); FormulaUtilsTest (denoptim.utils); FPRunner (denoptim.programs.fitnessevaluator); GraphOperations.FragForClosabChains (denoptim.ga); FragIsomorphEdge (denoptim.graph); FragIsomorphNode (denoptim.graph); Fragment (denoptim.graph); FragmentAlignement (denoptim.fragmenter); FragmentAlignementTest (denoptim.fragmenter); FragmentClusterer (denoptim.fragmenter); FragmentClustererTest (denoptim.fragmenter); Fragmenter (denoptim.programs.fragmenter); FragmenterParameters (denoptim.programs.fragmenter); FragmenterTask (denoptim.fragmenter); FragmenterTools (denoptim.fragmenter); FragmenterToolsTest (denoptim.fragmenter); FragmentIsomorphismInspector (denoptim.graph); FragmentIsomorphismInspectorTest (denoptim.graph); FragmentSpace (denoptim.fragspace); FragmentSpaceParameters (denoptim.fragspace); FragmentSpaceTest (denoptim.fragspace); FragmentSpaceUtils (denoptim.fragspace); FragmentTest (denoptim.graph); FragmentViewPanel (denoptim.gui); FragsCombination (denoptim.fragspace); FragsCombinationIterator (denoptim.fragspace); FragSpaceExplorer (denoptim.programs.combinatorial); FRParameters (denoptim.programs.fitnessevaluator); FSEParametersForm (denoptim.gui); FSParametersForm (denoptim.gui); FSParamsDialog (denoptim.gui)

G: GAParameters (denoptim.programs.denovo); GAParametersForm (denoptim.gui); GAParametersTest (denoptim.programs.denovo); GARunner (denoptim.programs.denovo); GeneOpsRunner (denoptim.programs.genetweeker); GeneOpsRunnerParameters (denoptim.programs.genetweeker); GeneralUtils (denoptim.utils); GUIInspectGARun.GenerationChoiceDialog (denoptim.gui); GenUtilsTest (denoptim.utils); GraphBuildingTask (denoptim.combinatorial); GraphConversionTool (denoptim.utils); GraphConversionToolTest (denoptim.utils); GraphEdit (denoptim.utils); GraphEditor (denoptim.programs.grapheditor); GraphEdParameters (denoptim.programs.grapheditor); GraphLinkFinder (denoptim.fragspace); GraphLinkFinderTest (denoptim.fragspace); GraphListsHandler (denoptim.programs.graphlisthandler); GraphListsHandlerParameters (denoptim.programs.graphlisthandler); GraphOperations (denoptim.ga); GraphOperationsTest (denoptim.ga); GraphViewerPanel.GraphOptsPopup (denoptim.gui); GraphPattern (denoptim.graph); GUIGraphHandler.GraphSpinnerChangeEvent (denoptim.gui); GraphUtils (denoptim.utils); GraphVertexMolViewerPanel (denoptim.gui); GraphViewerPanel (denoptim.gui); GUI (denoptim.gui); GUIAPClassDefinitionDialog (denoptim.gui); GUICardPanel (denoptim.gui); GUICompatibilityMatrixTab (denoptim.gui); GUIEmptyVertexMaker (denoptim.gui); GUIFileOpener (denoptim.gui); GUIFileSaver (denoptim.gui); GUIGraphHandler (denoptim.gui); GUIInspectFSERun (denoptim.gui); GUIInspectGARun (denoptim.gui); GUIMainPanel (denoptim.gui); GUIModalDialog (denoptim.gui); GUIPreferences (denoptim.gui); GUIPreferencesDialog (denoptim.gui); GUIPrepare (denoptim.gui); GUIPrepareFitnessRunner (denoptim.gui); GUIPrepareFSERun (denoptim.gui); GUIPrepareGARun (denoptim.gui); GUITextReader (denoptim.gui); GUIVertexInspector (denoptim.gui); GUIVertexSelector (denoptim.gui)

H: HomePanel (denoptim.gui); HTMLLogFormatter (denoptim.logging)

J: GraphViewerPanel.JEdge (denoptim.gui); JmolPanel (denoptim.gui); JUNGGraphSnapshot (denoptim.gui); GraphViewerPanel.JVertex (denoptim.gui); GraphViewerPanel.JVertexType (denoptim.gui)

L: GraphViewerPanel.LabelType (denoptim.gui); LWAtom (denoptim.json); LWBond (denoptim.json)

M: Main (denoptim.main); MainTest (denoptim.main); MainToolBar (denoptim.gui); ManySMARTSQuery (denoptim.utils); MatchedBond (denoptim.programs.fragmenter); MathUtils (denoptim.utils); MMBuilderParameters (denoptim.programs.moldecularmodelbuilder); MMBuilderUtils (denoptim.molecularmodeling); Mol2Graph (denoptim.programs.mol2graph); Mol2GraphParameters (denoptim.programs.mol2graph); MolecularModelBuilder (denoptim.programs.moldecularmodelbuilder); MoleculeUtils (denoptim.utils); MoleculeUtilsTest (denoptim.utils); MoleculeViewPanel (denoptim.gui); MolToGraphParametersDialog (denoptim.gui); Monitor (denoptim.logging); GraphVertexMolViewerPanel.MouseModeChoiceListener (denoptim.gui); MultiMolecularModelBuilder (denoptim.molecularmodeling); MutationType (denoptim.utils); CuttingRulesSelectionDialog.MyJSVGCanvas (denoptim.gui); SocketProvidedDescriptorTest.MySocketServer (denoptim.fitness.descriptors)

N: Node (denoptim.graph.simplified); GraphVertexMolViewerPanel.NodeClickedListener (denoptim.gui); NodeConnection (denoptim.graph.simplified)

O: ObjectPair (denoptim.utils); OffspringEvaluationTask (denoptim.ga); GeneOpsRunnerParameters.Operator (denoptim.programs.genetweeker)

P: ParallelAsynchronousTaskExecutor (denoptim.task); ParallelConformerExtractionAlgorithm (denoptim.fragmenter); ParallelFragmentationAlgorithm (denoptim.fragmenter); ParallelFragmentationAlgorithmTest (denoptim.fragmenter); ParametersForm (denoptim.gui); RunTimeParameters.ParametersType (denoptim.programs); FitnessParametersForm.ParametrizedDescriptorDefinition (denoptim.gui); PathClosabilityTools (denoptim.graph.rings); PathClosabilityToolsTest (denoptim.graph.rings); PathSubGraph (denoptim.graph.rings); PathSubGraphTest (denoptim.graph.rings); FragmentViewPanel.PausableTableModelListener (denoptim.gui); VertexAsTwoDimStructureViewPanel.PausableTableModelListener (denoptim.gui); VertexAsGraphViewPanel.PausableTableModelListener (denoptim.gui); GUIInspectGARun.PlottedCandidatesComparator (denoptim.gui); Population (denoptim.ga); PopulationTest (denoptim.ga); GraphViewerPanel.PopupGraphMousePlugin (denoptim.gui); GAParametersForm.ProbabilityFuncitonShape (denoptim.gui); ProcessHandler (denoptim.task); ProgramTask (denoptim.task); Py4JGetawayServer (denoptim.integration.python)

R: RandomCombOfRingIteratorTest (denoptim.graph.rings); RandomCombOfRingsIterator (denoptim.graph.rings); Randomizer (denoptim.utils); RandomizerTest (denoptim.utils); ParametersForm.RdbFieldChange (denoptim.gui); MainToolBar.RecentFileItem (denoptim.gui); DNPSpringLayout.RecreateKnownPositions (denoptim.gui); RelatedAPPair (denoptim.graph); RelatedAPPairTest (denoptim.graph); GUICardPanel.removeCardActionListener (denoptim.gui); SocketProvidedDescriptorTest.RequestHandler (denoptim.fitness.descriptors); Ring (denoptim.graph); RingClosureTool.RingClosedMolComparator (denoptim.molecularmodeling); RingClosingAttractor (denoptim.graph.rings); RingClosingConformations (denoptim.graph.rings); RingClosingUtils (denoptim.utils); RingClosure (denoptim.graph.rings); RingClosureFinder (denoptim.graph.rings); RingClosureParameters (denoptim.graph.rings); RingClosuresArchive (denoptim.graph.rings); RingClosureTool (denoptim.molecularmodeling); RingSizeManager (denoptim.graph.rings); RingSizeManagerTest (denoptim.graph.rings); RingTest (denoptim.graph); RotationalSpaceUtils (denoptim.utils); RunTimeParameters (denoptim.programs); Main.RunType (denoptim.main)

S: ScaffoldingPolicy (denoptim.fragmenter); ScrollableJPupupMenu (denoptim.gui); SeelctionHelperTest (denoptim.ga); SelectionHelper (denoptim.ga); GUIGraphHandler.showHideLabelsListener (denoptim.gui); StaticTaskManager.ShutDownHook (denoptim.task); SingletonFileAccess (denoptim.files); SizeControlledSet (denoptim.utils); SizeControlledSetTest (denoptim.utils); CuttingRulesSelectionDialog.SMARTSVisualizationButton (denoptim.gui); SMILESListFormat (denoptim.io); SMILESListFormatTest (denoptim.io); GUIPreferences.SMITo3DEngine (denoptim.gui); SocketProvidedDescriptor (denoptim.fitness.descriptors); SocketProvidedDescriptorTest (denoptim.fitness.descriptors); StaticLogger (denoptim.logging); StaticTaskManager (denoptim.task); StatUtils (denoptim.utils); StreamGobbler (denoptim.task); DGraph.StringFormat (denoptim.graph); SymmetricAPs (denoptim.graph); SymmetricAPs.SymmetricAPsSerializer (denoptim.graph); SymmetricAPsTest (denoptim.graph); SymmetricSet (denoptim.graph); SymmetricSetWithMode (denoptim.graph); SymmetricSetWithModeTest (denoptim.graph); SymmetricVertexes (denoptim.graph); SymmetricVertexes.SymmetricVertexesSerializer (denoptim.graph)

T: ParametersForm.TabFieldChange (denoptim.gui); TanimotoMolSimilarity (denoptim.fitness.descriptors); TanimotoMolSimilarityBySubstructure (denoptim.fitness.descriptors); TanimotoMolSimilarityTest (denoptim.fitness.descriptors); CompatibilityMatrixForm.TargetAPClassToken (denoptim.gui); Task (denoptim.task); TasksBatchManager (denoptim.task); TaskUtils (denoptim.utils); Template (denoptim.graph); GUIGraphHandler.ConfigTemplateDialog.TemplateConfiguration (denoptim.gui); TemplateTest (denoptim.graph); FragmentSpaceTest.TestCase (denoptim.fragspace); ThreeDimTreeBuilder (denoptim.molecularmodeling); ThreeDimTreeBuilderTest (denoptim.molecularmodeling); TinkerAtom (denoptim.integration.tinker); TinkerBond (denoptim.integration.tinker); TinkerConstants (denoptim.integration.tinker); TinkerException (denoptim.integration.tinker); TinkerMolecule (denoptim.integration.tinker); TinkerUtils (denoptim.integration.tinker); CompatibilityMatrixForm.TrgRemovalListener (denoptim.gui); VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel (denoptim.gui)

U: UndetectedFileFormatException (denoptim.files); UndirectedEdge (denoptim.graph.simplified); UndirectedEdgeRelationTest (denoptim.graph); Utils (denoptim.gui)

X: XoverSite (denoptim.ga); Population.XoverSitesAmongCandidates (denoptim.ga); XoverSiteTest (denoptim.ga)