Unit test. More...

Collaboration diagram for denoptim.ga.EAUtilsTest:

Public Member Functions
void	testBuildGraphFromTemplateScaffold () throws Exception

void	testAvoidRedundantXOver () throws Exception

void	testBuildByXOver_SubGraph () throws Exception

void	testBuildByXOver_Embedded_Free () throws Exception
	NB: the graphs from methods `getPairOfTestGraphsB()` and `getPairOfTestGraphsBxo()` and `getPairOfTestGraphsBxoxo()` are a sequence resulting from crossover operations. More...

void	testBuildByXOver_Embedded_FreeBackwards () throws Exception
	NB: the graphs from methods `getPairOfTestGraphsB()` and `getPairOfTestGraphsBxo()` and `getPairOfTestGraphsBxoxo()` are a sequence resulting from crossover operations. More...

void	testBuildByXOver_Embedded_FixedStructure () throws Exception

void	testCandidateGenerationMethod () throws Exception

void	testCandidateGenerationMethodReproducibility () throws Exception

void	testCrowdingProbability () throws Exception

void	testSelectNonScaffoldNonCapVertex () throws Exception

void	testChooseNumberOfSitesToMutate () throws Exception

void	testMakeGraphFromFragmentationOfMol () throws Exception

void	testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy () throws Exception

void	testMakeGraphFromFragmentationOfMol_Symmetry () throws Exception

void	testMakeGraphFromFragmentationOfMol_linearities () throws Exception

void	testMakeGraphFromFragmentationOfMol_symmetry () throws Exception
	Test the detection of "some" symmetry. More...

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")

Detailed Description

Unit test.

Author: Marco Foscato

Definition at line 76 of file EAUtilsTest.java.

Member Function Documentation

◆ prepare()

FragmentSpaceParameters denoptim.ga.EAUtilsTest.prepare ( ) throws DENOPTIMException

private

Definition at line 95 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().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ testAvoidRedundantXOver()

void denoptim.ga.EAUtilsTest.testAvoidRedundantXOver ( ) throws Exception

Definition at line 219 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().

Here is the call graph for this function:

◆ testBuildByXOver_Embedded_FixedStructure()

void denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure ( ) throws Exception

Definition at line 445 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().

Here is the call graph for this function:

◆ testBuildByXOver_Embedded_Free()

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 337 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().

Here is the call graph for this function:

◆ testBuildByXOver_Embedded_FreeBackwards()

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 396 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().

Here is the call graph for this function:

◆ testBuildByXOver_SubGraph()

void denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph ( ) throws Exception

Definition at line 260 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().

Here is the call graph for this function:

◆ testBuildGraphFromTemplateScaffold()

void denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold ( ) throws Exception

Definition at line 189 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().

Here is the call graph for this function:

◆ testCandidateGenerationMethod()

void denoptim.ga.EAUtilsTest.testCandidateGenerationMethod ( ) throws Exception

Definition at line 554 of file EAUtilsTest.java.

References denoptim.ga.EAUtilsTest.c, and denoptim.ga.EAUtils.pickNewCandidateGenerationMode().

Here is the call graph for this function:

◆ testCandidateGenerationMethodReproducibility()

void denoptim.ga.EAUtilsTest.testCandidateGenerationMethodReproducibility ( ) throws Exception

Definition at line 594 of file EAUtilsTest.java.

References denoptim.ga.EAUtils.pickNewCandidateGenerationMode().

Here is the call graph for this function:

◆ testChooseNumberOfSitesToMutate()

void denoptim.ga.EAUtilsTest.testChooseNumberOfSitesToMutate ( ) throws Exception

Definition at line 720 of file EAUtilsTest.java.

References denoptim.ga.EAUtils.chooseNumberOfSitesToMutate().

Here is the call graph for this function:

◆ testCrowdingProbability()

void denoptim.ga.EAUtilsTest.testCrowdingProbability ( ) throws Exception

Definition at line 643 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().

Here is the call graph for this function:

◆ testMakeGraphFromFragmentationOfMol()

void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol ( ) throws Exception

Definition at line 746 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().

Here is the call graph for this function:

◆ testMakeGraphFromFragmentationOfMol_linearities()

void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities ( ) throws Exception

Definition at line 1038 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().

Here is the call graph for this function:

◆ testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy()

void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy ( ) throws Exception

Definition at line 875 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.

Here is the call graph for this function:

◆ testMakeGraphFromFragmentationOfMol_Symmetry()

void denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_Symmetry ( ) throws Exception

Definition at line 936 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().

Here is the call graph for this function:

◆ testMakeGraphFromFragmentationOfMol_symmetry()

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 1135 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(), and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().

Here is the call graph for this function: