├── .classpath ├── .github └── workflows │ ├── documentation.yml │ ├── maven.yml │ └── publish_conda.yml ├── .gitignore ├── .project ├── .settings ├── org.eclipse.core.resources.prefs ├── org.eclipse.jdt.core.prefs ├── org.eclipse.jdt.ui.prefs └── org.eclipse.m2e.core.prefs ├── CHANGELOG.md ├── CONTRIBUTING.md ├── COPYING ├── README.md ├── conda ├── bld.bat ├── build.sh ├── build_local_pkg_for_testing.sh ├── environment.yml └── meta.yaml ├── contrib ├── README.md └── monitoring │ ├── .gitignore │ └── plot_EA_monitors.ipynb ├── doc ├── .gitignore ├── Doxyfile ├── DoxygenLayout.xml ├── README.md ├── developer_manual.md ├── doxygen_custom.css ├── doxygen_custom_header.html ├── figures │ ├── ea.gif │ ├── exp_diff.png │ ├── fragmentation.png │ ├── fse_levels.odg │ ├── fse_levels.png │ ├── fse_levels.svg │ ├── ga_folders.png │ ├── graph_levels.png │ ├── graph_levels.svg │ ├── graphs.png │ ├── graphs.pptx │ ├── graphs.svg │ ├── gui_snapshots.png │ ├── gui_snapshots.xcf │ ├── icon.png │ ├── logo.png │ ├── logo_header.png │ ├── sigma.png │ ├── subs_prob.png │ └── tanh.png └── user_manual.md ├── environment.yml ├── licenses ├── .gitignore ├── README.md ├── THIRD-PARTY.txt ├── cached │ ├── Apache-2.0.txt │ ├── GPL-2.0-only.txt │ ├── LGPL-2.1-only.txt │ ├── LGPL-2.1-or-later.txt │ ├── apache 2.0 - license-2.0.txt │ ├── apache license, version 2.0 - license-2.0.txt │ ├── eclipse public license v. 2.0 - epl-2.0.txt │ ├── gplv2+ce.txt │ ├── revised bsd license - licence.txt │ ├── the apache software license, version 2.0 - license-2.0.txt │ └── the w3c license - java-binding.txt ├── license_files │ ├── Apache-2.0.txt │ ├── GPL-2.0-only.txt │ ├── LGPL-2.1-only.txt │ ├── LGPL-2.1-or-later.txt │ ├── apache 2.0 - license-2.0.txt │ ├── apache license, version 2.0 - license-2.0.txt │ ├── bsd-3-clause - bsd-3-clause.html │ ├── cddl + gplv2 with classpath exception - license.html │ ├── eclipse distribution license - v 1.0 - edl-v10.html │ ├── eclipse public license (epl) 2.0 - epl-v20.html │ ├── eclipse public license 1.0 - epl-v10.html │ ├── eclipse public license 2.0 - epl-2.0.html │ ├── eclipse public license v. 2.0 - epl-2.0.txt │ ├── eclipse public license v2.0 - epl-v20.html │ ├── gnu general public license, version 2 with the gnu classpath exception - secondary-gpl-2.0-cp.html │ ├── gnu lesser general public license (lgpl), version 2.1 or later - lgpl-2.1.html │ ├── gplv2+ce.txt │ ├── mit licence - mit.html │ ├── mit license - mit-license.html │ ├── mit license - mit.html │ ├── new bsd license - bsd-license.html │ ├── public domain - publicdomain.html │ ├── revised bsd license - licence.txt │ ├── the apache software license, version 2.0 - license-2.0.txt │ ├── the bsd 2-clause license - bsd-2-clause.html │ ├── the bsd license - license.html │ ├── the new bsd license - bsd-license.html │ ├── the sax license - copying.html │ └── the w3c license - java-binding.txt ├── manually_configured_licenses.xml └── resolve_missing.properties ├── pom.xml ├── src ├── main │ ├── java │ │ └── denoptim │ │ │ ├── combinatorial │ │ │ ├── CEBLUtils.java │ │ │ ├── CheckPoint.java │ │ │ ├── CombinatorialExplorerByLayer.java │ │ │ └── GraphBuildingTask.java │ │ │ ├── constants │ │ │ └── DENOPTIMConstants.java │ │ │ ├── exception │ │ │ ├── DENOPTIMException.java │ │ │ └── ExceptionUtils.java │ │ │ ├── files │ │ │ ├── FileAndFormat.java │ │ │ ├── FileFormat.java │ │ │ ├── FileUtils.java │ │ │ ├── SingletonFileAccess.java │ │ │ └── UndetectedFileFormatException.java │ │ │ ├── fitness │ │ │ ├── DescriptorForFitness.java │ │ │ ├── DescriptorUtils.java │ │ │ ├── FitnessExpressionParser.java │ │ │ ├── FitnessParameters.java │ │ │ ├── FitnessProvider.java │ │ │ ├── IDenoptimDescriptor.java │ │ │ ├── Variable.java │ │ │ └── descriptors │ │ │ │ ├── SocketProvidedDescriptor.java │ │ │ │ ├── TanimotoMolSimilarity.java │ │ │ │ └── TanimotoMolSimilarityBySubstructure.java │ │ │ ├── fragmenter │ │ │ ├── BridgeHeadFindingRule.java │ │ │ ├── ClusterableFragment.java │ │ │ ├── ConformerExtractorTask.java │ │ │ ├── DynamicCentroidCluster.java │ │ │ ├── FragmentAlignement.java │ │ │ ├── FragmentClusterer.java │ │ │ ├── FragmenterTask.java │ │ │ ├── FragmenterTools.java │ │ │ ├── ParallelConformerExtractionAlgorithm.java │ │ │ ├── ParallelFragmentationAlgorithm.java │ │ │ └── ScaffoldingPolicy.java │ │ │ ├── fragspace │ │ │ ├── APMapFinder.java │ │ │ ├── FragmentSpace.java │ │ │ ├── FragmentSpaceParameters.java │ │ │ ├── FragmentSpaceUtils.java │ │ │ ├── FragsCombination.java │ │ │ ├── FragsCombinationIterator.java │ │ │ ├── GraphLinkFinder.java │ │ │ └── IdFragmentAndAP.java │ │ │ ├── ga │ │ │ ├── EAUtils.java │ │ │ ├── EvolutionaryAlgorithm.java │ │ │ ├── ExternalCmdsListener.java │ │ │ ├── GraphOperations.java │ │ │ ├── OffspringEvaluationTask.java │ │ │ ├── Population.java │ │ │ ├── SelectionHelper.java │ │ │ └── XoverSite.java │ │ │ ├── graph │ │ │ ├── APClass.java │ │ │ ├── APMapping.java │ │ │ ├── APTreeMap.java │ │ │ ├── AttachmentPoint.java │ │ │ ├── AttachmentPointComparator.java │ │ │ ├── Candidate.java │ │ │ ├── CandidateLW.java │ │ │ ├── DGraph.java │ │ │ ├── Edge.java │ │ │ ├── EdgeQuery.java │ │ │ ├── EmptyVertex.java │ │ │ ├── FragIsomorphEdge.java │ │ │ ├── FragIsomorphNode.java │ │ │ ├── Fragment.java │ │ │ ├── FragmentIsomorphismInspector.java │ │ │ ├── GraphPattern.java │ │ │ ├── RelatedAPPair.java │ │ │ ├── Ring.java │ │ │ ├── SymmetricAPs.java │ │ │ ├── SymmetricSet.java │ │ │ ├── SymmetricSetWithMode.java │ │ │ ├── SymmetricVertexes.java │ │ │ ├── Template.java │ │ │ ├── Vertex.java │ │ │ ├── VertexQuery.java │ │ │ ├── rings │ │ │ │ ├── ChainLink.java │ │ │ │ ├── ClosableChain.java │ │ │ │ ├── CyclicGraphHandler.java │ │ │ │ ├── PathClosabilityTools.java │ │ │ │ ├── PathSubGraph.java │ │ │ │ ├── RandomCombOfRingsIterator.java │ │ │ │ ├── RingClosingAttractor.java │ │ │ │ ├── RingClosingConformations.java │ │ │ │ ├── RingClosure.java │ │ │ │ ├── RingClosureFinder.java │ │ │ │ ├── RingClosureParameters.java │ │ │ │ ├── RingClosuresArchive.java │ │ │ │ └── RingSizeManager.java │ │ │ └── simplified │ │ │ │ ├── Node.java │ │ │ │ ├── NodeConnection.java │ │ │ │ └── UndirectedEdge.java │ │ │ ├── gui │ │ │ ├── ButtonsBar.java │ │ │ ├── CompatibilityMatrixForm.java │ │ │ ├── CuttingRulesSelectionDialog.java │ │ │ ├── DNPSpringLayout.java │ │ │ ├── FSEParametersForm.java │ │ │ ├── FSParametersForm.java │ │ │ ├── FSParamsDialog.java │ │ │ ├── FitnessParametersForm.java │ │ │ ├── FragmentViewPanel.java │ │ │ ├── GAParametersForm.java │ │ │ ├── GUI.java │ │ │ ├── GUIAPClassDefinitionDialog.java │ │ │ ├── GUICardPanel.java │ │ │ ├── GUICompatibilityMatrixTab.java │ │ │ ├── GUIEmptyVertexMaker.java │ │ │ ├── GUIFileOpener.java │ │ │ ├── GUIFileSaver.java │ │ │ ├── GUIGraphHandler.java │ │ │ ├── GUIInspectFSERun.java │ │ │ ├── GUIInspectGARun.java │ │ │ ├── GUIMainPanel.java │ │ │ ├── GUIModalDialog.java │ │ │ ├── GUIPreferences.java │ │ │ ├── GUIPreferencesDialog.java │ │ │ ├── GUIPrepare.java │ │ │ ├── GUIPrepareFSERun.java │ │ │ ├── GUIPrepareFitnessRunner.java │ │ │ ├── GUIPrepareGARun.java │ │ │ ├── GUITextReader.java │ │ │ ├── GUIVertexInspector.java │ │ │ ├── GUIVertexSelector.java │ │ │ ├── GraphVertexMolViewerPanel.java │ │ │ ├── GraphViewerPanel.java │ │ │ ├── HomePanel.java │ │ │ ├── ILoadFragSpace.java │ │ │ ├── IParametersForm.java │ │ │ ├── IVertexAPSelection.java │ │ │ ├── JUNGGraphSnapshot.java │ │ │ ├── JmolPanel.java │ │ │ ├── MainToolBar.java │ │ │ ├── MolToGraphParametersDialog.java │ │ │ ├── MoleculeViewPanel.java │ │ │ ├── ParametersForm.java │ │ │ ├── ScrollableJPupupMenu.java │ │ │ ├── Utils.java │ │ │ ├── VertexAsGraphViewPanel.java │ │ │ ├── VertexAsTwoDimStructureViewPanel.java │ │ │ └── VertexViewPanel.java │ │ │ ├── integration │ │ │ ├── python │ │ │ │ └── Py4JGetawayServer.java │ │ │ └── tinker │ │ │ │ ├── ConformationalSearchPSSROT.java │ │ │ │ ├── TinkerAtom.java │ │ │ │ ├── TinkerBond.java │ │ │ │ ├── TinkerConstants.java │ │ │ │ ├── TinkerException.java │ │ │ │ ├── TinkerMolecule.java │ │ │ │ └── TinkerUtils.java │ │ │ ├── io │ │ │ ├── DenoptimIO.java │ │ │ ├── IteratingAtomContainerReader.java │ │ │ └── SMILESListFormat.java │ │ │ ├── json │ │ │ ├── DENOPTIMgson.java │ │ │ ├── IAtomContainerDeserializer.java │ │ │ ├── IAtomContainerSerializer.java │ │ │ ├── LWAtom.java │ │ │ └── LWBond.java │ │ │ ├── logging │ │ │ ├── CounterID.java │ │ │ ├── HTMLLogFormatter.java │ │ │ ├── Monitor.java │ │ │ ├── StaticLogger.java │ │ │ └── Version.java │ │ │ ├── main │ │ │ ├── Behavior.java │ │ │ ├── CLIOptions.java │ │ │ └── Main.java │ │ │ ├── molecularmodeling │ │ │ ├── ChemicalObjectModel.java │ │ │ ├── MMBuilderUtils.java │ │ │ ├── MultiMolecularModelBuilder.java │ │ │ ├── RingClosureTool.java │ │ │ └── ThreeDimTreeBuilder.java │ │ │ ├── programs │ │ │ ├── RunTimeParameters.java │ │ │ ├── combinatorial │ │ │ │ ├── CEBLParameters.java │ │ │ │ └── FragSpaceExplorer.java │ │ │ ├── denovo │ │ │ │ ├── GAParameters.java │ │ │ │ └── GARunner.java │ │ │ ├── fitnessevaluator │ │ │ │ ├── FPRunner.java │ │ │ │ ├── FRParameters.java │ │ │ │ ├── FitnessEvaluationTask.java │ │ │ │ └── FitnessRunner.java │ │ │ ├── fragmenter │ │ │ │ ├── CuttingRule.java │ │ │ │ ├── Fragmenter.java │ │ │ │ ├── FragmenterParameters.java │ │ │ │ └── MatchedBond.java │ │ │ ├── genetweeker │ │ │ │ ├── GeneOpsRunner.java │ │ │ │ └── GeneOpsRunnerParameters.java │ │ │ ├── grapheditor │ │ │ │ ├── GraphEdParameters.java │ │ │ │ └── GraphEditor.java │ │ │ ├── graphlisthandler │ │ │ │ ├── GraphListsHandler.java │ │ │ │ └── GraphListsHandlerParameters.java │ │ │ ├── isomorphism │ │ │ │ ├── Isomorphism.java │ │ │ │ └── IsomorphismParameters.java │ │ │ ├── mol2graph │ │ │ │ ├── Mol2Graph.java │ │ │ │ └── Mol2GraphParameters.java │ │ │ └── moldecularmodelbuilder │ │ │ │ ├── MMBuilderParameters.java │ │ │ │ └── MolecularModelBuilder.java │ │ │ ├── task │ │ │ ├── FitnessTask.java │ │ │ ├── ParallelAsynchronousTaskExecutor.java │ │ │ ├── ProcessHandler.java │ │ │ ├── ProgramTask.java │ │ │ ├── StaticTaskManager.java │ │ │ ├── StreamGobbler.java │ │ │ ├── Task.java │ │ │ └── TasksBatchManager.java │ │ │ └── utils │ │ │ ├── AtomOrganizer.java │ │ │ ├── CartesianSpaceUtils.java │ │ │ ├── ConnectedLigand.java │ │ │ ├── ConnectedLigandComparator.java │ │ │ ├── CrossoverType.java │ │ │ ├── DummyAtomHandler.java │ │ │ ├── FormulaUtils.java │ │ │ ├── GeneralUtils.java │ │ │ ├── GraphConversionTool.java │ │ │ ├── GraphEdit.java │ │ │ ├── GraphUtils.java │ │ │ ├── ManySMARTSQuery.java │ │ │ ├── MathUtils.java │ │ │ ├── MoleculeUtils.java │ │ │ ├── MutationType.java │ │ │ ├── ObjectPair.java │ │ │ ├── Randomizer.java │ │ │ ├── RingClosingUtils.java │ │ │ ├── RotBndConstraint.java │ │ │ ├── RotationalSpaceUtils.java │ │ │ ├── SizeControlledSet.java │ │ │ ├── StatUtils.java │ │ │ └── TaskUtils.java │ └── resources │ │ ├── data │ │ ├── bridge-head_finding_rules.json │ │ ├── build_rc-uff.key │ │ ├── build_uff.key │ │ ├── cutting_rules │ │ ├── rotatableBonds-1.0 │ │ ├── submit_pssrot │ │ ├── submit_rc-pssrot │ │ └── uff_vdw.prm │ │ ├── images │ │ └── DENOPTIM_extended_logo.png │ │ └── project.properties ├── misc │ ├── CheckpointReader │ │ └── src │ │ │ └── checkpointreader │ │ │ └── CheckpointReader.java │ ├── DenoptimRND │ │ └── .gitignore │ ├── JSONConverter │ │ ├── convert_symmetric_sets_in_JSON.py │ │ └── test │ │ │ ├── .gitignore │ │ │ ├── editing_task │ │ │ ├── editing_task_EXPECTED │ │ │ ├── graph_w_template_w_sym_APs.sdf │ │ │ ├── graph_w_template_w_sym_APs_EXPECTED.sdf │ │ │ ├── graph_w_vertex_w_sym_APs.json │ │ │ ├── graph_w_vertex_w_sym_APs_EXPECTED.json │ │ │ ├── graphs_w_sym_APs_and_sym_vertexes.sdf │ │ │ ├── graphs_w_sym_APs_and_sym_vertexes_EXPECTED.sdf │ │ │ ├── graphs_w_vertex_w_sym_APs.json │ │ │ ├── graphs_w_vertex_w_sym_APs.sdf │ │ │ ├── graphs_w_vertex_w_sym_APs_EXPECTED.json │ │ │ ├── graphs_w_vertex_w_sym_APs_EXPECTED.sdf │ │ │ ├── run.sh │ │ │ ├── vertex_w_sym_APs.sdf │ │ │ ├── vertex_w_sym_APs_EXPECTED.sdf │ │ │ ├── vertex_w_template_w_sym_APs.sdf │ │ │ └── vertex_w_template_w_sym_APs_EXPECTED.sdf │ ├── PrepareFitnessOutput │ │ └── src │ │ │ └── preparefitnessoutput │ │ │ └── PrepareFitnessOutput.java │ ├── PrepareMOPAC │ │ └── src │ │ │ └── preparemopac │ │ │ └── PrepareMOPAC.java │ ├── SerConverter │ │ └── src │ │ │ └── serconverter │ │ │ ├── SerConvParameters.java │ │ │ └── SerConverter.java │ └── StringConverter │ │ └── src │ │ └── stringconverter │ │ ├── StringConverter.java │ │ └── StringConverterParameters.java └── test │ ├── java │ └── denoptim │ │ ├── fitness │ │ ├── DescriptorUtilsTest.java │ │ ├── FitnessExpressionParserTest.java │ │ ├── FitnessProviderTest.java │ │ └── descriptors │ │ │ ├── SocketProvidedDescriptorTest.java │ │ │ └── TanimotoMolSimilarityTest.java │ │ ├── fragmenter │ │ ├── ClusterableFragmentTest.java │ │ ├── ConformerExtractorTaskTest.java │ │ ├── DynamicCentroidClusterTest.java │ │ ├── FragmentAlignementTest.java │ │ ├── FragmentClustererTest.java │ │ ├── FragmenterToolsTest.java │ │ └── ParallelFragmentationAlgorithmTest.java │ │ ├── fragspace │ │ ├── APMapFinderTest.java │ │ ├── FragmentSpaceTest.java │ │ └── GraphLinkFinderTest.java │ │ ├── ga │ │ ├── EAUtilsTest.java │ │ ├── GraphOperationsTest.java │ │ ├── PopulationTest.java │ │ ├── SeelctionHelperTest.java │ │ └── XoverSiteTest.java │ │ ├── graph │ │ ├── APClassTest.java │ │ ├── AttachmentPointTest.java │ │ ├── DGraphTest.java │ │ ├── EdgeTest.java │ │ ├── FragmentIsomorphismInspectorTest.java │ │ ├── FragmentTest.java │ │ ├── RelatedAPPairTest.java │ │ ├── RingTest.java │ │ ├── SymmetricAPsTest.java │ │ ├── SymmetricSetWithModeTest.java │ │ ├── TemplateTest.java │ │ ├── UndirectedEdgeRelationTest.java │ │ ├── VertexTest.java │ │ └── rings │ │ │ ├── PathClosabilityToolsTest.java │ │ │ ├── PathSubGraphTest.java │ │ │ ├── RandomCombOfRingIteratorTest.java │ │ │ └── RingSizeManagerTest.java │ │ ├── io │ │ ├── DenoptimIOTest.java │ │ └── SMILESListFormatTest.java │ │ ├── json │ │ └── DENOPTIMgsonTest.java │ │ ├── main │ │ └── MainTest.java │ │ ├── molecularmodeling │ │ └── ThreeDimTreeBuilderTest.java │ │ ├── programs │ │ └── denovo │ │ │ └── GAParametersTest.java │ │ └── utils │ │ ├── FormulaUtilsTest.java │ │ ├── GenUtilsTest.java │ │ ├── GraphConversionToolTest.java │ │ ├── MoleculeUtilsTest.java │ │ ├── RandomizerTest.java │ │ └── SizeControlledSetTest.java │ └── resources │ ├── fromCOD.cif │ └── multipleStructure.cif └── test ├── PtCOLX2 ├── data │ ├── DB.sdf.tar.gz │ ├── TCFS-1_CPMap.par │ ├── TCFS-1_caps.sdf │ ├── TCFS-1_frags.sdf │ ├── TCFS-1_scaff.sdf │ ├── UIDsToAtomClash │ ├── UIDsToFitness │ ├── fitness_provider_fromDB.py │ ├── fitness_provider_fromDB.sh │ └── initPopulation.sdf ├── input_parameters ├── input_parameters_bash └── runEvolutionaryExperiment.sh ├── PtCOLX2_FSE ├── data │ ├── DB.sdf.tar.gz │ ├── TCFS-1_CPMap.par │ ├── TCFS-1_caps.sdf │ ├── TCFS-1_frags.sdf │ ├── TCFS-1_scaff.sdf │ ├── UIDsToAtomClash │ ├── UIDsToFitness │ ├── fitness_provider_fromDB.py │ ├── fitness_provider_fromDB.sh │ └── root.sdf ├── input_parameters ├── input_parameters_bash └── runCombinatorialExperiment.sh ├── README.md ├── cyclicpeptide ├── data │ ├── CPMap │ ├── NOTEs │ ├── goal.sdf │ ├── lib_frags.sdf │ └── lib_scaff.sdf ├── input_parameters ├── run.sh └── utils │ ├── .gitignore │ └── make_amino_acid_3D_fragments.py ├── diamonds ├── data │ ├── CPMap.par │ ├── RC-CPMap │ ├── conf_search.key │ ├── conf_search_rcp.key │ ├── fitness_provider_w3D.sh │ ├── goal.sdf │ ├── goal_7-5-6-membered_rings.sdf │ ├── goal_7-6-6-5-4-3-membered_rings.sdf │ ├── goal_7-membered_ring.sdf │ ├── goal_C35.sdf │ ├── goal_OK.sdf │ ├── lib_cap.sdf │ ├── lib_frags.sdf │ ├── lib_frags_with_C6ring.sdf │ ├── lib_scaff.sdf │ ├── rotatableBonds-1.0 │ ├── submit_PSSROT │ ├── submit_RC-PSSROT │ └── uff_vdw.prm ├── input_parameters_GA ├── input_parameters_GA_3D ├── input_parameters_GA_3D_bis ├── input_parameters_GA_7-5-6 ├── input_parameters_GA_7-6-6-5-4-3 ├── input_parameters_GA_C35 ├── input_parameters_GA_nice-run_pop20 ├── runDiamondsGA.sh └── utils │ ├── .ipynb_checkpoints │ └── Generate_substructure_SMARTS_for_fingerprinter-checkpoint.ipynb │ ├── create_substructure_SMARTS │ ├── Generate_substructure_SMARTS_for_fingerprinter.ipynb │ ├── fragments.sdf │ ├── goal.sdf │ └── smarts │ ├── make_initial_population │ ├── acyclic_molecules.sdf │ ├── fitness.params │ ├── goal.sdf │ ├── initial_population.sdf │ ├── make_initial_population.sh │ └── substructures.smarts │ ├── test_fingerprinters │ ├── 7-5-6.sdf │ ├── 7-6-5.sdf │ ├── 756.sdf │ ├── 765.sdf │ ├── fp.params │ ├── goal.sdf │ └── input.sdf │ └── very_complex.sdf ├── functional_tests ├── README ├── p6 │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds-1.2 │ ├── p6.params │ └── runp6.sh ├── runTests.sh ├── t1 │ ├── expected_results │ │ ├── MOL000001_3Dbuilt.sdf │ │ ├── MOL000002_3Dbuilt.sdf │ │ ├── MOL000003_3Dbuilt.sdf │ │ ├── MOL000004_3Dbuilt.sdf │ │ ├── MOL000005_3Dbuilt.sdf │ │ ├── MOL000006_3Dbuilt.sdf │ │ ├── MOL000007_3Dbuilt.sdf │ │ ├── MOL000008_3Dbuilt.sdf │ │ └── MOL000009_3Dbuilt.sdf │ ├── fragment_space │ │ ├── CPMap.par │ │ ├── FS.params │ │ ├── cap.sdf │ │ ├── frags.sdf │ │ └── scaff.sdf │ ├── input │ │ ├── MOL000001.sdf │ │ ├── MOL000002.sdf │ │ ├── MOL000003.sdf │ │ ├── MOL000004.sdf │ │ ├── MOL000005.sdf │ │ ├── MOL000006.sdf │ │ ├── MOL000007.sdf │ │ ├── MOL000008.sdf │ │ ├── MOL000009.sdf │ │ └── MOL000009_tor_cnstr │ ├── rotatableBonds-1.0 │ └── runt1.sh ├── t10 │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt10.sh │ └── t10.params ├── t11 │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt11.sh │ └── t11.params ├── t12 │ ├── data │ │ ├── CPMap.par │ │ ├── expected_results │ │ ├── fitness_provider.sh │ │ ├── initialPop.sdf │ │ ├── knownUID.txt │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12.sh │ └── t12.params ├── t12a │ ├── data │ │ ├── CPMap.par │ │ ├── initialPop.sdf │ │ ├── knownUID.txt │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12a.sh │ └── t12a.params ├── t12b │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── initialPop.sdf │ │ ├── knownUID.txt │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12b.sh │ └── t12b.params ├── t12c │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── initialPop.sdf │ │ ├── knownUID.txt │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12c.sh │ └── t12c.params ├── t12d │ ├── data │ │ ├── CPMap.par │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12d.sh │ └── t12d.params ├── t12e │ ├── data │ │ ├── CPMap.par │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12e.sh │ └── t12e.params ├── t12f │ ├── data │ │ ├── CPMap.par │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12f.sh │ └── t12f.params ├── t12g │ ├── data │ │ ├── CPMap.par │ │ ├── cutting_rules │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── molsToFragment.smi │ ├── runt12g.sh │ └── t12g.params ├── t12h │ ├── data │ │ ├── CPMap.par │ │ ├── cutting_rules │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── molsToFragment.sdf │ ├── runt12h.sh │ └── t12h.params ├── t12i │ ├── data │ │ ├── 5ok.sdf │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── aromatic_bridges.sdf │ │ ├── cutting_rules │ │ ├── initial_pop.sdf │ │ ├── initial_pop.smi │ │ ├── initial_pop_graph_no5.sdf │ │ ├── initial_pop_mix.sdf │ │ ├── initial_pop_whole_mol.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt12i.sh │ └── t12i.params ├── t12j │ ├── data │ │ ├── CPMap.par │ │ ├── cutting_rules │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── molsToFragment.sdf │ ├── runt12h.sh │ └── t12h.params ├── t13 │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── initialPop.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt13.sh │ └── t13.params ├── t14 │ ├── data │ │ ├── CPMap.par │ │ ├── female.sdf │ │ ├── female_ok.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── male.sdf │ │ └── male_ok.sdf │ ├── runt14.sh │ ├── t14-check-1.params │ ├── t14-check-2.params │ └── t14.params ├── t15 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── female.sdf │ │ ├── female_ok.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── male.sdf │ │ ├── male_ok.sdf │ │ └── rotatableBonds-1.2 │ ├── runt15.sh │ ├── t15-check-1.params │ ├── t15-check-2.params │ └── t15.params ├── t16 │ ├── data │ │ ├── CPMap.par │ │ ├── editingTasks │ │ ├── editingTasks_doc │ │ ├── editingTasks_with_APID │ │ ├── inGraphs.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ └── lib_scaff.sdf │ ├── runt16.sh │ └── t16.params ├── t17 │ ├── data │ │ ├── TCFS-1_CPMap.par │ │ ├── TCFS-1_caps.sdf │ │ ├── TCFS-1_frags.sdf │ │ ├── TCFS-1_scaff.sdf │ │ └── allGrafsWithFitness.sdf │ ├── runt17.sh │ └── t17.params ├── t19 │ ├── WARNING │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── input.txt │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── reference.sdf │ │ ├── rotatableBonds │ │ ├── template_7 │ │ └── template_8 │ ├── runt19.sh │ ├── t19.params_1 │ └── t19.params_2 ├── t2 │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2.sh │ └── t2.params ├── t20 │ ├── README │ ├── data │ │ ├── CPMap.par │ │ ├── female.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── male.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ ├── female_xo.sdf │ │ └── male_xo.sdf │ ├── runt20.sh │ └── t20.params ├── t21 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── graph.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ └── graph_mut.sdf │ ├── runt21.sh │ └── t21.params ├── t22 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── graph.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ └── graph_mut.sdf │ ├── runt22.sh │ └── t22.params ├── t23 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── graph.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ └── graph_mut.sdf │ ├── runt23.sh │ └── t23.params ├── t24 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── graph.sdf │ │ ├── graph10.sdf │ │ ├── graph11.sdf │ │ ├── graph2.sdf │ │ ├── graph3.sdf │ │ ├── graph4.sdf │ │ ├── graph5.sdf │ │ ├── graph6.sdf │ │ ├── graph7.sdf │ │ ├── graph8.sdf │ │ ├── graph9.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds │ ├── runt24.sh │ ├── t24-1.params │ ├── t24-2.params │ ├── t24-3.params │ ├── t24-4.params │ ├── t24-5.params │ ├── t24-6.params │ ├── t24-7.params │ ├── t24-8.params │ └── t24-9.params ├── t25 │ ├── goal.sdf │ ├── runt25.sh │ ├── t25.params │ └── t25_in.sdf ├── t26 │ ├── data │ │ ├── CPMap.par │ │ ├── CPMap_t26-30.par │ │ ├── RC-CPMap.par │ │ ├── RC-CPMap_t26-30.par │ │ ├── RC-CPMap_t26-32.par │ │ ├── bridge-head_finding_rules_t26-30.json │ │ ├── bridge-head_finding_rules_t26-31.json │ │ ├── graph-1.sdf │ │ ├── graph-10.sdf │ │ ├── graph-11.sdf │ │ ├── graph-12.sdf │ │ ├── graph-13.sdf │ │ ├── graph-14.sdf │ │ ├── graph-15.sdf │ │ ├── graph-16.sdf │ │ ├── graph-17.sdf │ │ ├── graph-18.sdf │ │ ├── graph-19.sdf │ │ ├── graph-2.sdf │ │ ├── graph-20.sdf │ │ ├── graph-21.sdf │ │ ├── graph-22.sdf │ │ ├── graph-23.sdf │ │ ├── graph-28.sdf │ │ ├── graph-3.sdf │ │ ├── graph-30.sdf │ │ ├── graph-31.sdf │ │ ├── graph-32.sdf │ │ ├── graph-4.sdf │ │ ├── graph-5.sdf │ │ ├── graph-6.sdf │ │ ├── graph-7.sdf │ │ ├── graph-8.sdf │ │ ├── graph-9.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_frags_t26-30.sdf │ │ ├── lib_frags_t26-31.sdf │ │ ├── lib_frags_t26-32.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ ├── graph_mut-1.sdf │ │ ├── graph_mut-10.sdf │ │ ├── graph_mut-11.sdf │ │ ├── graph_mut-12.sdf │ │ ├── graph_mut-13.sdf │ │ ├── graph_mut-14.sdf │ │ ├── graph_mut-15.sdf │ │ ├── graph_mut-16.sdf │ │ ├── graph_mut-17.sdf │ │ ├── graph_mut-18.sdf │ │ ├── graph_mut-19.sdf │ │ ├── graph_mut-2.sdf │ │ ├── graph_mut-20.sdf │ │ ├── graph_mut-21.sdf │ │ ├── graph_mut-22.sdf │ │ ├── graph_mut-23.sdf │ │ ├── graph_mut-24.sdf │ │ ├── graph_mut-25.sdf │ │ ├── graph_mut-26.sdf │ │ ├── graph_mut-27.sdf │ │ ├── graph_mut-28.sdf │ │ ├── graph_mut-29.sdf │ │ ├── graph_mut-3.sdf │ │ ├── graph_mut-30.sdf │ │ ├── graph_mut-31.sdf │ │ ├── graph_mut-32.sdf │ │ ├── graph_mut-4.sdf │ │ ├── graph_mut-5.sdf │ │ ├── graph_mut-6.sdf │ │ ├── graph_mut-7.sdf │ │ ├── graph_mut-8.sdf │ │ └── graph_mut-9.sdf │ ├── runt26.sh │ ├── t26-1.params │ ├── t26-10.params │ ├── t26-11.params │ ├── t26-12.params │ ├── t26-13.params │ ├── t26-14.params │ ├── t26-15.params │ ├── t26-16.params │ ├── t26-17.params │ ├── t26-18.params │ ├── t26-19.params │ ├── t26-2.params │ ├── t26-20.params │ ├── t26-21.params │ ├── t26-22.params │ ├── t26-23.params │ ├── t26-24.params │ ├── t26-25.params │ ├── t26-26.params │ ├── t26-27.params │ ├── t26-28.params │ ├── t26-29.params │ ├── t26-3.params │ ├── t26-30.params │ ├── t26-31.params │ ├── t26-32.params │ ├── t26-4.params │ ├── t26-5.params │ ├── t26-6.params │ ├── t26-7.params │ ├── t26-8.params │ └── t26-9.params ├── t27 │ ├── data │ │ ├── CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── newCandSrc.json │ ├── runt27.sh │ └── t27.params ├── t28 │ ├── data │ │ ├── CPMap.par │ │ ├── RC-CPMap.par │ │ ├── female-1.sdf │ │ ├── female-2.sdf │ │ ├── female-3.sdf │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── male-1.sdf │ │ ├── male-2.sdf │ │ ├── male-3.sdf │ │ └── rotatableBonds │ ├── expected_output │ │ ├── female-1_xo.sdf │ │ ├── female-2_xo.sdf │ │ ├── female-3_xo.sdf │ │ ├── male-1_xo.sdf │ │ ├── male-2_xo.sdf │ │ └── male-3_xo.sdf │ ├── runt28.sh │ ├── t28-1.params │ ├── t28-2.params │ └── t28-3.params ├── t29 │ ├── data │ │ ├── CPMap-1.par │ │ ├── editingTasks-1 │ │ ├── editingTasks-2 │ │ ├── editingTasks-3 │ │ ├── editingTasks-4 │ │ ├── editingTasks-5 │ │ ├── editingTasks-7 │ │ ├── editingTasks-9 │ │ ├── inGraphs-1.sdf │ │ ├── inGraphs-2.sdf │ │ ├── inGraphs-3.sdf │ │ ├── inGraphs-4.sdf │ │ ├── inGraphs-5.sdf │ │ ├── inGraphs-9.sdf │ │ ├── lib_frag-4.sdf │ │ ├── lib_frag-5.sdf │ │ └── lib_scaff-1.sdf │ ├── expected_output │ │ ├── outGraphs-1.sdf │ │ ├── outGraphs-10.sdf │ │ ├── outGraphs-2.sdf │ │ ├── outGraphs-3.sdf │ │ ├── outGraphs-4.sdf │ │ ├── outGraphs-5.sdf │ │ ├── outGraphs-6.sdf │ │ ├── outGraphs-7.sdf │ │ ├── outGraphs-8.sdf │ │ └── outGraphs-9.sdf │ ├── runt29.sh │ ├── t29-1.params │ ├── t29-10.params │ ├── t29-2.params │ ├── t29-3.params │ ├── t29-4.params │ ├── t29-5.params │ ├── t29-6.params │ ├── t29-7.params │ ├── t29-8.params │ └── t29-9.params ├── t2a │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2a.sh │ └── t2a.params ├── t2b │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2b.sh │ └── t2b.params ├── t2c │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2c.sh │ └── t2c.params ├── t2d │ ├── WARNING │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.py │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2d.sh │ └── t2d.params ├── t2e │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.py │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt2e.sh │ └── t2e.params ├── t3 │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds-1.2 │ ├── runt3.sh │ └── t3.params ├── t30 │ ├── data │ │ ├── customCuttingRules-17.rul │ │ ├── cutting_rules │ │ ├── cutting_rules_noH │ │ ├── formula-1.txt │ │ ├── formula-2.txt │ │ ├── ignorable-5.sdf │ │ ├── inputFrags-10.sdf │ │ ├── inputFrags-11.sdf │ │ ├── inputFrags-12.sdf │ │ ├── inputFrags-13.sdf │ │ ├── inputFrags-14.sdf │ │ ├── isomorphicFamily-16.sdf │ │ ├── mols-1.sdf │ │ ├── mols-15.sdf │ │ ├── mols-17.sdf │ │ ├── mols-18.sdf │ │ ├── mols-19.cif │ │ ├── mols-2.sdf │ │ ├── mols-20.smi │ │ ├── mols-21.smi │ │ ├── mols-22.smi │ │ ├── mols-23.smi │ │ ├── mols-3.sdf │ │ ├── mols-4.sdf │ │ ├── mols-5.sdf │ │ ├── mols-6.sdf │ │ ├── mols-7.sdf │ │ └── targets-6.sdf │ ├── runt30.sh │ ├── t30-1.params │ ├── t30-10.params │ ├── t30-11.params │ ├── t30-12.params │ ├── t30-13.params │ ├── t30-14.params │ ├── t30-15.params │ ├── t30-16.params │ ├── t30-17.params │ ├── t30-18.params │ ├── t30-19.params │ ├── t30-2.params │ ├── t30-20.params │ ├── t30-21.params │ ├── t30-22.params │ ├── t30-23.params │ ├── t30-24.params │ ├── t30-3.params │ ├── t30-4.params │ ├── t30-5.params │ ├── t30-6.params │ ├── t30-7.params │ ├── t30-8.params │ └── t30-9.params ├── t31 │ ├── client-1.py │ ├── data │ │ └── graph-1.sdf │ └── runt31.sh ├── t32 │ ├── mol-3.sdf │ ├── mols.sdf │ ├── runt32.sh │ ├── t32-1.params │ ├── t32-2.cutRul │ ├── t32-2.params │ ├── t32-3.cutRul │ └── t32-3.params ├── t4 │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── roots.json │ │ └── rotatableBonds-1.2 │ ├── runt4.sh │ └── t4.params ├── t5 │ ├── data │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ └── rotatableBonds-1.2 │ ├── runt5.sh │ └── t5.params ├── t6 │ ├── README │ ├── data │ │ ├── .gitignore │ │ ├── CPMap.par │ │ ├── MOLUID.txt │ │ ├── RC-CPMap.par │ │ ├── fitness_provider.sh │ │ ├── lib_cap.sdf │ │ ├── lib_frags.sdf │ │ ├── lib_scaff.sdf │ │ ├── prev_dbRoot │ │ │ └── .placeholder │ │ └── rotatableBonds-1.2 │ ├── runt6.sh │ └── t6.params └── t9 │ ├── data │ ├── CPMap.par │ ├── fitness_provider.sh │ ├── lib_cap.sdf │ ├── lib_frags.sdf │ └── lib_scaff.sdf │ ├── runt9.sh │ └── t9.params └── polycycle ├── data ├── CPMap.par ├── RC-CPMap ├── conf_search.key ├── conf_search_rcp.key ├── fitness_provider_w3D.sh ├── goal.sdf ├── goal_7-5-6-membered_rings.sdf ├── goal_7-6-6-5-4-3-membered_rings.sdf ├── goal_7-membered_ring.sdf ├── goal_C35.sdf ├── goal_OK.sdf ├── initial_population.sdf ├── lib_cap.sdf ├── lib_frags.sdf ├── lib_scaff.sdf ├── mm2.prm ├── mmff.prm ├── rotatableBonds-1.0 ├── submit_PSSROT ├── submit_RC-PSSROT ├── substructures.smarts └── uff_vdw.prm ├── input_parameters ├── input_parameters_2D └── run_muplitple_runs.sh /.classpath: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/denoptim-project/DENOPTIM/HEAD/.classpath -------------------------------------------------------------------------------- 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