Unit test. More...

Collaboration diagram for denoptim.ga.GraphOperationsTest:

Classes
class	ExtractPatternCase

Public Member Functions
void	testExtractPattern_singleRingSystem () throws Throwable

void	testExtractPattern_returnsEmptyListIfNoRings () throws Throwable

void	testExtractPattern_fusedRings () throws Throwable

void	testLocateCompatibleXOverPoints () throws Exception

void	testAddRing () throws Exception

void	testAddFusedRings () throws Exception

void	testExtendGraph () throws Exception

Static Package Functions
static void	setUpClass ()

Package Attributes
IChemObjectBuilder	chemBuilder = DefaultChemObjectBuilder.getInstance()

Private Member Functions
ExtractPatternCase	getFusedRings () throws Throwable
	Returns a molecule consisting of two pairs of fused rings connected by an oxygen atom. More...

DGraph	buildGraph (List< Vertex > vertices, List< List< Integer > > edges) throws DENOPTIMException

void	addRings (List< Vertex > vertices, DGraph g)

Set< DGraph >	getExpectedSubgraphs (DGraph graph)

Vertex	buildFragment (String elementSymbol, int apCount, boolean isRCV)

Point3d	getRandomVector ()

DGraph	getThreeCycle () throws DENOPTIMException
	Returns a 3-cycle. More...

DGraph[]	getPairOfTestGraphs () throws Exception
	Generates a pair of graphs that include templates with free content. More...

FragmentSpace	prepare () throws Exception
	Sets the compatibility matrix (src -> trg);. More...

Private Attributes
final Random	rng = new Random()

Static Private Attributes
static APClass	APCA

static APClass	APCB

static APClass	APCC

static APClass	APCD

static APClass	DEFAULT_APCLASS

Detailed Description

Unit test.

Author: Marco Foscato

Definition at line 90 of file GraphOperationsTest.java.

Member Function Documentation

◆ addRings()

void denoptim.ga.GraphOperationsTest.addRings	(	List< Vertex >	vertices,
		DGraph	g
	)

private

Definition at line 282 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.addRing(), and denoptim.graph.Ring.addVertex().

Referenced by denoptim.ga.GraphOperationsTest.getFusedRings().

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◆ buildFragment()

Vertex denoptim.ga.GraphOperationsTest.buildFragment	(	String	elementSymbol,
		int	apCount,
		boolean	isRCV
	)

private

Definition at line 335 of file GraphOperationsTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.ga.GraphOperationsTest.chemBuilder, denoptim.ga.GraphOperationsTest.DEFAULT_APCLASS, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.ga.GraphOperationsTest.getRandomVector(), and denoptim.utils.GraphUtils.getUniqueVertexIndex().

Referenced by denoptim.ga.GraphOperationsTest.getFusedRings().

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◆ buildGraph()

DGraph denoptim.ga.GraphOperationsTest.buildGraph	(	List< Vertex >	vertices,
		List< List< Integer > >	edges
	)		throws DENOPTIMException

private

Definition at line 246 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), and denoptim.graph.Vertex.getAttachmentPoints().

Referenced by denoptim.ga.GraphOperationsTest.getFusedRings().

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◆ getExpectedSubgraphs()

Set< DGraph > denoptim.ga.GraphOperationsTest.getExpectedSubgraphs ( DGraph graph )

private

Definition at line 307 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.DGraph.removeVertex().

Referenced by denoptim.ga.GraphOperationsTest.getFusedRings().

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◆ getFusedRings()

ExtractPatternCase denoptim.ga.GraphOperationsTest.getFusedRings ( ) throws Throwable

private

Returns a molecule consisting of two pairs of fused rings connected by an oxygen atom.

The dots represents chords. The molecule looks as follows: Cl | ↑ O - C - C → ← N - | . | . ↑ . | . N - C - O - C - C - C → . | . | . ↓ . . N . . O . .

The atoms are labelled in order of the leftmost then topmost. 2 | ↑ 0 - 1 - 4 → ← 12 - | . | . ↑ . | . 3 - 6 - 7 - 8 - 10 - 11 → . | . | . ↓ . . 5 . . 9 . .

Definition at line 178 of file GraphOperationsTest.java.

References denoptim.ga.GraphOperationsTest.addRings(), denoptim.ga.GraphOperationsTest.buildFragment(), denoptim.ga.GraphOperationsTest.buildGraph(), denoptim.ga.GraphOperationsTest.getExpectedSubgraphs(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.DGraph.setScaffold().

Referenced by denoptim.ga.GraphOperationsTest.testExtractPattern_fusedRings().

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◆ getPairOfTestGraphs()

DGraph[] denoptim.ga.GraphOperationsTest.getPairOfTestGraphs ( ) throws Exception

private

Generates a pair of graphs that include templates with free content.

The first graph is

               (A)--(A)-m5
              /
 m1-(A)--(A)-T1-(A)--(A)-m2-(B)--(B)-m3
              \
               (C)--(C)-m4

where template 'T1' is:

 
    (A)         (C)
   /           /
 tv0-(A)--(A)-tv1-(B)--(C)-tv2-(A)--(A)-tv3-(A)-
               \
                (A)--(A)-tv4-(A)--(A)-tv5-(A)-

And the second graph is

 f1-(A)--(A)-T1-(A)--(A)-f2-(B)--(B)-f3-(C)--(C)-f4
              \
               (C)--(C)-f5

where template 'T2' is:

 
        (C)
       /
 -(A)-tw1-(B)--(C)-tw2-(B)--(B)-tw3-(A)-(A)-tw4-(A)

Definition at line 650 of file GraphOperationsTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.ga.GraphOperationsTest.APCA, denoptim.ga.GraphOperationsTest.APCB, denoptim.ga.GraphOperationsTest.APCC, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Template.ContractLevel.FREE, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.BBType.NONE, denoptim.ga.GraphOperationsTest.prepare(), denoptim.graph.Template.setContractLevel(), denoptim.graph.DGraph.setGraphId(), denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Vertex.setProperty().

Referenced by denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints().

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◆ getRandomVector()

Point3d denoptim.ga.GraphOperationsTest.getRandomVector ( )

private

Definition at line 361 of file GraphOperationsTest.java.

References denoptim.ga.GraphOperationsTest.rng.

Referenced by denoptim.ga.GraphOperationsTest.buildFragment().

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◆ getThreeCycle()

DGraph denoptim.ga.GraphOperationsTest.getThreeCycle ( ) throws DENOPTIMException

private

Returns a 3-cycle.

The S marks the scaffold vertex: /— S —\ / \ RCV -(chord)- RCV

Definition at line 379 of file GraphOperationsTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.ga.GraphOperationsTest.testExtractPattern_returnsEmptyListIfNoRings(), and denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem().

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◆ prepare()

FragmentSpace denoptim.ga.GraphOperationsTest.prepare ( ) throws Exception

private

Sets the compatibility matrix (src -> trg);.

     |  A  |  B  |  C  |  D  |
   ---------------------------
   A |  T  |     |     |     |
   ---------------------------
   B |     |  T  |  T  |     |
   ---------------------------
   C |     |     |  T   |     |
   ---------------------------
   D |     |     |     |  T  |

Definition at line 825 of file GraphOperationsTest.java.

References denoptim.ga.GraphOperationsTest.APCA, denoptim.ga.GraphOperationsTest.APCB, denoptim.ga.GraphOperationsTest.APCC, denoptim.ga.GraphOperationsTest.APCD, denoptim.graph.APClass.make(), and denoptim.fragspace.FragmentSpace.setAPclassBasedApproach().

Referenced by denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), and denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints().

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◆ setUpClass()

static void denoptim.ga.GraphOperationsTest.setUpClass ( )

staticpackage

Definition at line 101 of file GraphOperationsTest.java.

References denoptim.ga.GraphOperationsTest.DEFAULT_APCLASS, and denoptim.graph.APClass.make().

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◆ testAddFusedRings()

void denoptim.ga.GraphOperationsTest.testAddFusedRings ( ) throws Exception

Definition at line 995 of file GraphOperationsTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.ga.GraphOperations.addFusedRing(), denoptim.graph.DGraph.addVertex(), denoptim.ga.GraphOperationsTest.chemBuilder, denoptim.utils.MoleculeUtils.countAtomsOfElement(), denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.APClass.make(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.ga.EAUtilsTest.replaceHatomWithAP(), denoptim.programs.RunTimeParameters.setParameters(), denoptim.programs.RunTimeParameters.setRandomizer(), denoptim.graph.rings.RingClosureParameters.setRingSizeBias(), and denoptim.graph.Vertex.setVertexId().

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◆ testAddRing()

void denoptim.ga.GraphOperationsTest.testAddRing ( ) throws Exception

Definition at line 866 of file GraphOperationsTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.ga.GraphOperations.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.ga.GraphOperationsTest.chemBuilder, denoptim.graph.Fragment.clone(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.rings.RingClosureParameters.getMaxRingSize(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.APClass.make(), denoptim.graph.APClass.RCACLASSMINUS, denoptim.graph.APClass.RCACLASSPLUS, denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS, denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), denoptim.graph.Vertex.setAsRCV(), denoptim.programs.RunTimeParameters.setParameters(), denoptim.graph.rings.RingClosureParameters.setRingSizeBias(), and denoptim.graph.Vertex.setVertexId().

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◆ testExtendGraph()

void denoptim.ga.GraphOperationsTest.testExtendGraph ( ) throws Exception

Definition at line 1178 of file GraphOperationsTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.ga.GraphOperationsTest.APCA, denoptim.ga.GraphOperationsTest.APCB, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Fragment.clone(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymVerticesForVertex(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.APClass.make(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), denoptim.programs.RunTimeParameters.setParameters(), and denoptim.graph.Vertex.setVertexId().

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◆ testExtractPattern_fusedRings()

void denoptim.ga.GraphOperationsTest.testExtractPattern_fusedRings ( ) throws Throwable

Definition at line 146 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.extractPattern(), denoptim.ga.GraphOperationsTest.ExtractPatternCase.g, denoptim.ga.GraphOperationsTest.getFusedRings(), denoptim.ga.GraphOperationsTest.ExtractPatternCase.matchesExpected(), and denoptim.graph.GraphPattern.RING.

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◆ testExtractPattern_returnsEmptyListIfNoRings()

void denoptim.ga.GraphOperationsTest.testExtractPattern_returnsEmptyListIfNoRings ( ) throws Throwable

Definition at line 133 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.extractPattern(), denoptim.graph.DGraph.getRings(), denoptim.ga.GraphOperationsTest.getThreeCycle(), denoptim.graph.DGraph.removeRing(), and denoptim.graph.GraphPattern.RING.

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◆ testExtractPattern_singleRingSystem()

void denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem ( ) throws Throwable

Definition at line 112 of file GraphOperationsTest.java.

References denoptim.graph.DGraph.compareGraphNodes(), denoptim.graph.DGraph.extractPattern(), denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getSourceVertex(), denoptim.ga.GraphOperationsTest.getThreeCycle(), denoptim.graph.DGraph.getVertexCount(), and denoptim.graph.GraphPattern.RING.

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◆ testLocateCompatibleXOverPoints()

void denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints ( ) throws Exception

Definition at line 454 of file GraphOperationsTest.java.

References denoptim.graph.Template.ContractLevel.FIXED, denoptim.graph.Template.ContractLevel.FIXED_STRUCT, denoptim.graph.Template.ContractLevel.FREE, denoptim.graph.Template.getInnerGraph(), denoptim.utils.GraphUtils.getLabel(), denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.indexOf(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.ga.GraphOperationsTest.prepare(), denoptim.graph.Template.setContractLevel(), denoptim.graph.Vertex.setProperty(), and denoptim.graph.Vertex.setUniquefyingProperty().

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Member Data Documentation

◆ APCA

APClass denoptim.ga.GraphOperationsTest.APCA

staticprivate

Definition at line 92 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), denoptim.ga.GraphOperationsTest.prepare(), and denoptim.ga.GraphOperationsTest.testExtendGraph().

◆ APCB

APClass denoptim.ga.GraphOperationsTest.APCB

staticprivate

Definition at line 92 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), denoptim.ga.GraphOperationsTest.prepare(), and denoptim.ga.GraphOperationsTest.testExtendGraph().

◆ APCC

APClass denoptim.ga.GraphOperationsTest.APCC

staticprivate

Definition at line 92 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), and denoptim.ga.GraphOperationsTest.prepare().

◆ APCD

APClass denoptim.ga.GraphOperationsTest.APCD

staticprivate

Definition at line 92 of file GraphOperationsTest.java.

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

◆ chemBuilder

IChemObjectBuilder denoptim.ga.GraphOperationsTest.chemBuilder = DefaultChemObjectBuilder.getInstance()

package

Definition at line 94 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.buildFragment(), denoptim.ga.GraphOperationsTest.testAddFusedRings(), and denoptim.ga.GraphOperationsTest.testAddRing().

◆ DEFAULT_APCLASS

APClass denoptim.ga.GraphOperationsTest.DEFAULT_APCLASS

staticprivate

Definition at line 96 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.buildFragment(), and denoptim.ga.GraphOperationsTest.setUpClass().

◆ rng

final Random denoptim.ga.GraphOperationsTest.rng = new Random()

private

Definition at line 95 of file GraphOperationsTest.java.

Referenced by denoptim.ga.GraphOperationsTest.getRandomVector().

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

/github/workspace/src/test/java/denoptim/ga/GraphOperationsTest.java

Classes

Public Member Functions

Static Package Functions

Package Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Function Documentation

◆ addRings()

◆ buildFragment()

◆ buildGraph()

◆ getExpectedSubgraphs()

◆ getFusedRings()

◆ getPairOfTestGraphs()

◆ getRandomVector()

◆ getThreeCycle()

◆ prepare()

◆ setUpClass()

◆ testAddFusedRings()

◆ testAddRing()

◆ testExtendGraph()

◆ testExtractPattern_fusedRings()

◆ testExtractPattern_returnsEmptyListIfNoRings()

◆ testExtractPattern_singleRingSystem()

◆ testLocateCompatibleXOverPoints()

Member Data Documentation

◆ APCA

◆ APCB

◆ APCC

◆ APCD

◆ chemBuilder

◆ DEFAULT_APCLASS

◆ rng