Utilities for graphs. More...

Collaboration diagram for denoptim.utils.GraphUtils:

Static Public Member Functions
static synchronized void	ensureVertexIDConsistency (long l) throws DENOPTIMException
	Method used to ensure consistency between internal atomic integer and vertex id from imported graphs. More...

static synchronized void	resetUniqueVertexCounter (long l) throws DENOPTIMException
	Reset the unique vertex counter to the given value. More...

static synchronized long	getUniqueVertexIndex ()
	Unique counter for the number of graph vertices generated. More...

static synchronized void	resetUniqueGraphCounter (int val) throws DENOPTIMException
	Reset the unique graph counter to the given value. More...

static synchronized int	getUniqueGraphIndex ()
	Unique counter for the number of graphs generated. More...

static synchronized void	resetUniqueMoleculeCounter (int val) throws DENOPTIMException
	Reset the unique mol counter to the given value. More...

static synchronized int	getUniqueMoleculeIndex ()
	Unique counter for the number of molecules generated. More...

static void	writeSDFFields (IAtomContainer iac, DGraph g) throws DENOPTIMException

static String	getLabel (Vertex v)

static String	getLabel (DGraph g, int vIdx)

Static Public Attributes
static AtomicLong	vertexCounter = new AtomicLong(1)

Static Private Attributes
static AtomicInteger	graphCounter = new AtomicInteger(1)

static AtomicInteger	molCounter = new AtomicInteger(1)

Detailed Description

Utilities for graphs.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 39 of file GraphUtils.java.

Member Function Documentation

◆ ensureVertexIDConsistency()

static synchronized void denoptim.utils.GraphUtils.ensureVertexIDConsistency ( long l ) throws DENOPTIMException

static

Method used to ensure consistency between internal atomic integer and vertex id from imported graphs.

The latter can be greater than the first, thus requiring a reset of the atomic integer to a new, larger than before, value.

Parameters

g

Exceptions

DENOPTIMException

Definition at line 55 of file GraphUtils.java.

References denoptim.utils.GraphUtils.getUniqueVertexIndex(), and denoptim.utils.GraphUtils.resetUniqueVertexCounter().

Referenced by denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.DGraph.insertVertex(), denoptim.graph.DGraph.removeVertexAndWeld(), denoptim.graph.DGraph.replaceSubGraph(), denoptim.graph.DGraph.replaceVertex(), and denoptim.ga.EAUtils.setVertexCounterValue().

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◆ getLabel() [1/2]

static String denoptim.utils.GraphUtils.getLabel	(	DGraph	g,
		int	vIdx
	)

static

Definition at line 220 of file GraphUtils.java.

References denoptim.graph.DGraph.getGraphId(), denoptim.graph.Vertex.getProperty(), denoptim.graph.DGraph.getVertexAtPosition(), and denoptim.graph.Vertex.hasProperty().

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◆ getLabel() [2/2]

static String denoptim.utils.GraphUtils.getLabel ( Vertex v )

static

Definition at line 210 of file GraphUtils.java.

References denoptim.graph.DGraph.getGraphId(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.Vertex.getProperty(), and denoptim.graph.Vertex.hasProperty().

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

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◆ getUniqueGraphIndex()

static synchronized int denoptim.utils.GraphUtils.getUniqueGraphIndex ( )

static

Unique counter for the number of graphs generated.

Returns: a new Graph id (number)

Exceptions

DENOPTIMException

Definition at line 142 of file GraphUtils.java.

References denoptim.utils.GraphUtils.graphCounter.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.buildGraph(), denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.ga.EAUtils.getPopulationFromFile(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), and denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold().

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◆ getUniqueMoleculeIndex()

static synchronized int denoptim.utils.GraphUtils.getUniqueMoleculeIndex ( )

static

Unique counter for the number of molecules generated.

Returns: the new molecule id (number)

Definition at line 184 of file GraphUtils.java.

References denoptim.utils.GraphUtils.molCounter.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.getPopulationFromFile(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), denoptim.ga.EAUtils.readCandidateFromFile(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

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◆ getUniqueVertexIndex()

static synchronized long denoptim.utils.GraphUtils.getUniqueVertexIndex ( )

static

Unique counter for the number of graph vertices generated.

Returns: the new vertex id (number)

Definition at line 97 of file GraphUtils.java.

References denoptim.utils.GraphUtils.vertexCounter.

Referenced by denoptim.graph.DGraph.addCappingGroups(), denoptim.ga.GraphOperations.addRing(), denoptim.ga.GraphOperations.attachFragmentInClosableChain(), denoptim.ga.GraphOperationsTest.buildFragment(), denoptim.graph.EmptyVertex.EmptyVertex(), denoptim.utils.GraphUtils.ensureVertexIDConsistency(), denoptim.ga.GraphOperations.extendGraph(), denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), denoptim.graph.TemplateTest.getAmideFragment(), denoptim.fragspace.FragmentSpaceTest.getCarbonVertex(), denoptim.graph.TemplateTest.getCH2Fragment(), denoptim.graph.TemplateTest.getOHFragment(), denoptim.fragspace.FragmentSpaceTest.getRCV(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), denoptim.graph.DGraph.insertVertex(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), denoptim.fragspace.FragmentSpace.makeRandomScaffold(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.fragspace.FragsCombinationIterator.next(), denoptim.graph.DGraph.renumberVerticesGetMap(), denoptim.graph.DGraph.replaceVertex(), denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold(), denoptim.fragspace.FragmentSpaceTest.testSymmetry(), and denoptim.graph.Vertex.Vertex().

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◆ resetUniqueGraphCounter()

static synchronized void denoptim.utils.GraphUtils.resetUniqueGraphCounter ( int val ) throws DENOPTIMException

static

Reset the unique graph counter to the given value.

In order to keep the uniqueness on the index, this method accepts only reset values that are higher that the current one. Attempts to reset to lower values return an exception.

Parameters

val	the new value for the counter. This value will be given to next call of the getUniqueGraphIndex method.

Exceptions

DENOPTIMException if the reset value is lower than the current value of the index.

Definition at line 121 of file GraphUtils.java.

References denoptim.utils.GraphUtils.graphCounter.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ resetUniqueMoleculeCounter()

static synchronized void denoptim.utils.GraphUtils.resetUniqueMoleculeCounter ( int val ) throws DENOPTIMException

static

Reset the unique mol counter to the given value.

In order to keep the uniqueness on the index, this method accepts only reset values that are higher that the current one. Attempts to reset to lower values return an exception.

Parameters

val	the new value for the counter. This value will be given to next call of the getUniqueMoleculeIndex method.

Exceptions

DENOPTIMException if the reset value is lower than the current value of the index.

Definition at line 164 of file GraphUtils.java.

References denoptim.utils.GraphUtils.molCounter.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ resetUniqueVertexCounter()

static synchronized void denoptim.utils.GraphUtils.resetUniqueVertexCounter ( long l ) throws DENOPTIMException

static

Reset the unique vertex counter to the given value.

In order to keep the uniqueness on the index, this method accepts only reset values that are higher that the current one. Attempts to reset to lower values return an exception.

Parameters

l	the new value for the counter. This value will be given to next call of the getUniqueVertexIndex method.

Exceptions

DENOPTIMException if the reset value is lower than the current value of the index.

Definition at line 77 of file GraphUtils.java.

References denoptim.utils.GraphUtils.vertexCounter.

Referenced by denoptim.utils.GraphUtils.ensureVertexIDConsistency(), and denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ writeSDFFields()

static void denoptim.utils.GraphUtils.writeSDFFields	(	IAtomContainer	iac,
		DGraph	g
	)		throws DENOPTIMException

static

Definition at line 195 of file GraphUtils.java.

References denoptim.constants.DENOPTIMConstants.GCODETAG, denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, denoptim.constants.DENOPTIMConstants.GRAPHTAG, and denoptim.constants.DENOPTIMConstants.PROVENANCE.

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), and denoptim.io.DenoptimIO.writeGraphsToSDF().

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Member Data Documentation

◆ graphCounter

AtomicInteger denoptim.utils.GraphUtils.graphCounter = new AtomicInteger(1)

staticprivate

Definition at line 42 of file GraphUtils.java.

Referenced by denoptim.utils.GraphUtils.getUniqueGraphIndex(), and denoptim.utils.GraphUtils.resetUniqueGraphCounter().

◆ molCounter

AtomicInteger denoptim.utils.GraphUtils.molCounter = new AtomicInteger(1)

staticprivate

Definition at line 43 of file GraphUtils.java.

Referenced by denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), and denoptim.utils.GraphUtils.resetUniqueMoleculeCounter().

◆ vertexCounter

AtomicLong denoptim.utils.GraphUtils.vertexCounter = new AtomicLong(1)

static

Definition at line 41 of file GraphUtils.java.

Referenced by denoptim.utils.GraphUtils.getUniqueVertexIndex(), and denoptim.utils.GraphUtils.resetUniqueVertexCounter().

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

/github/workspace/src/main/java/denoptim/utils/GraphUtils.java

Static Public Member Functions

Static Public Attributes

Static Private Attributes

Detailed Description

Member Function Documentation

◆ ensureVertexIDConsistency()

◆ getLabel() [1/2]

◆ getLabel() [2/2]

◆ getUniqueGraphIndex()

◆ getUniqueMoleculeIndex()

◆ getUniqueVertexIndex()

◆ resetUniqueGraphCounter()

◆ resetUniqueMoleculeCounter()

◆ resetUniqueVertexCounter()

◆ writeSDFFields()

Member Data Documentation

◆ graphCounter

◆ molCounter

◆ vertexCounter