Utility class to calculate and manage the alternative ring sizes achievable by formation of Rings. More...

Collaboration diagram for denoptim.graph.rings.RingSizeManager:

Public Member Functions
	RingSizeManager (FragmentSpace fragSpace, RingClosureParameters rcParams)
	Creates a tool that will work according to the given system-aspecific settings. More...

void	initialize (IAtomContainer origMol, DGraph graph)
	Makes this ring size manager work on a specific system that has a molecular representation and a DENOPTIM's graph representation. More...

List< Vertex >	getRSBiasedListOfCandidates ()

List< Vertex >	getRSBiasedListOfCandidates (Vertex vI)

void	addRingClosingBond (Vertex vI, Vertex vJ)

void	setVertexAsDone (Vertex v)

boolean	getCompatibilityOfPair (Vertex vI, Vertex vJ)

Private Member Functions
void	fillTopologicalMatrix ()

void	calculateCompatibilityOfAllRCAPairs ()

boolean	evaluateRCVPair (Vertex vI, Vertex vJ, FragmentSpace fragSpace)
	Method to analyze a pair of vertices and evaluate whether they respect the criteria for being the two ends of a candidate closable chain: a pair of Ring Closing Vertices (RCV). More...

Private Attributes
IAtomContainer	mol
	Molecular representation of the current system. More...

int[][]	topoMat
	Topological matrix: contains the number of bonds (shortest path) separating the two atoms having index i and j in the current system. More...

ArrayList< Vertex >	lstVert
	List of Ring Closing Vertices (RCV as DENOPTIMVerex) each containing an available Ring Closing Attractor (RCA) More...

int	sz
	Size of the list of available RCAs. More...

boolean[][]	compatibilityOfPairs
	Compatibility matrix between pairs of RCAs in the current system. More...

List< Double >	weigths
	List of weight factors used to control the likeliness of choosing rings of a given size for the current system. More...

List< Boolean >	done
	List of flags defining if an RCA has been "used", i.e., not used to make an actual chord, but used to make a plan to make a chord and update the molecular representation accordingly. More...

Map< Vertex, ArrayList< Integer > >	vIdToAtmId
	Map linking the list of vertices and atoms. More...

List< Integer >	ringSizeBias
	Parameters setting the bias for selecting rings of given size. More...

FragmentSpace	fragSpace = null
	Definition of the fragment space. More...

RingClosureParameters	settings
	Parameters related to rings. More...

Logger	logger
	tool managing the logs More...

Static Private Attributes
static final String	NL = DENOPTIMConstants.EOL
	New line character. More...

Detailed Description

Utility class to calculate and manage the alternative ring sizes achievable by formation of Rings.

Definition at line 35 of file RingSizeManager.java.

Constructor & Destructor Documentation

◆ RingSizeManager()

denoptim.graph.rings.RingSizeManager.RingSizeManager	(	FragmentSpace	fragSpace,
		RingClosureParameters	rcParams
	)

Creates a tool that will work according to the given system-aspecific settings.

Parameters

fragSpace	the space of building blocks.
rcParams	the parameters pertaining ring closures.

Definition at line 115 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.fragSpace, denoptim.programs.RunTimeParameters.getLogger(), and denoptim.graph.rings.RingClosureParameters.getRingSizeBias().

Here is the call graph for this function:

Member Function Documentation

◆ addRingClosingBond()

void denoptim.graph.rings.RingSizeManager.addRingClosingBond	(	Vertex	vI,
		Vertex	vJ
	)

Definition at line 466 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix(), denoptim.graph.Edge.getBondType(), denoptim.graph.Edge.BondType.getCDKOrder(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.Edge.BondType.hasCDKAnalogue(), denoptim.graph.rings.RingSizeManager.logger, denoptim.graph.rings.RingSizeManager.mol, and denoptim.graph.rings.RingSizeManager.vIdToAtmId.

Referenced by denoptim.graph.rings.RandomCombOfRingsIterator.next().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ calculateCompatibilityOfAllRCAPairs()

void denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs ( )

private

Definition at line 199 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), and denoptim.graph.rings.RingSizeManager.initialize().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ evaluateRCVPair()

boolean denoptim.graph.rings.RingSizeManager.evaluateRCVPair	(	Vertex	vI,
		Vertex	vJ,
		FragmentSpace	fragSpace
	)

private

Method to analyze a pair of vertices and evaluate whether they respect the criteria for being the two ends of a candidate closable chain: a pair of Ring Closing Vertices (RCV).

Parameters

vI	first vertex
vJ	second vertex

Returns: true is the path satisfies the criteria

Definition at line 316 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.fragSpace, denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.Vertex.getParent(), denoptim.fragspace.FragmentSpace.getRCCompatibilityMatrix(), denoptim.graph.Edge.getSrcAPClass(), denoptim.graph.Edge.getSrcAPID(), and denoptim.graph.rings.RingSizeManager.logger.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ fillTopologicalMatrix()

void denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix ( )

private

Definition at line 167 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.logger, denoptim.graph.rings.RingSizeManager.mol, denoptim.graph.rings.RingSizeManager.NL, and denoptim.graph.rings.RingSizeManager.topoMat.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), and denoptim.graph.rings.RingSizeManager.initialize().

Here is the caller graph for this function:

◆ getCompatibilityOfPair()

boolean denoptim.graph.rings.RingSizeManager.getCompatibilityOfPair	(	Vertex	vI,
		Vertex	vJ
	)

Definition at line 516 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.compatibilityOfPairs, and denoptim.graph.rings.RingSizeManager.lstVert.

Referenced by denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), and denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair().

Here is the caller graph for this function:

◆ getRSBiasedListOfCandidates() [1/2]

List< Vertex > denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates ( )

Definition at line 391 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.done, denoptim.graph.rings.RingSizeManager.logger, denoptim.graph.rings.RingSizeManager.lstVert, denoptim.graph.rings.RingSizeManager.sz, and denoptim.graph.rings.RingSizeManager.weigths.

Referenced by denoptim.graph.rings.RandomCombOfRingsIterator.next(), and denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair().

Here is the caller graph for this function:

◆ getRSBiasedListOfCandidates() [2/2]

List< Vertex > denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates ( Vertex vI )

Definition at line 414 of file RingSizeManager.java.

Here is the call graph for this function:

◆ initialize()

void denoptim.graph.rings.RingSizeManager.initialize	(	IAtomContainer	origMol,
		DGraph	graph
	)

Makes this ring size manager work on a specific system that has a molecular representation and a DENOPTIM's graph representation.

Parameters

origMol	the molecular representation.
graph	the graph representation.

Exceptions

DENOPTIMException

Definition at line 133 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.done, denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.utils.MoleculeUtils.getVertexToAtomIdMap(), denoptim.graph.rings.RingSizeManager.lstVert, denoptim.graph.rings.RingSizeManager.mol, denoptim.graph.rings.RingSizeManager.sz, and denoptim.graph.rings.RingSizeManager.vIdToAtmId.

Referenced by denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), and denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ setVertexAsDone()

void denoptim.graph.rings.RingSizeManager.setVertexAsDone ( Vertex v )

Definition at line 509 of file RingSizeManager.java.

References denoptim.graph.rings.RingSizeManager.done, and denoptim.graph.rings.RingSizeManager.lstVert.

Referenced by denoptim.graph.rings.RandomCombOfRingsIterator.next().

Here is the caller graph for this function:

Member Data Documentation

◆ compatibilityOfPairs

boolean [][] denoptim.graph.rings.RingSizeManager.compatibilityOfPairs

private

Compatibility matrix between pairs of RCAs in the current system.

Definition at line 62 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.getCompatibilityOfPair(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

◆ done

List<Boolean> denoptim.graph.rings.RingSizeManager.done

private

List of flags defining if an RCA has been "used", i.e., not used to make an actual chord, but used to make a plan to make a chord and update the molecular representation accordingly.

Definition at line 75 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), denoptim.graph.rings.RingSizeManager.initialize(), and denoptim.graph.rings.RingSizeManager.setVertexAsDone().

◆ fragSpace

FragmentSpace denoptim.graph.rings.RingSizeManager.fragSpace = null

private

Definition of the fragment space.

Definition at line 90 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.evaluateRCVPair(), and denoptim.graph.rings.RingSizeManager.RingSizeManager().

◆ logger

Logger denoptim.graph.rings.RingSizeManager.logger

private

tool managing the logs

Definition at line 100 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.evaluateRCVPair(), denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

◆ lstVert

ArrayList<Vertex> denoptim.graph.rings.RingSizeManager.lstVert

private

List of Ring Closing Vertices (RCV as DENOPTIMVerex) each containing an available Ring Closing Attractor (RCA)

Definition at line 52 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.getCompatibilityOfPair(), denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), denoptim.graph.rings.RingSizeManager.initialize(), and denoptim.graph.rings.RingSizeManager.setVertexAsDone().

◆ mol

IAtomContainer denoptim.graph.rings.RingSizeManager.mol

private

Molecular representation of the current system.

Definition at line 40 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix(), and denoptim.graph.rings.RingSizeManager.initialize().

◆ NL

final String denoptim.graph.rings.RingSizeManager.NL = DENOPTIMConstants.EOL

staticprivate

New line character.

Definition at line 105 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), and denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix().

◆ ringSizeBias

List<Integer> denoptim.graph.rings.RingSizeManager.ringSizeBias

private

Parameters setting the bias for selecting rings of given size.

Definition at line 85 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

◆ settings

RingClosureParameters denoptim.graph.rings.RingSizeManager.settings

private

Parameters related to rings.

Definition at line 95 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

◆ sz

int denoptim.graph.rings.RingSizeManager.sz

private

Size of the list of available RCAs.

Definition at line 57 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), and denoptim.graph.rings.RingSizeManager.initialize().

◆ topoMat

int [][] denoptim.graph.rings.RingSizeManager.topoMat

private

Topological matrix: contains the number of bonds (shortest path) separating the two atoms having index i and j in the current system.

Definition at line 46 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.fillTopologicalMatrix(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

◆ vIdToAtmId

Map<Vertex,ArrayList<Integer> > denoptim.graph.rings.RingSizeManager.vIdToAtmId

private

Map linking the list of vertices and atoms.

Definition at line 80 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.addRingClosingBond(), denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), and denoptim.graph.rings.RingSizeManager.initialize().

◆ weigths

List<Double> denoptim.graph.rings.RingSizeManager.weigths

private

List of weight factors used to control the likeliness of choosing rings of a given size for the current system.

Definition at line 68 of file RingSizeManager.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), and denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RingSizeManager()

Member Function Documentation

◆ addRingClosingBond()

◆ calculateCompatibilityOfAllRCAPairs()

◆ evaluateRCVPair()

◆ fillTopologicalMatrix()

◆ getCompatibilityOfPair()

◆ getRSBiasedListOfCandidates() [1/2]

◆ getRSBiasedListOfCandidates() [2/2]

◆ initialize()

◆ setVertexAsDone()

Member Data Documentation

◆ compatibilityOfPairs

◆ done

◆ fragSpace

◆ logger

◆ lstVert

◆ mol

◆ NL

◆ ringSizeBias

◆ settings

◆ sz

◆ topoMat

◆ vIdToAtmId

◆ weigths