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DENOPTIM
denoptim.ga.EAUtilsTest Class Reference

Unit test. More...

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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...
 
void testMakeGraphFromFragmentationOfMol_cappingGroups () throws Exception
 
void testSearchForApPairsSuitableToRingFusion () throws Exception
 
void testFusionSiteDetection_ImposeSymmetry () throws Exception
 
void testGetUsableAromaticBridges () throws Exception
 
void testGetUsableAliphaticBridges () throws Exception
 

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")
 

Detailed Description

Unit test.

Author
Marco Foscato

Definition at line 87 of file EAUtilsTest.java.

Member Function Documentation

◆ prepare()

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

◆ replaceHatomWithAP()

static void denoptim.ga.EAUtilsTest.replaceHatomWithAP ( Fragment  frag,
int  srcId,
APClass  apc 
)
static

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().

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◆ testAvoidRedundantXOver()

◆ testBuildByXOver_Embedded_FixedStructure()

◆ 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 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().

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◆ 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 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().

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◆ testBuildByXOver_SubGraph()

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

◆ testBuildGraphFromTemplateScaffold()

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().

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◆ testCandidateGenerationMethod()

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().

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◆ testCandidateGenerationMethodReproducibility()

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

Definition at line 605 of file EAUtilsTest.java.

References denoptim.ga.EAUtils.pickNewCandidateGenerationMode().

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◆ testChooseNumberOfSitesToMutate()

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

Definition at line 731 of file EAUtilsTest.java.

References denoptim.ga.EAUtils.chooseNumberOfSitesToMutate().

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◆ testCrowdingProbability()

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().

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◆ testFusionSiteDetection_ImposeSymmetry()

◆ testGetUsableAliphaticBridges()

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().

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◆ testGetUsableAromaticBridges()

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().

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◆ testMakeGraphFromFragmentationOfMol()

◆ testMakeGraphFromFragmentationOfMol_cappingGroups()

◆ testMakeGraphFromFragmentationOfMol_linearities()

◆ testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy()

◆ testMakeGraphFromFragmentationOfMol_Symmetry()

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

◆ 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 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().

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◆ testSearchForApPairsSuitableToRingFusion()

◆ testSelectNonScaffoldNonCapVertex()

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

Member Data Documentation

◆ a

String denoptim.ga.EAUtilsTest.a ="A"
staticprivate

◆ APCA

APClass denoptim.ga.EAUtilsTest.APCA
staticprivate

Definition at line 90 of file EAUtilsTest.java.

Referenced by denoptim.ga.EAUtilsTest.prepare().

◆ APCB

APClass denoptim.ga.EAUtilsTest.APCB
staticprivate

Definition at line 90 of file EAUtilsTest.java.

Referenced by denoptim.ga.EAUtilsTest.prepare().

◆ APCC

APClass denoptim.ga.EAUtilsTest.APCC
staticprivate

Definition at line 90 of file EAUtilsTest.java.

Referenced by denoptim.ga.EAUtilsTest.prepare().

◆ b

String denoptim.ga.EAUtilsTest.b ="B"
staticprivate

Definition at line 91 of file EAUtilsTest.java.

Referenced by denoptim.ga.EAUtilsTest.prepare().

◆ builder

◆ c

String denoptim.ga.EAUtilsTest.c ="C"
staticprivate

◆ NL

final String denoptim.ga.EAUtilsTest.NL = System.getProperty("line.separator")
staticprivate

◆ SEP

final String denoptim.ga.EAUtilsTest.SEP = System.getProperty("file.separator")
staticprivate

◆ tempDir

File denoptim.ga.EAUtilsTest.tempDir
staticpackage

The documentation for this class was generated from the following file: