Collection of operators meant to alter graphs and associated utilities. More...

Classes
class	FragForClosabChains
	Private class representing a selected closable chain of fragments. More...

Static Public Member Functions
static List< XoverSite >	locateCompatibleXOverPoints (DGraph graphA, DGraph graphB, FragmentSpace fragSpace, int maxSizeXoverSubGraph) throws DENOPTIMException
	Identify crossover sites, i.e., subgraphs that can be swapped between two graphs (i.e., the parents). More...

static boolean	extendLink (Vertex vertex, int chosenAPId, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Inserts a vertex in between two connected vertexes that are identified by the one vertex holding the "source" end of the edge, and the identifier of the attachment point used by that edge. More...

static boolean	extendLink (Vertex vertex, int chosenAPId, int chosenNewVrtxId, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Inserts a vertex in between two connected vertexes that are identified by the one vertex holding the "source" end of the edge, and the identifier of the attachment point used by that edge. More...

static boolean	extendLink (Edge edge, int chosenBBIdx, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Replace an edge with two edges with a new vertex in between, thus inserting a vertex in between two directly connected vertexes, which will no longer be directly connected. More...

static boolean	performCrossover (XoverSite site, FragmentSpace fragSpace) throws DENOPTIMException
	Performs the crossover that swaps the two subgraphs defining the given `XoverSite`. More...

static boolean	performMutation (DGraph graph, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Tries to do mutate the given graph. More...

static boolean	performMutation (Vertex vertex, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Tries to do mutate the given vertex. More...

static boolean	performMutation (Vertex vertex, MutationType mType, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Mutates the given vertex according to the given mutation type, if possible. More...

static boolean	performMutation (Vertex vertex, MutationType mType, boolean force, int chosenVrtxIdx, int chosenApId, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Mutates the given vertex according to the given mutation type, if possible. More...

Static Protected Member Functions
static boolean	deleteLink (Vertex vertex, int chosenVrtxIdx, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Removes a vertex while merging as many of the child branches into the parent vertex. More...

static boolean	substituteLink (Vertex vertex, int chosenVrtxIdx, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Substitutes a vertex while keeping its surrounding. More...

static boolean	rebuildBranch (Vertex vertex, boolean force, int chosenVrtxIdx, int chosenApId, GAParameters settings) throws DENOPTIMException
	Substitutes a vertex and any child branch. More...

static boolean	deleteFragment (Vertex vertex) throws DENOPTIMException
	Deletion mutation removes the vertex and also the symmetric partners on its parent. More...

static boolean	deleteChain (Vertex vertex, Monitor mnt, FragmentSpace fragSpace) throws DENOPTIMException
	Deletes the given vertex and all other vertexes that are not connected to more than 2 non-capping group vertexes. More...

static boolean	addRing (Vertex vertex, Monitor mnt, boolean force, FragmentSpace fragSpace, GAParameters settings) throws DENOPTIMException
	Tries to use any free AP of the given vertex to close ring in the graph by adding a chord. More...

static boolean	extendGraph (Vertex curVertex, boolean extend, boolean symmetryOnAps, GAParameters settings) throws DENOPTIMException
	function that will keep extending the graph according to the growth/substitution probability. More...

static boolean	extendGraph (Vertex curVrtx, boolean extend, boolean symmetryOnAps, boolean force, int chosenVrtxIdx, int chosenApId, GAParameters settings) throws DENOPTIMException
	function that will keep extending the graph. More...

static IdFragmentAndAP	getFrgApForSrcAp (Vertex curVertex, int dapidx, FragmentSpace fragSpace) throws DENOPTIMException
	Select a compatible fragment for the given attachment point. More...

static IdFragmentAndAP	getFrgApForSrcAp (Vertex curVertex, int dapidx, int chosenVrtxIdx, int chosenApId, FragmentSpace fragSpace) throws DENOPTIMException
	Select a compatible fragment for the given attachment point. More...

static IdFragmentAndAP	getRCVForSrcAp (Vertex curVertex, int dapidx, FragmentSpace fragSpace) throws DENOPTIMException
	Select a compatible ring-closing vertex for the given attachment point. More...

static boolean	attachFragmentInClosableChain (Vertex curVertex, int dapidx, DGraph molGraph, ArrayList< Long > addedVertices, GAParameters settings) throws DENOPTIMException

static ArrayList< FragForClosabChains >	getFragmentForClosableChain (Vertex curVertex, int dapidx, DGraph molGraph) throws DENOPTIMException
	Method to select fragments that increase the likeliness of generating closable chains. More...

static boolean	applySymmetry (boolean apclassImposed, double symmetryProbability, Randomizer randomizer)
	Decides whether to apply constitutional symmetry or not. More...

Static Private Member Functions
static void	processCombinationOfEndPoints (Vertex[] pair, List< Vertex[]> cominationOfEnds, List< XoverSite > collector, FragmentSpace fragSpace)
	Given a pair of seed vertexes that define where a pair of subgraphs stars in the corresponding original graphs, this method evaluates the use of a given list of candidate subgraph end points. More...

static void	processPermutationOfEndPoints (Vertex[] pair, List< Vertex[]> chosenSequenceOfEndpoints, List< XoverSite > collector, FragmentSpace fragSpace)
	Given a pair of seed vertexes that define where a pair of subgraphs stars in the corresponding original graphs, this method evaluates the use of a given ordered list of candidate subgraph end points. More...

static void	checkAndAddXoverSites (FragmentSpace fragSpace, List< Vertex > subGraphA, List< Vertex > subGraphB, CrossoverType xoverType, List< XoverSite > collector)
	Here we check that the given subgraphs have a mapping that allows to swap them, and full fill any other requirement other than not being isomorphic (which is done in parent methods calling this one). More...

static boolean	isCrossoverPossible (Edge eA, Edge eB, FragmentSpace fragSpace)
	Evaluate AP class-compatibility of a pair of edges with respect to crossover. More...

Detailed Description

Collection of operators meant to alter graphs and associated utilities.

Definition at line 76 of file GraphOperations.java.

Member Function Documentation

◆ addRing()

static boolean denoptim.ga.GraphOperations.addRing	(	Vertex	vertex,
		Monitor	mnt,
		boolean	force,
		FragmentSpace	fragSpace,
		GAParameters	settings
	)		throws DENOPTIMException

staticprotected

Tries to use any free AP of the given vertex to close ring in the graph by adding a chord.

Parameters

vertex	the vertex on which we start to close a the ring.
mnt	monitoring tool to keep count of events.
force	use `true` to by-pass random decisions and force the creation of rings.
fragSpace	the fragment space controlling how we put together building blocks.
settings	the GA settings controlling how we work.

Returns: true when at least one ring was added to the graph.

Exceptions

DENOPTIMException

Definition at line 966 of file GraphOperations.java.

References denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.DGraph.clone(), denoptim.graph.Vertex.clone(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.graph.APClass.equals(), denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOADDRING_NOFREEAP, denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOADDRING_NORINGCOMB, denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.DGraph.getAvailableAPsThroughout(), denoptim.graph.Vertex.getFreeAPThroughout(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.indexOf(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), denoptim.utils.Randomizer.randomlyChooseOne(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.rings.RingClosingAttractor.RCAAPCMAP, denoptim.graph.DGraph.removeVertex(), denoptim.molecularmodeling.ThreeDimTreeBuilder.setAlignBBsIn3D(), and denoptim.graph.Vertex.setVertexId().

Referenced by denoptim.ga.GraphOperations.performMutation(), and denoptim.ga.GraphOperationsTest.testAddRing().

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◆ applySymmetry()

static boolean denoptim.ga.GraphOperations.applySymmetry	(	boolean	apclassImposed,
		double	symmetryProbability,
		Randomizer	randomizer
	)

staticprotected

Decides whether to apply constitutional symmetry or not.

Application of this type of symmetry implies that the operation on the graph/molecule is to be performed on all the attachment point/vertices related to each other by "constitutional symmetry". Such type symmetry is defined by getMatchingAP for a single fragment, and symmetric vertices in a graph are found by getSymmetricVertices. This method takes into account the effect of the symmetric substitution probability, and the symmetry-related keywords.

Returns: true if symmetry is to be applied

Definition at line 2110 of file GraphOperations.java.

References denoptim.utils.Randomizer.nextBoolean().

Referenced by denoptim.ga.GraphOperations.attachFragmentInClosableChain(), and denoptim.ga.GraphOperations.extendGraph().

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◆ attachFragmentInClosableChain()

static boolean denoptim.ga.GraphOperations.attachFragmentInClosableChain	(	Vertex	curVertex,
		int	dapidx,
		DGraph	molGraph,
		ArrayList< Long >	addedVertices,
		GAParameters	settings
	)		throws DENOPTIMException

staticprotected

Definition at line 1624 of file GraphOperations.java.

References denoptim.ga.GraphOperations.applySymmetry(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.graph.Vertex.getAP(), denoptim.ga.GraphOperations.FragForClosabChains.getFragIDs(), denoptim.ga.GraphOperations.getFragmentForClosableChain(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.ga.GraphOperations.FragForClosabChains.getIncompatibleCC(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.fragspace.FragmentSpace.imposeSymmetryOnAPsOfClass(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.Vertex.BBType.parseInt().

Referenced by denoptim.ga.GraphOperations.extendGraph().

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◆ checkAndAddXoverSites()

static void denoptim.ga.GraphOperations.checkAndAddXoverSites	(	FragmentSpace	fragSpace,
		List< Vertex >	subGraphA,
		List< Vertex >	subGraphB,
		CrossoverType	xoverType,
		List< XoverSite >	collector
	)

staticprivate

Here we check that the given subgraphs have a mapping that allows to swap them, and full fill any other requirement other than not being isomorphic (which is done in parent methods calling this one).

Then, we create the corresponding crossover site and place it in the collector of such sites.

NB: This method assumes that no crossover can involve seed of the spanning tree (whether scaffold, of anything else).

Definition at line 493 of file GraphOperations.java.

References denoptim.utils.CrossoverType.BRANCH, denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.Template.ContractLevel.FIXED_STRUCT, denoptim.fragspace.APMapFinder.foundMapping(), denoptim.graph.Template.getContractLevel(), denoptim.graph.DGraph.getDeepestAmongThese(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.DGraph.getInterfaceAPs(), denoptim.graph.DGraph.getRingsInvolvingVertex(), denoptim.graph.DGraph.getSubgraphAPs(), denoptim.graph.DGraph.getTemplateJacket(), denoptim.graph.Edge.getTrgAP(), and denoptim.graph.DGraph.isIsostructuralTo().

Referenced by denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), and denoptim.ga.GraphOperations.processPermutationOfEndPoints().

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◆ deleteChain()

static boolean denoptim.ga.GraphOperations.deleteChain	(	Vertex	vertex,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Deletes the given vertex and all other vertexes that are not connected to more than 2 non-capping group vertexes.

Effectively, it removes an entire branch (in acyclic graphs) or the part of a cyclic graph between two branching points (in a ring, thus opening the ring wide). The same is done on symmetric partners on its parent.

Parameters

vertex	the vertex at which the deletion begins.
mnt	monitoring tool to keep count of events.

Returns: true if deletion is successful

Exceptions

DENOPTIMException

Definition at line 921 of file GraphOperations.java.

References denoptim.utils.MutationType.DELETECHAIN, denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexWithId(), denoptim.graph.DGraph.hasSymmetryInvolvingVertex(), and denoptim.graph.DGraph.removeChainUpToBranching().

Referenced by denoptim.ga.GraphOperations.performMutation().

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◆ deleteFragment()

static boolean denoptim.ga.GraphOperations.deleteFragment ( Vertex vertex ) throws DENOPTIMException

staticprotected

Deletion mutation removes the vertex and also the symmetric partners on its parent.

Parameters

vertex

Returns: true if deletion is successful

Exceptions

DENOPTIMException

Definition at line 881 of file GraphOperations.java.

References denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexWithId(), denoptim.graph.DGraph.hasSymmetryInvolvingVertex(), and denoptim.graph.DGraph.removeBranchStartingAt().

Referenced by denoptim.ga.GraphOperations.performMutation(), and denoptim.ga.GraphOperations.rebuildBranch().

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◆ deleteLink()

static boolean denoptim.ga.GraphOperations.deleteLink	(	Vertex	vertex,
		int	chosenVrtxIdx,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Removes a vertex while merging as many of the child branches into the parent vertex.

Parameters

vertex	the vertex to remove.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 626 of file GraphOperations.java.

References denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NODELLINK_EDIT, and denoptim.graph.DGraph.removeVertexAndWeld().

Referenced by denoptim.ga.GraphOperations.performMutation().

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◆ extendGraph() [1/2]

static boolean denoptim.ga.GraphOperations.extendGraph	(	Vertex	curVertex,
		boolean	extend,
		boolean	symmetryOnAps,
		GAParameters	settings
	)		throws DENOPTIMException

staticprotected

function that will keep extending the graph according to the growth/substitution probability.

Parameters

curVertex	vertex to which further fragments will be appended
extend	if `true`, then the graph will be grown further (recursive mode)
symmetryOnAps	if `true`, then symmetry will be applied on the APs, no matter what. This is mostly needed to retain symmetry when performing mutations on the root vertex of a symmetric graph.

Exceptions

DENOPTIMException

Returns: true if the graph has been modified

Definition at line 1180 of file GraphOperations.java.

References denoptim.ga.GraphOperations.extendGraph().

Referenced by denoptim.ga.EAUtils.buildGraph(), denoptim.ga.GraphOperations.extendGraph(), denoptim.ga.GraphOperations.performMutation(), denoptim.ga.GraphOperations.rebuildBranch(), and denoptim.ga.GraphOperationsTest.testExtendGraph().

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◆ extendGraph() [2/2]

static boolean denoptim.ga.GraphOperations.extendGraph	(	Vertex	curVrtx,
		boolean	extend,
		boolean	symmetryOnAps,
		boolean	force,
		int	chosenVrtxIdx,
		int	chosenApId,
		GAParameters	settings
	)		throws DENOPTIMException

staticprotected

function that will keep extending the graph.

The probability of addition depends on the growth probability scheme.

Parameters

curVrtx	vertex to which further fragments will be appended
extend	if `true`, then the graph will be grown further (recursive mode)
symmetryOnAps	if `true`, then symmetry will be applied on the APs, no matter what. This is mostly needed to retain symmetry when performing mutations on the root vertex of a symmetric graph.
force	set to `true` to ignore growth probability.
chosenVrtxIdx	if greater than or equals to zero, sets the choice of the vertex to the given index. This selection applies only to the first extension, not to further recursions.
chosenApId	if greater than or equals to zero, sets the choice of the AP to the given index. This selection applies only to the first extension, not to further recursions.
maxHeavyAtoms	maximum number of heavy atoms.

Exceptions

DENOPTIMException

Returns: true if the graph has been modified

Definition at line 1215 of file GraphOperations.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.ga.GraphOperations.applySymmetry(), denoptim.ga.GraphOperations.attachFragmentInClosableChain(), denoptim.utils.GraphUtils.ensureVertexIDConsistency(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.fragspace.IdFragmentAndAP.getApId(), denoptim.ga.EAUtils.getCrowdedness(), denoptim.ga.EAUtils.getCrowdingProbability(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.ga.GraphOperations.getFrgApForSrcAp(), denoptim.ga.EAUtils.getGrowthByLevelProbability(), denoptim.graph.Vertex.getHeavyAtomsCount(), denoptim.graph.AttachmentPoint.getIndexInOwner(), denoptim.graph.DGraph.getLevel(), denoptim.fragspace.FragmentSpaceParameters.getMaxHeavyAtom(), denoptim.graph.DGraph.getMaxVertexId(), denoptim.ga.EAUtils.getMolSizeProbability(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.ga.GraphOperations.getRCVForSrcAp(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.fragspace.IdFragmentAndAP.getVertexMolId(), denoptim.graph.DGraph.getVertexWithId(), denoptim.graph.DGraph.hasSymmetryInvolvingVertex(), denoptim.fragspace.FragmentSpace.imposeSymmetryOnAPsOfClass(), denoptim.graph.AttachmentPoint.isAvailable(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, and denoptim.graph.rings.RingClosureParameters.selectFragmentsFromClosableChains().

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◆ extendLink() [1/3]

static boolean denoptim.ga.GraphOperations.extendLink	(	Edge	edge,
		int	chosenBBIdx,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

static

Replace an edge with two edges with a new vertex in between, thus inserting a vertex in between two directly connected vertexes, which will no longer be directly connected.

Parameters

vertex	holding the "source" end of the edge to
chosenBBIdx	the identifier of the building block to insert.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 774 of file GraphOperations.java.

References denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOADDLINK_EDIT, denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOADDLINK_FIND, denoptim.fragspace.GraphLinkFinder.foundAlternativeLink(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.fragspace.GraphLinkFinder.getChosenAlternativeLink(), denoptim.fragspace.GraphLinkFinder.getChosenAPMapping(), and denoptim.graph.DGraph.insertVertex().

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◆ extendLink() [2/3]

static boolean denoptim.ga.GraphOperations.extendLink	(	Vertex	vertex,
		int	chosenAPId,
		int	chosenNewVrtxId,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

static

Inserts a vertex in between two connected vertexes that are identified by the one vertex holding the "source" end of the edge, and the identifier of the attachment point used by that edge.

Effectively, this method asks to replace an edge with two edges with a new vertex in between.

Parameters

vertex	holding the "source" end of the edge to
chosenAPId	the identifier of the AP on the vertex.
chosenNewVrtxId	the identifier of the new building block to insert in the list.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException if the request cannot be performed because the vertex is not the source of an edge at the given AP, or because such AP does not exist on the given vertex.

Definition at line 735 of file GraphOperations.java.

References denoptim.ga.GraphOperations.extendLink(), denoptim.graph.AttachmentPoint.getEdgeUserThroughout(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Edge.getSrcAP().

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◆ extendLink() [3/3]

static boolean denoptim.ga.GraphOperations.extendLink	(	Vertex	vertex,
		int	chosenAPId,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

static

Inserts a vertex in between two connected vertexes that are identified by the one vertex holding the "source" end of the edge, and the identifier of the attachment point used by that edge.

Effectively, this method asks to replace an edge with two edges with a new vertex in between.

Parameters

vertex	holding the "source" end of the edge to
chosenAPId	the identifier of the AP on the vertex.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException if the request cannot be performed because the vertex is not the source of an edge at the given AP, or because such AP does not exist on the given vertex.

Definition at line 709 of file GraphOperations.java.

References denoptim.ga.GraphOperations.extendLink().

Referenced by denoptim.ga.GraphOperations.extendLink(), and denoptim.ga.GraphOperations.performMutation().

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◆ getFragmentForClosableChain()

static ArrayList< FragForClosabChains > denoptim.ga.GraphOperations.getFragmentForClosableChain	(	Vertex	curVertex,
		int	dapidx,
		DGraph	molGraph
	)		throws DENOPTIMException

staticprotected

Method to select fragments that increase the likeliness of generating closable chains.

Only works for scaffold.

Definition at line 1758 of file GraphOperations.java.

References denoptim.ga.GraphOperations.FragForClosabChains.addCompatibleCC(), denoptim.graph.rings.ChainLink.getApIdToLeft(), denoptim.graph.rings.ChainLink.getApIdToRight(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.rings.ChainLink.getFragType(), denoptim.graph.rings.ChainLink.getIdx(), denoptim.graph.Vertex.getParent(), denoptim.graph.Edge.getSrcAPID(), denoptim.graph.Edge.getTrgAPID(), denoptim.graph.Vertex.BBType.parseInt(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.Vertex.BBType.toOldInt(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.ga.GraphOperations.attachFragmentInClosableChain().

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◆ getFrgApForSrcAp() [1/2]

static IdFragmentAndAP denoptim.ga.GraphOperations.getFrgApForSrcAp	(	Vertex	curVertex,
		int	dapidx,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Select a compatible fragment for the given attachment point.

Compatibility can either be class based or based on the free connections

Parameters

curVertex	the source graph vertex
dapidx	the attachment point index on the src vertex

Returns: the vector of indexes identifying the molId (fragment index) of a fragment with a compatible attachment point, and the index of such attachment point.

Exceptions

DENOPTIMException

Definition at line 1521 of file GraphOperations.java.

References denoptim.ga.GraphOperations.getFrgApForSrcAp().

Referenced by denoptim.ga.GraphOperations.extendGraph(), and denoptim.ga.GraphOperations.getFrgApForSrcAp().

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◆ getFrgApForSrcAp() [2/2]

static IdFragmentAndAP denoptim.ga.GraphOperations.getFrgApForSrcAp	(	Vertex	curVertex,
		int	dapidx,
		int	chosenVrtxIdx,
		int	chosenApId,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Select a compatible fragment for the given attachment point.

Compatibility can either be class based or based on the free connections

Parameters

curVertex	the source graph vertex
dapidx	the attachment point index on the src vertex
chosenVrtxIdx	if greater than or equals to zero, sets the choice of the incoming vertex to the given index.
chosenApId	if greater than or equals to zero, sets the choice of the AP (of the incoming vertex) to the given index.

Returns: the vector of indeces identifying the molId (fragment index) of a fragment with a compatible attachment point, and the index of such attachment point.

Exceptions

DENOPTIMException

Definition at line 1546 of file GraphOperations.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, and denoptim.graph.AttachmentPoint.getAPClass().

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◆ getRCVForSrcAp()

static IdFragmentAndAP denoptim.ga.GraphOperations.getRCVForSrcAp	(	Vertex	curVertex,
		int	dapidx,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Select a compatible ring-closing vertex for the given attachment point.

Parameters

curVertex	the source graph vertex
dapidx	the attachment point index on the src vertex
fragSpace	the space of building blocks with all the settings.

Returns: the vector of indeces identifying the molId (fragment index) of a fragment with a compatible attachment point, and the index of such attachment point.

Exceptions

DENOPTIMException

Definition at line 1595 of file GraphOperations.java.

References denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), and denoptim.utils.Randomizer.randomlyChooseOne().

Referenced by denoptim.ga.GraphOperations.extendGraph().

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◆ isCrossoverPossible()

static boolean denoptim.ga.GraphOperations.isCrossoverPossible	(	Edge	eA,
		Edge	eB,
		FragmentSpace	fragSpace
	)

staticprivate

Evaluate AP class-compatibility of a pair of edges with respect to crossover.

The condition for performing AP class-compatible crossover is that the AP class on source vertex of edge A is compatible with the AP class on target vertex of edge B, and that AP class on source vertex of edgeB is compatible with the AP class on target vertex of edge A.

Parameters

eA	first edge of the pair.
eB	second edge of the pair.

Returns: true if the condition is satisfied.

Definition at line 595 of file GraphOperations.java.

References denoptim.graph.Edge.getSrcAPClass(), denoptim.graph.Edge.getTrgAPClass(), and denoptim.graph.APClass.isCPMapCompatibleWith().

Referenced by denoptim.ga.GraphOperations.locateCompatibleXOverPoints().

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◆ locateCompatibleXOverPoints()

static List< XoverSite > denoptim.ga.GraphOperations.locateCompatibleXOverPoints	(	DGraph	graphA,
		DGraph	graphB,
		FragmentSpace	fragSpace,
		int	maxSizeXoverSubGraph
	)		throws DENOPTIMException

static

Identify crossover sites, i.e., subgraphs that can be swapped between two graphs (i.e., the parents).

This method will try to locate as many as possible crossover sites without falling into combinatorial explosion.

Parameters

gA	one of the parent graphs.
gB	the other of the parent graphs.
fragSpace	the space of building blocks defining how to generate graphs.
maxSizeXoverSubGraph	the limit to the size of subgraphs that can can be exchanged by crossover.

Returns: the list of pairs of crossover sites.

Exceptions

DENOPTIMException

Definition at line 94 of file GraphOperations.java.

Referenced by denoptim.ga.Population.getXoverPartners(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.programs.genetweeker.GeneOpsRunner.runXOver(), and denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints().

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◆ performCrossover()

static boolean denoptim.ga.GraphOperations.performCrossover	(	XoverSite	site,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

static

Performs the crossover that swaps the two subgraphs defining the given XoverSite.

The operation is performed on the graphs that own the vertexes referred in the XoverSite, so the original version of the graphs is lost. We expect the graphs to have an healthy set of vertex IDs. This can be ensured by running DGraph#renumberGraphVertices().

Parameters

site	the definition of the crossover site.

Exceptions

DENOPTIMException

Definition at line 1985 of file GraphOperations.java.

References denoptim.graph.DGraph.extractSubgraph(), denoptim.fragspace.APMapFinder.foundMapping(), denoptim.graph.Vertex.getAP(), denoptim.fragspace.APMapFinder.getChosenAPMapping(), denoptim.graph.AttachmentPoint.getIndexInOwner(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.DGraph.getSubgraphAPs(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.getVertexWithId(), and denoptim.graph.DGraph.replaceSubGraph().

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), and denoptim.programs.genetweeker.GeneOpsRunner.runXOver().

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◆ performMutation() [1/4]

static boolean denoptim.ga.GraphOperations.performMutation	(	DGraph	graph,
		Monitor	mnt,
		GAParameters	settings
	)		throws DENOPTIMException

static

Tries to do mutate the given graph.

The mutation site and type are chosen randomly according to the possibilities declared by the graph. The graph that owns the vertex will be altered and the original structure and content of the graph will be lost.

Parameters

graph	the graph to mutate.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 2139 of file GraphOperations.java.

References denoptim.ga.EAUtils.chooseNumberOfSitesToMutate(), denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOMUTSITE, and denoptim.ga.GraphOperations.performMutation().

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildGraph(), denoptim.ga.GraphOperations.performMutation(), and denoptim.programs.genetweeker.GeneOpsRunner.runMutation().

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◆ performMutation() [2/4]

static boolean denoptim.ga.GraphOperations.performMutation	(	Vertex	vertex,
		Monitor	mnt,
		GAParameters	settings
	)		throws DENOPTIMException

static

Tries to do mutate the given vertex.

We assume the vertex belongs to a graph, if not no mutation is done. The mutation type is chosen randomly according to the possibilities declared by the vertex. The graph that owns the vertex will be altered and the original structure and content of the graph will be lost.

Parameters

vertex	the vertex to mutate.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 2188 of file GraphOperations.java.

References denoptim.ga.GraphOperations.performMutation().

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◆ performMutation() [3/4]

static boolean denoptim.ga.GraphOperations.performMutation	(	Vertex	vertex,
		MutationType	mType,
		boolean	force,
		int	chosenVrtxIdx,
		int	chosenApId,
		Monitor	mnt,
		GAParameters	settings
	)		throws DENOPTIMException

static

Mutates the given vertex according to the given mutation type, if possible.

Vertex that do not belong to any graph or that do not allow the requested kind of mutation, are not mutated. The graph that owns the vertex will be altered and the original structure and content of the graph will be lost.

Parameters

vertex	the vertex to mutate.
mType	the type of mutation to perform.
force	set to `true` to ignore growth probability.
chosenVrtxIdx	if greater than or equals to zero, sets the choice of the incoming vertex to the given index. This parameter is ignored for mutation types that do not define an incoming vertex (i.e., `MutationType#DELETE`).
chosenApId	if greater than or equals to zero, sets the choice of the AP to the given index. Depending on the type of mutation, the AP can be on the incoming vertex (i.e., the vertex that will be added to the graph) or on the target vertex (i.e., the vertex that already belongs to the graph and that is the focus of the mutation). This parameter is ignored for mutation types that do not define an incoming vertex (i.e., `MutationType#DELETE`).

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 2264 of file GraphOperations.java.

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◆ performMutation() [4/4]

static boolean denoptim.ga.GraphOperations.performMutation	(	Vertex	vertex,
		MutationType	mType,
		Monitor	mnt,
		GAParameters	settings
	)		throws DENOPTIMException

static

Mutates the given vertex according to the given mutation type, if possible.

Vertex that do not belong to any graph or that do not allow the requested kind of mutation, are not mutated. The graph that owns the vertex ill be altered and the original structure and content of the graph will be lost.

Parameters

vertex	the vertex to mutate.
mType	the type of mutation to perform.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 2214 of file GraphOperations.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.indexOf(), denoptim.ga.GraphOperations.performMutation(), and denoptim.io.DenoptimIO.writeGraphToSDF().

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◆ processCombinationOfEndPoints()

static void denoptim.ga.GraphOperations.processCombinationOfEndPoints	(	Vertex[]	pair,
		List< Vertex[]>	cominationOfEnds,
		List< XoverSite >	collector,
		FragmentSpace	fragSpace
	)

staticprivate

Given a pair of seed vertexes that define where a pair of subgraphs stars in the corresponding original graphs, this method evaluates the use of a given list of candidate subgraph end points.

When it finds a pair of subgraphs that can be used to do crossover it stores them as a XoverSite in the given collector.

Parameters

pair	the seed vertexes in each of the graph
cominationOfEnds	the combination of subgraph end points to be evaluated. The order of the entries does not matter as we will consider the permutations of this list.
collector	this is where the crossover sites are stored.

Definition at line 356 of file GraphOperations.java.

References denoptim.ga.GraphOperations.processPermutationOfEndPoints().

Referenced by denoptim.ga.GraphOperations.locateCompatibleXOverPoints().

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◆ processPermutationOfEndPoints()

static void denoptim.ga.GraphOperations.processPermutationOfEndPoints	(	Vertex[]	pair,
		List< Vertex[]>	chosenSequenceOfEndpoints,
		List< XoverSite >	collector,
		FragmentSpace	fragSpace
	)

staticprivate

Given a pair of seed vertexes that define where a pair of subgraphs stars in the corresponding original graphs, this method evaluates the use of a given ordered list of candidate subgraph end points.

When it finds a pair of subgraphs that can be used to do crossover it stores them as a XoverSite in the given collector.

Parameters

pair	the seed vertexes in each of the graph
chosenSequenceOfEndpoints	the specific permutation of subgraph end points to be evaluated.
collector	this is where the crossover sites are stored.

Definition at line 405 of file GraphOperations.java.

References denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getChildTreeLimited(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.rings.PathSubGraph.getVertecesPath(), denoptim.graph.DGraph.isIsomorphicTo(), and denoptim.utils.CrossoverType.SUBGRAPH.

Referenced by denoptim.ga.GraphOperations.processCombinationOfEndPoints().

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◆ rebuildBranch()

static boolean denoptim.ga.GraphOperations.rebuildBranch	(	Vertex	vertex,
		boolean	force,
		int	chosenVrtxIdx,
		int	chosenApId,
		GAParameters	settings
	)		throws DENOPTIMException

staticprotected

Substitutes a vertex and any child branch.

Deletes the given vertex from the graph that owns it, and removes any child vertex (i.e., reachable from the given vertex by a directed path). Then it tries to extent the graph from the parent vertex (i.e., the one that was originally holding the given vertex). Moreover, additional extension may occur on any available attachment point of the parent vertex.

Parameters

vertex	to mutate (the given vertex).
force	set to `true` to ignore growth probability.
chosenVrtxIdx	if greater than or equals to zero, sets the choice of the vertex to the given index.
chosenApId	if greater than or equals to zero, sets the choice of the AP to the given index.
maxHeavyAtoms	maximum number of heavy atoms.

Returns: true if substitution is successful

Exceptions

DENOPTIMException

Definition at line 840 of file GraphOperations.java.

References denoptim.ga.GraphOperations.deleteFragment(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.DGraph.getVertexWithId(), and denoptim.graph.DGraph.hasSymmetryInvolvingVertex().

Referenced by denoptim.ga.GraphOperations.performMutation().

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◆ substituteLink()

static boolean denoptim.ga.GraphOperations.substituteLink	(	Vertex	vertex,
		int	chosenVrtxIdx,
		Monitor	mnt,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

staticprotected

Substitutes a vertex while keeping its surrounding.

Does not replace with same vertex (i.e., new vertex will have different building block ID, but might look the same wrt content and properties).

Parameters

vertex	the vertex to replace with another one.
chosenVrtxIdx	if greater than or equals to zero, sets the choice of the incoming vertex to the given index. AP mapping between old and new vertex is not controllable in this method.
mnt	the monitor keeping track of what happens in EA operations. This does not affect the mutation. It only measures how many attempts and failures occur.

Returns: true if the mutation is successful.

Exceptions

DENOPTIMException

Definition at line 657 of file GraphOperations.java.

References denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOCHANGELINK_EDIT, denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM_NOCHANGELINK_FIND, denoptim.fragspace.GraphLinkFinder.foundAlternativeLink(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.fragspace.GraphLinkFinder.getChosenAlternativeLink(), denoptim.fragspace.GraphLinkFinder.getChosenAPMapping(), denoptim.graph.DGraph.replaceVertex(), and denoptim.graph.APMapping.toIntMappig().

Referenced by denoptim.ga.GraphOperations.performMutation().

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

/github/workspace/src/main/java/denoptim/ga/GraphOperations.java

Classes

Static Public Member Functions

Static Protected Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ addRing()

◆ applySymmetry()

◆ attachFragmentInClosableChain()

◆ checkAndAddXoverSites()

◆ deleteChain()

◆ deleteFragment()

◆ deleteLink()

◆ extendGraph() [1/2]

◆ extendGraph() [2/2]

◆ extendLink() [1/3]

◆ extendLink() [2/3]

◆ extendLink() [3/3]

◆ getFragmentForClosableChain()

◆ getFrgApForSrcAp() [1/2]

◆ getFrgApForSrcAp() [2/2]

◆ getRCVForSrcAp()

◆ isCrossoverPossible()

◆ locateCompatibleXOverPoints()

◆ performCrossover()

◆ performMutation() [1/4]

◆ performMutation() [2/4]

◆ performMutation() [3/4]

◆ performMutation() [4/4]

◆ processCombinationOfEndPoints()

◆ processPermutationOfEndPoints()

◆ rebuildBranch()

◆ substituteLink()