This object represents a path in a DGraph. More...

Collaboration diagram for denoptim.graph.rings.PathSubGraph:

Public Member Functions
	PathSubGraph (Vertex vA, Vertex vB, DGraph molGraph)
	Constructs a new PathSubGraph specifying the first and last vertex of the path. More...

void	makeMolecularRepresentation (IAtomContainer mol, boolean make3D, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Creates the molecular representation, list of atoms and bonds involved in the path between the head and tail. More...

String	getChainID ()
	Returns the string representation of the path. More...

List< String >	getAllAlternativeChainIDs ()
	Returns all the possible IDs for this chain. More...

Vertex	getHeadVertex ()
	Returns the vertex representing the head of the chain. More...

Vertex	getTailVertex ()
	Returns the vertex representing the tail of the chain. More...

int	getPathLength ()
	Returns the length of the list of edges involved in this path. More...

List< Vertex >	getVertecesPath ()
	Returns the list of verteces involved. More...

List< Edge >	getEdgesPath ()
	Returns the list of edges involved. More...

boolean	hasMolecularRepresentation ()
	Returns true if the molecular representation has been set. More...

IAtomContainer	getMolecularRepresentation ()
	Returns the molecular representation. More...

List< IAtom >	getAtomPath ()
	Returns the list of atoms in the path between the head and the tail. More...

String	getAtomRefStr ()
	Returns the string with atom symbols and number for an easy identification of the path in a molecular structure. More...

List< IBond >	getBondPath ()
	Returns the list of bonds in the path between the head and the tail. More...

ArrayList< ArrayList< Point3d > >	getDihedralRefPoints ()
	Returns the list of point to be used to define the torsion of a bond uniquely (independently on the substituents present in this chain) as a dihedral angle. More...

RingClosingConformations	getRCC ()
	Returns the ring closing conformations. More...

void	setRCC (RingClosingConformations rcc)
	Set the ring closing conformations to this object. More...

String	toString ()

DGraph	getGraph ()

Static Public Member Functions
static DGraph	findPath (Vertex from, Vertex to)
	Returns a path as a DENOPTIMGraph from the first argument to the second one. More...

static List< IAtom >	findAtomPath (IAtomContainer iac)
	Finds the shortest path of atoms between the first and last atom in the given atom container. More...

Private Member Functions
long	getVertexIdInPath (IAtom a)

Static Private Member Functions
static Iterable< AttachmentPoint >	findPath (Vertex from, Vertex to, Set< Long > visited)
	Returns a sequence of APs that is the path from vertex from to vertex to. More...

Private Attributes
DGraph	graph
	The graph representation of this path. More...

String	chainID
	The string identifier of this path. More...

String	revChainID

ArrayList< String >	allPossibleChainIDs = new ArrayList<String>()

Vertex	vA
	The vertex representing the first RCA: head of the path. More...

Vertex	vB
	The vertex representing the second RCA: the tail of the path. More...

Vertex	turningPointVert
	The turning point in the graph: after this point the direction of edges becomes opposite than before. More...

List< Vertex >	vertPathVAVB
	The list of vertices of the original graph and involved in the path. More...

List< Edge >	edgesPathVAVB
	The list of edges of the original graph and involved in the path. More...

IAtomContainer	iacPathVAVB
	The molecular representation of the fragment in the path. More...

List< IAtom >	atomsPathVAVB
	The list of atoms in the shortest path. More...

List< IBond >	bondsPathVAVB
	The list of bonds in the shortest path. More...

ArrayList< ArrayList< Point3d > >	dihedralRefPts
	Per each bond the pair of point used to define the torsion. More...

boolean	hasMolRepr = false
	The flag defining whether this object has already a molecular representation or not. More...

String	atmNumStr
	The string of atoms involved (atom numbers from full molecule list) More...

RingClosingConformations	rcc
	The list of closable conformations, if any is found. More...

boolean	debug = false

Detailed Description

This object represents a path in a DGraph.

The path involving more than one Vertex and Edge.

Author: Marco Foscato

Definition at line 56 of file PathSubGraph.java.

Constructor & Destructor Documentation

◆ PathSubGraph()

denoptim.graph.rings.PathSubGraph.PathSubGraph	(	Vertex	vA,
		Vertex	vB,
		DGraph	molGraph
	)

Constructs a new PathSubGraph specifying the first and last vertex of the path.

Definition at line 145 of file PathSubGraph.java.

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Member Function Documentation

◆ findAtomPath()

static List< IAtom > denoptim.graph.rings.PathSubGraph.findAtomPath ( IAtomContainer iac )

static

Finds the shortest path of atoms between the first and last atom in the given atom container.

Parameters

iac	the atom container

Returns: the path as a list of atoms where the first is the beginning and the last is the end.

Definition at line 735 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

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◆ findPath() [1/2]

static DGraph denoptim.graph.rings.PathSubGraph.findPath	(	Vertex	from,
		Vertex	to
	)

static

Returns a path as a DENOPTIMGraph from the first argument to the second one.

The vertices in the path have vacant APs where they would connect to another vertex in the graph that from and to belongs to. The direction of the edges are the same as the graph that from and to belongs to.

An empty graph is returned if from == to.

Parameters

from	start of path.
to	end of path.

Exceptions

IllegalArgumentException if from cannot reach to.

Definition at line 328 of file PathSubGraph.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.AttachmentPoint.clone(), denoptim.graph.Vertex.clone(), denoptim.graph.rings.PathSubGraph.findPath(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.AttachmentPoint.setOwner().

Referenced by denoptim.graph.rings.PathSubGraph.findPath().

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◆ findPath() [2/2]

static Iterable< AttachmentPoint > denoptim.graph.rings.PathSubGraph.findPath	(	Vertex	from,
		Vertex	to,
		Set< Long >	visited
	)

staticprivate

Returns a sequence of APs that is the path from vertex from to vertex to.

An empty sequence is returned if from cannot reach to. This usually happens if from and to are not part of the same graph.

Parameters

from	start of path
to	end of path
visited	vertices already visited.

Returns: the path of APs from vertex from to vertex to.

Definition at line 382 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.findPath(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.Edge.getTrgAP(), and denoptim.graph.Vertex.getVertexId().

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◆ getAllAlternativeChainIDs()

List< String > denoptim.graph.rings.PathSubGraph.getAllAlternativeChainIDs ( )

Returns all the possible IDs for this chain.

The alternatives differ in the position of the chord.

Definition at line 771 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.allPossibleChainIDs.

Referenced by denoptim.graph.rings.RingClosuresArchive.containsChain().

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◆ getAtomPath()

List< IAtom > denoptim.graph.rings.PathSubGraph.getAtomPath ( )

Returns the list of atoms in the path between the head and the tail.

Definition at line 857 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.atomsPathVAVB.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getAtomRefStr()

String denoptim.graph.rings.PathSubGraph.getAtomRefStr ( )

Returns the string with atom symbols and number for an easy identification of the path in a molecular structure.

Definition at line 869 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.atmNumStr.

◆ getBondPath()

List< IBond > denoptim.graph.rings.PathSubGraph.getBondPath ( )

Returns the list of bonds in the path between the head and the tail.

Note that the IBonds are those of the entire molecule not of the IAtomContainer representing only this path.

Definition at line 882 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.bondsPathVAVB.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkClosabilityOfInterdependentPaths(), and denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getChainID()

String denoptim.graph.rings.PathSubGraph.getChainID ( )

Returns the string representation of the path.

Definition at line 759 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.chainID.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getDihedralRefPoints()

ArrayList< ArrayList< Point3d > > denoptim.graph.rings.PathSubGraph.getDihedralRefPoints ( )

Returns the list of point to be used to define the torsion of a bond uniquely (independently on the substituents present in this chain) as a dihedral angle.

Definition at line 895 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.dihedralRefPts.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getEdgesPath()

List< Edge > denoptim.graph.rings.PathSubGraph.getEdgesPath ( )

Returns the list of edges involved.

Definition at line 825 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.edgesPathVAVB.

Referenced by denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), and denoptim.graph.DGraphTest.testReplaceSubGraph().

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◆ getGraph()

DGraph denoptim.graph.rings.PathSubGraph.getGraph ( )

Definition at line 945 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.graph.

◆ getHeadVertex()

Vertex denoptim.graph.rings.PathSubGraph.getHeadVertex ( )

Returns the vertex representing the head of the chain.

Definition at line 782 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.vA.

Referenced by denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), and denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability().

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◆ getMolecularRepresentation()

IAtomContainer denoptim.graph.rings.PathSubGraph.getMolecularRepresentation ( )

Returns the molecular representation.

Definition at line 846 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.iacPathVAVB.

Referenced by denoptim.graph.rings.PathSubGraphTest.testMakePathSubGraph().

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◆ getPathLength()

int denoptim.graph.rings.PathSubGraph.getPathLength ( )

Returns the length of the list of edges involved in this path.

Definition at line 804 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.edgesPathVAVB.

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

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◆ getRCC()

RingClosingConformations denoptim.graph.rings.PathSubGraph.getRCC ( )

Returns the ring closing conformations.

Definition at line 906 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.rcc.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkClosabilityOfInterdependentPaths().

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◆ getTailVertex()

Vertex denoptim.graph.rings.PathSubGraph.getTailVertex ( )

Returns the vertex representing the tail of the chain.

Definition at line 793 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.vB.

Referenced by denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), and denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability().

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◆ getVertecesPath()

List< Vertex > denoptim.graph.rings.PathSubGraph.getVertecesPath ( )

Returns the list of verteces involved.

Definition at line 814 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.vertPathVAVB.

Referenced by denoptim.graph.DGraph.addRing(), denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), denoptim.ga.GraphOperations.processPermutationOfEndPoints(), and denoptim.graph.DGraph.replaceSingleSubGraph().

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◆ getVertexIdInPath()

long denoptim.graph.rings.PathSubGraph.getVertexIdInPath ( IAtom a )

private

Definition at line 747 of file PathSubGraph.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID.

Referenced by denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

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◆ hasMolecularRepresentation()

boolean denoptim.graph.rings.PathSubGraph.hasMolecularRepresentation ( )

Returns true if the molecular representation has been set.

Definition at line 836 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.hasMolRepr.

◆ makeMolecularRepresentation()

void denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation	(	IAtomContainer	mol,
		boolean	make3D,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

Creates the molecular representation, list of atoms and bonds involved in the path between the head and tail.

Parameters

mol	the full molecule
make3D	if `true` makes the method generate the 3D coordinates of the chain of fragments by rototranslation of the 3D fragments so that to align the APvectors

Exceptions

DENOPTIMException if we cannot make the molecular representation.

Definition at line 427 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), and denoptim.graph.rings.PathSubGraphTest.testMakePathSubGraph().

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◆ setRCC()

void denoptim.graph.rings.PathSubGraph.setRCC ( RingClosingConformations rcc )

Set the ring closing conformations to this object.

Definition at line 917 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.rcc.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ toString()

String denoptim.graph.rings.PathSubGraph.toString ( )

Returns: a string describing this path to a human reader

Definition at line 929 of file PathSubGraph.java.

References denoptim.graph.rings.PathSubGraph.vertPathVAVB.

Member Data Documentation

◆ allPossibleChainIDs

ArrayList<String> denoptim.graph.rings.PathSubGraph.allPossibleChainIDs = new ArrayList<String>()

private

Definition at line 69 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getAllAlternativeChainIDs(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ atmNumStr

String denoptim.graph.rings.PathSubGraph.atmNumStr

private

The string of atoms involved (atom numbers from full molecule list)

Definition at line 128 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getAtomRefStr().

◆ atomsPathVAVB

List<IAtom> denoptim.graph.rings.PathSubGraph.atomsPathVAVB

private

The list of atoms in the shortest path.

Definition at line 105 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getAtomPath(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ bondsPathVAVB

List<IBond> denoptim.graph.rings.PathSubGraph.bondsPathVAVB

private

The list of bonds in the shortest path.

Note that the IBonds are those of the entire molecule not of the container representing only this path.

Definition at line 112 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getBondPath(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ chainID

String denoptim.graph.rings.PathSubGraph.chainID

private

The string identifier of this path.

Definition at line 67 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getChainID(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ debug

boolean denoptim.graph.rings.PathSubGraph.debug = false

private

Definition at line 136 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ dihedralRefPts

ArrayList<ArrayList<Point3d> > denoptim.graph.rings.PathSubGraph.dihedralRefPts

private

Per each bond the pair of point used to define the torsion.

Definition at line 117 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getDihedralRefPoints(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ edgesPathVAVB

List<Edge> denoptim.graph.rings.PathSubGraph.edgesPathVAVB

private

The list of edges of the original graph and involved in the path.

Definition at line 95 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getEdgesPath(), denoptim.graph.rings.PathSubGraph.getPathLength(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ graph

DGraph denoptim.graph.rings.PathSubGraph.graph

private

The graph representation of this path.

Neither vertexes nor edges belong to the original graph.

Definition at line 62 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getGraph(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ hasMolRepr

boolean denoptim.graph.rings.PathSubGraph.hasMolRepr = false

private

The flag defining whether this object has already a molecular representation or not.

Definition at line 123 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.hasMolecularRepresentation(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ iacPathVAVB

IAtomContainer denoptim.graph.rings.PathSubGraph.iacPathVAVB

private

The molecular representation of the fragment in the path.

Definition at line 100 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getMolecularRepresentation(), and denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation().

◆ rcc

RingClosingConformations denoptim.graph.rings.PathSubGraph.rcc

private

The list of closable conformations, if any is found.

Definition at line 133 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getRCC(), and denoptim.graph.rings.PathSubGraph.setRCC().

◆ revChainID

String denoptim.graph.rings.PathSubGraph.revChainID

private

Definition at line 68 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ turningPointVert

Vertex denoptim.graph.rings.PathSubGraph.turningPointVert

private

The turning point in the graph: after this point the direction of edges becomes opposite than before.

Definition at line 85 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ vA

Vertex denoptim.graph.rings.PathSubGraph.vA

private

The vertex representing the first RCA: head of the path.

Definition at line 74 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getHeadVertex(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ vB

Vertex denoptim.graph.rings.PathSubGraph.vB

private

The vertex representing the second RCA: the tail of the path.

Definition at line 79 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getTailVertex(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

◆ vertPathVAVB

List<Vertex> denoptim.graph.rings.PathSubGraph.vertPathVAVB

private

The list of vertices of the original graph and involved in the path.

Definition at line 90 of file PathSubGraph.java.

Referenced by denoptim.graph.rings.PathSubGraph.getVertecesPath(), denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation(), denoptim.graph.rings.PathSubGraph.PathSubGraph(), and denoptim.graph.rings.PathSubGraph.toString().

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

/github/workspace/src/main/java/denoptim/graph/rings/PathSubGraph.java

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PathSubGraph()

Member Function Documentation

◆ findAtomPath()

◆ findPath() [1/2]

◆ findPath() [2/2]

◆ getAllAlternativeChainIDs()

◆ getAtomPath()

◆ getAtomRefStr()

◆ getBondPath()

◆ getChainID()

◆ getDihedralRefPoints()

◆ getEdgesPath()

◆ getGraph()

◆ getHeadVertex()

◆ getMolecularRepresentation()

◆ getPathLength()

◆ getRCC()

◆ getTailVertex()

◆ getVertecesPath()

◆ getVertexIdInPath()

◆ hasMolecularRepresentation()

◆ makeMolecularRepresentation()

◆ setRCC()

◆ toString()

Member Data Documentation

◆ allPossibleChainIDs

◆ atmNumStr

◆ atomsPathVAVB

◆ bondsPathVAVB

◆ chainID

◆ debug

◆ dihedralRefPts

◆ edgesPathVAVB

◆ graph

◆ hasMolRepr

◆ iacPathVAVB

◆ rcc

◆ revChainID

◆ turningPointVert

◆ vA

◆ vB

◆ vertPathVAVB