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DENOPTIM
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Unit test. More...
Static Public Member Functions | |
| static void | replaceHatomWithAP (Fragment frag, int srcId, APClass apc) |
Static Package Attributes | |
| static File | tempDir |
Private Member Functions | |
| FragmentSpaceParameters | prepare () throws DENOPTIMException |
Private Attributes | |
| IChemObjectBuilder | builder = SilentChemObjectBuilder.getInstance() |
| Private builder of atom containers. More... | |
Static Private Attributes | |
| static APClass | APCA |
| static APClass | APCB |
| static APClass | APCC |
| static String | a ="A" |
| static String | b ="B" |
| static String | c ="C" |
| static final String | SEP = System.getProperty("file.separator") |
| static final String | NL = System.getProperty("line.separator") |
Unit test.
Definition at line 87 of file EAUtilsTest.java.
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Definition at line 106 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.a, denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.ga.EAUtilsTest.APCA, denoptim.ga.EAUtilsTest.APCB, denoptim.ga.EAUtilsTest.APCC, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.fragspace.FragmentSpace.appendVertexToLibrary(), denoptim.ga.EAUtilsTest.b, denoptim.ga.EAUtilsTest.c, denoptim.graph.Template.ContractLevel.FIXED_STRUCT, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpace.getScaffoldLibrary(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.APClass.make(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), denoptim.graph.Vertex.setAsRCV(), denoptim.graph.Vertex.setBuildingBlockType(), and denoptim.graph.Edge.BondType.SINGLE.
Referenced by denoptim.ga.EAUtilsTest.testAvoidRedundantXOver(), and denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold().
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Definition at line 2373 of file EAUtilsTest.java.
References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.getAtom(), denoptim.graph.Fragment.getConnectedAtomsList(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), and denoptim.graph.Fragment.removeAtom().
Referenced by denoptim.ga.GraphOperationsTest.testAddFusedRings(), denoptim.ga.EAUtilsTest.testFusionSiteDetection_ImposeSymmetry(), denoptim.ga.EAUtilsTest.testGetUsableAliphaticBridges(), and denoptim.ga.EAUtilsTest.testSearchForApPairsSuitableToRingFusion().
| void denoptim.ga.EAUtilsTest.testAvoidRedundantXOver | ( | ) | throws Exception |
Definition at line 230 of file EAUtilsTest.java.
References denoptim.ga.Population.add(), denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.graph.DGraph.clone(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.ga.EAUtilsTest.prepare(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.Vertex.setBuildingBlockType(), and denoptim.programs.RunTimeParameters.setParameters().
| void denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure | ( | ) | throws Exception |
Definition at line 456 of file EAUtilsTest.java.
References denoptim.ga.Population.add(), denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.graph.Template.ContractLevel.FIXED_STRUCT, denoptim.graph.Candidate.getGraph(), denoptim.graph.Template.getInnerGraph(), denoptim.ga.PopulationTest.getPairOfTestGraphsB(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.DGraph.isIsomorphicTo(), denoptim.graph.DGraph.isIsostructuralTo(), denoptim.ga.PopulationTest.prepare(), and denoptim.graph.Template.setContractLevel().
| void denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_Free | ( | ) | throws Exception |
NB: the graphs from methods getPairOfTestGraphsB() and getPairOfTestGraphsBxo() and
getPairOfTestGraphsBxoxo() are a sequence resulting from crossover operations.
Note that the order of APs in on the templates changes as a result of the crossover. For this reason, the backwards crossover of the graphs from getPairOfTestGraphsBxo() does not produce the graphs from getPairOfTestGraphsB(), but those from getPairOfTestGraphsBxoxo().
Definition at line 348 of file EAUtilsTest.java.
References denoptim.ga.Population.add(), denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.graph.Template.ContractLevel.FREE, denoptim.graph.Candidate.getGraph(), denoptim.ga.PopulationTest.getPairOfTestGraphsB(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxo(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.ga.PopulationTest.prepare(), and denoptim.graph.DGraph.sameAs().
| void denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FreeBackwards | ( | ) | throws Exception |
NB: the graphs from methods getPairOfTestGraphsB() and getPairOfTestGraphsBxo() and
getPairOfTestGraphsBxoxo() are a sequence resulting from crossover operations.
Note that the order of APs in on the templates changes as a result of the crossover. For this reason, the backwards crossover of the graphs from getPairOfTestGraphsBxo() does not produce the graphs from getPairOfTestGraphsB(), but those from getPairOfTestGraphsBxoxo().
Definition at line 407 of file EAUtilsTest.java.
References denoptim.ga.Population.add(), denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.graph.Template.ContractLevel.FREE, denoptim.graph.Candidate.getGraph(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxo(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxoxo(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.ga.PopulationTest.prepare(), and denoptim.graph.DGraph.sameAs().
| void denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph | ( | ) | throws Exception |
Definition at line 271 of file EAUtilsTest.java.
References denoptim.ga.Population.add(), denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.Candidate.getGraph(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), denoptim.ga.PopulationTest.makeGraphA(), denoptim.ga.PopulationTest.makeGraphE(), denoptim.ga.PopulationTest.prepare(), and denoptim.graph.Candidate.setFitness().
| void denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold | ( | ) | throws Exception |
Definition at line 200 of file EAUtilsTest.java.
References denoptim.ga.EAUtils.buildGraph(), denoptim.graph.Template.getMutationSites(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.ga.EAUtilsTest.prepare(), and denoptim.programs.RunTimeParameters.setParameters().
| void denoptim.ga.EAUtilsTest.testCandidateGenerationMethod | ( | ) | throws Exception |
Definition at line 565 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.c, and denoptim.ga.EAUtils.pickNewCandidateGenerationMode().
| void denoptim.ga.EAUtilsTest.testCandidateGenerationMethodReproducibility | ( | ) | throws Exception |
Definition at line 605 of file EAUtilsTest.java.
References denoptim.ga.EAUtils.pickNewCandidateGenerationMode().
| void denoptim.ga.EAUtilsTest.testChooseNumberOfSitesToMutate | ( | ) | throws Exception |
Definition at line 731 of file EAUtilsTest.java.
References denoptim.ga.EAUtils.chooseNumberOfSitesToMutate().
| void denoptim.ga.EAUtilsTest.testCrowdingProbability | ( | ) | throws Exception |
Definition at line 654 of file EAUtilsTest.java.
References denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getAttachmentPoints(), denoptim.ga.EAUtils.getCrowdingProbability(), denoptim.graph.DGraph.getVertexAtPosition(), and denoptim.graph.DGraphTest.makeTestGraphA().
| void denoptim.ga.EAUtilsTest.testFusionSiteDetection_ImposeSymmetry | ( | ) | throws Exception |
Definition at line 2288 of file EAUtilsTest.java.
References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.DGraph.addVertex(), denoptim.ga.EAUtilsTest.builder, denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.APClass.make(), denoptim.ga.EAUtilsTest.replaceHatomWithAP(), denoptim.ga.EAUtils.searchRingFusionSites(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.fragspace.FragmentSpace.setSymmConstraints().
| void denoptim.ga.EAUtilsTest.testGetUsableAliphaticBridges | ( | ) | throws Exception |
Definition at line 2495 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.builder, denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.ga.EAUtils.getUsableAliphaticBridges(), denoptim.graph.APClass.make(), denoptim.ga.EAUtilsTest.replaceHatomWithAP(), and denoptim.graph.Vertex.setBuildingBlockId().
| void denoptim.ga.EAUtilsTest.testGetUsableAromaticBridges | ( | ) | throws Exception |
Definition at line 2394 of file EAUtilsTest.java.
References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.ga.EAUtils.getUsableAromaticBridges(), and denoptim.graph.APClass.make().
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol | ( | ) | throws Exception |
Definition at line 757 of file EAUtilsTest.java.
References denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.Template.ContractLevel.FIXED, denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.Template.getContractLevel(), denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.Template.getInnerGraph(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.ga.EAUtilsTest.NL, denoptim.io.DenoptimIO.readSDFFile(), denoptim.graph.GraphPattern.RING, denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.ga.EAUtilsTest.SEP, denoptim.ga.EAUtilsTest.tempDir, and denoptim.io.DenoptimIO.writeData().
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_cappingGroups | ( | ) | throws Exception |
Definition at line 1227 of file EAUtilsTest.java.
References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.ga.EAUtilsTest.builder, denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getVertexCount(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, denoptim.graph.APClass.make(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.graph.DGraph.removeCappingGroups(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.programs.RunTimeParameters.setParameters().
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities | ( | ) | throws Exception |
Definition at line 1037 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.a, denoptim.ga.EAUtilsTest.builder, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.graph.DGraph.getEdgeCount(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getRingCount(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy | ( | ) | throws Exception |
Definition at line 886 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.builder, denoptim.fragmenter.ScaffoldingPolicy.ELEMENT, denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.Vertex.getIAtomContainer(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.graph.Vertex.BBType.SCAFFOLD.
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_Symmetry | ( | ) | throws Exception |
Definition at line 941 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.builder, denoptim.fragmenter.ScaffoldingPolicy.ELEMENT, denoptim.graph.DGraph.getEdgeCount(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymSetsIterator(), denoptim.graph.DGraph.getVertexCount(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().
| void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_symmetry | ( | ) | throws Exception |
Test the detection of "some" symmetry.
: a topology that would result in something close to a C3 point group geometry. Three symmetric branches that form a three-cyclic system. This method tests the capacity to detect that vertexes that have no sym set of APs but can be flagged as symmetric because they are part of a chain rooted on a vertex with sym APs (i.e., the bridge head).
Definition at line 1134 of file EAUtilsTest.java.
References denoptim.ga.EAUtilsTest.builder, denoptim.fragmenter.ScaffoldingPolicy.ELEMENT, denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.getVertexWithId(), denoptim.fragmenter.ScaffoldingPolicy.LARGEST_FRAGMENT, and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().
| void denoptim.ga.EAUtilsTest.testSearchForApPairsSuitableToRingFusion | ( | ) | throws Exception |
Definition at line 1295 of file EAUtilsTest.java.
References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.RelatedAPPair.apA, denoptim.graph.RelatedAPPair.apB, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.ga.EAUtilsTest.builder, denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getAttachmentPoints(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.fragspace.FragmentSpace.getPolarizedRCV(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.APClass.make(), denoptim.graph.RelatedAPPair.propID, denoptim.ga.EAUtilsTest.replaceHatomWithAP(), denoptim.ga.EAUtils.searchRingFusionSites(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.graph.Vertex.setVertexId().
| void denoptim.ga.EAUtilsTest.testSelectNonScaffoldNonCapVertex | ( | ) | throws Exception |
Definition at line 681 of file EAUtilsTest.java.
References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.ga.EAUtils.selectNonScaffoldNonCapVertex(), and denoptim.graph.Vertex.setBuildingBlockType().
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Definition at line 91 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare(), and denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities().
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Definition at line 90 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare().
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Definition at line 90 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare().
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Definition at line 90 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare().
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Definition at line 91 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare().
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Private builder of atom containers.
Definition at line 99 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.testFusionSiteDetection_ImposeSymmetry(), denoptim.ga.EAUtilsTest.testGetUsableAliphaticBridges(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_cappingGroups(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_Symmetry(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_symmetry(), and denoptim.ga.EAUtilsTest.testSearchForApPairsSuitableToRingFusion().
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Definition at line 91 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.prepare(), and denoptim.ga.EAUtilsTest.testCandidateGenerationMethod().
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Definition at line 94 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().
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Definition at line 93 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().
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Definition at line 102 of file EAUtilsTest.java.
Referenced by denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().