This class represents the edge between two vertices. More...

Collaboration diagram for denoptim.graph.Edge:

Classes
enum	BondType
	Possible chemical bond types an edge can represent. More...

class	DENOPTIMEdgeSerializer

Public Member Functions
	Edge (AttachmentPoint srcAP, AttachmentPoint trgAP, BondType bondType)
	Constructor for an edge that connects two APs. More...

	Edge (AttachmentPoint srcAP, AttachmentPoint trgAP)
	Constructor for an edge that connects two APs. More...

AttachmentPoint	getSrcAP ()

AttachmentPoint	getSrcAPThroughout ()

AttachmentPoint	getTrgAPThroughout ()

AttachmentPoint	getTrgAP ()

long	getSrcVertex ()

int	getSrcAPID ()

int	getTrgAPID ()

long	getTrgVertex ()

APClass	getSrcAPClass ()

APClass	getTrgAPClass ()

BondType	getBondType ()

boolean	sameAs (Edge other, StringBuilder reason)
	Compares this and another edge ignoring edge and vertex IDs. More...

int	compareAsUndirected (Edge other)
	Compares this and another edge ignoring the directionality of both, i.e., as if both edges were undirected. More...

String	toString ()

void	flipEdge ()
	Exchanges source and target vertices and respective APs of this edge. More...

Private Attributes
AttachmentPoint	srcAP
	Attachment point at source end. More...

AttachmentPoint	trgAP
	Attachment point at target end. More...

BondType	bondType = BondType.UNDEFINED
	The bond type associated with the connection between the fragments. More...

Detailed Description

This class represents the edge between two vertices.

Definition at line 37 of file Edge.java.

Constructor & Destructor Documentation

◆ Edge() [1/2]

denoptim.graph.Edge.Edge	(	AttachmentPoint	srcAP,
		AttachmentPoint	trgAP,
		BondType	bondType
	)

Constructor for an edge that connects two APs.

The number of connections available in the APs is reduced upon creation of the edge and according the the bond type.

Parameters

srcAP	attachment point at source end
trgAP	attachment point at target end
bondType	defines what kind of bond type this edge should be converted to when converting a graph into a chemical representation.

Definition at line 67 of file Edge.java.

References denoptim.graph.Edge.bondType, denoptim.graph.AttachmentPoint.setUser(), denoptim.graph.Edge.srcAP, and denoptim.graph.Edge.trgAP.

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◆ Edge() [2/2]

denoptim.graph.Edge.Edge	(	AttachmentPoint	srcAP,
		AttachmentPoint	trgAP
	)

Constructor for an edge that connects two APs.

We assume a single bond. The number of connections available in the APs is reduced upon creation of the edge and according the the bond type.

Parameters

srcAP	attachment point at source end
trgAP	attachment point at target end

Definition at line 87 of file Edge.java.

References denoptim.graph.Edge.srcAP, denoptim.graph.Edge.trgAP, and denoptim.graph.Edge.BondType.UNDEFINED.

Member Function Documentation

◆ compareAsUndirected()

int denoptim.graph.Edge.compareAsUndirected ( Edge other )

Compares this and another edge ignoring the directionality of both, i.e., as if both edges were undirected.

Ranking and comparison is based on an invariant lexicographic string that combines, for each side of the edge, the following information:

type of the building block reached,
the ID of the building block,
the index of the attachment point.

Only for edges that link equivalent building blocks via the corresponding APs (i.e., edges belonging to the same invariant class), the bond type is considered as the final comparison criterion.

Parameters

other edge to compare with this.

Returns: a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Definition at line 221 of file Edge.java.

References denoptim.graph.Edge.getBondType(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.AttachmentPoint.getIndexInOwner(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.graph.Edge.srcAP, and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.EdgeTest.testUndirectedComparison().

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◆ flipEdge()

void denoptim.graph.Edge.flipEdge ( )

Exchanges source and target vertices and respective APs of this edge.

Definition at line 292 of file Edge.java.

References denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getTrgAP(), denoptim.graph.Edge.srcAP, and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.DGraph.fixEdgeDirections().

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◆ getBondType()

BondType denoptim.graph.Edge.getBondType ( )

Definition at line 164 of file Edge.java.

References denoptim.graph.Edge.bondType.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), denoptim.graph.Edge.compareAsUndirected(), denoptim.graph.DGraph.editGraph(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), denoptim.graph.rings.PathSubGraph.PathSubGraph(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.replaceSingleSubGraph(), denoptim.graph.Edge.sameAs(), and denoptim.graph.Edge.DENOPTIMEdgeSerializer.serialize().

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◆ getSrcAP()

AttachmentPoint denoptim.graph.Edge.getSrcAP ( )

Definition at line 94 of file Edge.java.

References denoptim.graph.Edge.srcAP.

Referenced by denoptim.graph.DGraph.changeSignOfVertexID(), denoptim.graph.AttachmentPointTest.checkGetEdgeUserThroughput(), denoptim.ga.GraphOperations.extendLink(), denoptim.graph.rings.PathSubGraph.findPath(), denoptim.graph.Edge.flipEdge(), denoptim.graph.DGraph.getAPOnLeftVertexID(), denoptim.graph.Vertex.getChilddren(), denoptim.utils.GraphConversionTool.getJGraphFromGraph(), denoptim.graph.AttachmentPoint.getLinkedAP(), denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), denoptim.graph.Vertex.getParent(), denoptim.graph.DGraph.getParent(), denoptim.graph.DGraph.insertVertex(), denoptim.graph.AttachmentPoint.isSrcInUser(), denoptim.graph.AttachmentPoint.isSrcInUserThroughout(), denoptim.graph.rings.PathSubGraph.PathSubGraph(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.removeEdge(), denoptim.graph.Edge.sameAs(), denoptim.graph.Edge.DENOPTIMEdgeSerializer.serialize(), and denoptim.graph.EdgeTest.testConnectionDeconnectionLoop().

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◆ getSrcAPClass()

APClass denoptim.graph.Edge.getSrcAPClass ( )

Definition at line 150 of file Edge.java.

References denoptim.graph.AttachmentPoint.getAPClass(), and denoptim.graph.Edge.srcAP.

Referenced by denoptim.graph.rings.RingSizeManager.evaluateRCVPair(), and denoptim.ga.GraphOperations.isCrossoverPossible().

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◆ getSrcAPID()

int denoptim.graph.Edge.getSrcAPID ( )

Definition at line 129 of file Edge.java.

References denoptim.graph.Vertex.getIndexOfAP(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Edge.srcAP.

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.graph.rings.RingSizeManager.evaluateRCVPair(), denoptim.graph.DGraph.getBondingAPIndex(), denoptim.ga.GraphOperations.getFragmentForClosableChain(), denoptim.graph.rings.PathSubGraph.PathSubGraph(), and denoptim.graph.Edge.toString().

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◆ getSrcAPThroughout()

AttachmentPoint denoptim.graph.Edge.getSrcAPThroughout ( )

Definition at line 101 of file Edge.java.

References denoptim.graph.AttachmentPoint.getEmbeddedAP(), and denoptim.graph.Edge.srcAP.

Referenced by denoptim.graph.Vertex.getAPsFromChildren(), denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), denoptim.graph.AttachmentPoint.isSrcInUserThroughout(), and denoptim.graph.AttachmentPointTest.testGetEmbeddedAP().

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◆ getSrcVertex()

long denoptim.graph.Edge.getSrcVertex ( )

Definition at line 122 of file Edge.java.

References denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Vertex.getVertexId(), and denoptim.graph.Edge.srcAP.

Referenced by denoptim.graph.DGraph.changeSignOfVertexID(), denoptim.graph.rings.PathSubGraph.findPath(), denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.DGraph.getBondingAPIndex(), denoptim.graph.DGraph.getEdgesWithChild(), denoptim.graph.DGraph.getIndexOfEdgesWithChild(), denoptim.ga.GraphOperations.rebuildBranch(), and denoptim.graph.DGraph.removeVertex().

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◆ getTrgAP()

AttachmentPoint denoptim.graph.Edge.getTrgAP ( )

Definition at line 115 of file Edge.java.

References denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.DGraph.changeSignOfVertexID(), denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.graph.AttachmentPointTest.checkGetEdgeUserThroughput(), denoptim.graph.rings.PathSubGraph.findPath(), denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.Edge.flipEdge(), denoptim.graph.DGraph.getAPOnLeftVertexID(), denoptim.graph.Vertex.getChilddren(), denoptim.graph.Vertex.getChildrenThroughout(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.AttachmentPoint.getLinkedAP(), denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), denoptim.graph.Vertex.getParent(), denoptim.graph.DGraph.insertVertex(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.removeEdge(), denoptim.graph.Edge.sameAs(), denoptim.graph.Edge.DENOPTIMEdgeSerializer.serialize(), and denoptim.graph.EdgeTest.testConnectionDeconnectionLoop().

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◆ getTrgAPClass()

APClass denoptim.graph.Edge.getTrgAPClass ( )

Definition at line 157 of file Edge.java.

References denoptim.graph.AttachmentPoint.getAPClass(), and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), and denoptim.ga.GraphOperations.isCrossoverPossible().

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◆ getTrgAPID()

int denoptim.graph.Edge.getTrgAPID ( )

Definition at line 136 of file Edge.java.

References denoptim.graph.Vertex.getIndexOfAP(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.DGraph.getBondingAPIndex(), denoptim.ga.GraphOperations.getFragmentForClosableChain(), denoptim.graph.rings.PathSubGraph.PathSubGraph(), and denoptim.graph.Edge.toString().

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◆ getTrgAPThroughout()

AttachmentPoint denoptim.graph.Edge.getTrgAPThroughout ( )

Definition at line 108 of file Edge.java.

References denoptim.graph.AttachmentPoint.getEmbeddedAP(), and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.Vertex.getAPsFromChildren(), denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), and denoptim.graph.AttachmentPointTest.testGetEmbeddedAP().

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◆ getTrgVertex()

long denoptim.graph.Edge.getTrgVertex ( )

Definition at line 143 of file Edge.java.

References denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Vertex.getVertexId(), and denoptim.graph.Edge.trgAP.

Referenced by denoptim.graph.DGraph.changeSignOfVertexID(), denoptim.graph.DGraph.compareGraphNodes(), denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.DGraph.getBondingAPIndex(), and denoptim.graph.DGraph.removeVertex().

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◆ sameAs()

boolean denoptim.graph.Edge.sameAs	(	Edge	other,
		StringBuilder	reason
	)

Compares this and another edge ignoring edge and vertex IDs.

Parameters

other	edge to compare against
reason	string builder used to build the message clarifying the reason for returning `false`.

Returns: true if the two edges represent the same connection even if the vertex IDs are different.

Definition at line 180 of file Edge.java.

References denoptim.graph.Edge.getBondType(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getTrgAP(), and denoptim.graph.Edge.sameAs().

Referenced by denoptim.graph.Edge.sameAs(), denoptim.graph.EdgeTest.testSameAs_DiffBndTyp(), and denoptim.graph.EdgeTest.testSameAs_Equal().

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◆ toString()

String denoptim.graph.Edge.toString ( )

Definition at line 265 of file Edge.java.

References denoptim.graph.Edge.bondType, denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Edge.getSrcAPID(), denoptim.graph.Edge.getTrgAPID(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.Edge.srcAP, and denoptim.graph.Edge.trgAP.

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Member Data Documentation

◆ bondType

BondType denoptim.graph.Edge.bondType = BondType.UNDEFINED

private

The bond type associated with the connection between the fragments.

Definition at line 52 of file Edge.java.

Referenced by denoptim.graph.Edge.Edge(), denoptim.graph.Edge.getBondType(), and denoptim.graph.Edge.toString().

◆ srcAP

AttachmentPoint denoptim.graph.Edge.srcAP

private

Attachment point at source end.

Definition at line 42 of file Edge.java.

Referenced by denoptim.graph.Edge.compareAsUndirected(), denoptim.graph.Edge.Edge(), denoptim.graph.Edge.flipEdge(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getSrcAPClass(), denoptim.graph.Edge.getSrcAPID(), denoptim.graph.Edge.getSrcAPThroughout(), denoptim.graph.Edge.getSrcVertex(), and denoptim.graph.Edge.toString().

◆ trgAP

AttachmentPoint denoptim.graph.Edge.trgAP

private

Attachment point at target end.

Definition at line 47 of file Edge.java.

Referenced by denoptim.graph.Edge.compareAsUndirected(), denoptim.graph.Edge.Edge(), denoptim.graph.Edge.flipEdge(), denoptim.graph.Edge.getTrgAP(), denoptim.graph.Edge.getTrgAPClass(), denoptim.graph.Edge.getTrgAPID(), denoptim.graph.Edge.getTrgAPThroughout(), denoptim.graph.Edge.getTrgVertex(), and denoptim.graph.Edge.toString().

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

/github/workspace/src/main/java/denoptim/graph/Edge.java

Classes

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Edge() [1/2]

◆ Edge() [2/2]

Member Function Documentation

◆ compareAsUndirected()

◆ flipEdge()

◆ getBondType()

◆ getSrcAP()

◆ getSrcAPClass()

◆ getSrcAPID()

◆ getSrcAPThroughout()

◆ getSrcVertex()

◆ getTrgAP()

◆ getTrgAPClass()

◆ getTrgAPID()

◆ getTrgAPThroughout()

◆ getTrgVertex()

◆ sameAs()

◆ toString()

Member Data Documentation

◆ bondType

◆ srcAP

◆ trgAP