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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().