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	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 84 of file GraphOperationsTest.java.

Member Function Documentation

◆ addRings()

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

private

Definition at line 276 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 329 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 240 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 301 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 172 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 644 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 355 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 373 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 819 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 95 of file GraphOperationsTest.java.

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

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◆ testAddRing()

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

Definition at line 860 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 995 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 140 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 127 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 106 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 448 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 86 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 86 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 86 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 86 of file GraphOperationsTest.java.

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

◆ chemBuilder

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

package

Definition at line 88 of file GraphOperationsTest.java.

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

◆ DEFAULT_APCLASS

APClass denoptim.ga.GraphOperationsTest.DEFAULT_APCLASS

staticprivate

Definition at line 90 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 89 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()

◆ testAddRing()

◆ testExtendGraph()

◆ testExtractPattern_fusedRings()

◆ testExtractPattern_returnsEmptyListIfNoRings()

◆ testExtractPattern_singleRingSystem()

◆ testLocateCompatibleXOverPoints()

Member Data Documentation

◆ APCA

◆ APCB

◆ APCC

◆ APCD

◆ chemBuilder

◆ DEFAULT_APCLASS

◆ rng