This is a tool to identify and manage vertices' connections not included in the DGraph, which is a spanning tree, thus connections that identify cyclic paths in the graph. More...

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Classes
class	ClosableConf
	Utility class to handle the simultaneous closeness condition. More...

Public Member Functions
	CyclicGraphHandler (RingClosureParameters settings, FragmentSpace fragSpace)
	Constructor from data structure. More...

List< Ring >	getRandomCombinationOfRings (IAtomContainer inMol, DGraph molGraph, int maxRingClosures) throws DENOPTIMException
	Identifies a random combination of ring closing paths and returns it as list of DENOPTIMRings ready to be appended to a DENOPTIMGraph. More...

ArrayList< List< Ring > >	getPossibleCombinationOfRings (IAtomContainer mol, DGraph molGraph) throws DENOPTIMException
	Identifies all possible ring closing paths and returns them as list of DENOPTIMRings ready to be appended to a DENOPTIMGraph. More...

boolean	checkChelatesGraph (DGraph molGraph, List< Ring > ringsSet)
	Evaluates the combination of a DENOPTIMGraph and a set of DENOPTIMRings and decides whether it's a proper candidate for the generation of a chelating ligand. More...

Private Member Functions
boolean	combineCompatPathSubGraphs (int ii0, ArrayList< Vertex > sortedKeys, Map< Vertex, ArrayList< Vertex > > compatMap, ArrayList< ObjectPair > lstPairs, ArrayList< Long > usedId, Map< ObjectPair, PathSubGraph > allGoodPaths, Map< IBond, List< PathSubGraph > > interdepPaths, ArrayList< List< Ring > > allCombsOfRings) throws DENOPTIMException
	Recursive method to identify all the combination of rings. More...

boolean	hasInterdependentPaths (ArrayList< ObjectPair > lstPairs, Map< IBond, List< PathSubGraph > > interdepPaths)
	Checks whether the combination of RCA's pairs leads to interdependent paths, that is, paths that share one or more bonds. More...

boolean	checkClosabilityOfInterdependentPaths (ArrayList< ObjectPair > lstPairs, Map< IBond, List< PathSubGraph > > interdepPaths, Map< ObjectPair, PathSubGraph > allGoodPaths)
	This method checks whether the interdependent paths are simultaneously closable. More...

Private Attributes
int	recCount = 0
	variables needed by recursive methods More...

int	maxLng = 0

RingClosureParameters	settings
	Parameters. More...

FragmentSpace	fragSpace
	Fragment space definition. More...

Logger	logger
	Logger to use. More...

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

Detailed Description

This is a tool to identify and manage vertices' connections not included in the DGraph, which is a spanning tree, thus connections that identify cyclic paths in the graph.

The three dimensional features of the vertices can be taken into account while defining the closability of a candidate chain. Since this is a computationally demanding task, we make use of serialized data that is recovered from previous experiments, updated on the fly, and stored for future used.

Author: Marco Foscato

Definition at line 75 of file CyclicGraphHandler.java.

Constructor & Destructor Documentation

◆ CyclicGraphHandler()

denoptim.graph.rings.CyclicGraphHandler.CyclicGraphHandler	(	RingClosureParameters	settings,
		FragmentSpace	fragSpace
	)

Constructor from data structure.

Parameters

libScaff	the library of scaffolds
libFrag	the library of fragments
libCap	the library of capping groups

Definition at line 112 of file CyclicGraphHandler.java.

References denoptim.graph.rings.CyclicGraphHandler.fragSpace, denoptim.programs.RunTimeParameters.getLogger(), and denoptim.graph.rings.CyclicGraphHandler.settings.

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Member Function Documentation

◆ checkChelatesGraph()

boolean denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph	(	DGraph	molGraph,
		List< Ring >	ringsSet
	)

Evaluates the combination of a DENOPTIMGraph and a set of DENOPTIMRings and decides whether it's a proper candidate for the generation of a chelating ligand.

Returns: true it this system is a good candidate

Definition at line 850 of file CyclicGraphHandler.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.Vertex.getChilddren(), denoptim.graph.DGraph.getEdgeWithParent(), denoptim.graph.DGraph.getLevel(), denoptim.graph.Edge.getTrgAPClass(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.DGraph.isVertexInRing(), denoptim.graph.rings.CyclicGraphHandler.logger, denoptim.graph.rings.RingClosureParameters.metalCoordinatingAPClasses, denoptim.graph.rings.CyclicGraphHandler.settings, and denoptim.graph.APClass.toString().

Referenced by denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), and denoptim.ga.EAUtils.setupRings().

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◆ checkClosabilityOfInterdependentPaths()

boolean denoptim.graph.rings.CyclicGraphHandler.checkClosabilityOfInterdependentPaths	(	ArrayList< ObjectPair >	lstPairs,
		Map< IBond, List< PathSubGraph > >	interdepPaths,
		Map< ObjectPair, PathSubGraph >	allGoodPaths
	)

private

This method checks whether the interdependent paths are simultaneously closable.

Returns: true is all interdependent sets are closable

Definition at line 592 of file CyclicGraphHandler.java.

References denoptim.graph.rings.PathSubGraph.getBondPath(), denoptim.graph.rings.RingClosingConformations.getListOfConformations(), and denoptim.graph.rings.PathSubGraph.getRCC().

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

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◆ combineCompatPathSubGraphs()

boolean denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs	(	int	ii0,
		ArrayList< Vertex >	sortedKeys,
		Map< Vertex, ArrayList< Vertex > >	compatMap,
		ArrayList< ObjectPair >	lstPairs,
		ArrayList< Long >	usedId,
		Map< ObjectPair, PathSubGraph >	allGoodPaths,
		Map< IBond, List< PathSubGraph > >	interdepPaths,
		ArrayList< List< Ring > >	allCombsOfRings
	)		throws DENOPTIMException

private

Recursive method to identify all the combination of rings.

Definition at line 339 of file CyclicGraphHandler.java.

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

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◆ getPossibleCombinationOfRings()

ArrayList< List< Ring > > denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings	(	IAtomContainer	mol,
		DGraph	molGraph
	)		throws DENOPTIMException

Identifies all possible ring closing paths and returns them as list of DENOPTIMRings ready to be appended to a DENOPTIMGraph.

Parameters

mol	the molecule
molGraph	the molecular graph

Returns: the candidate closable paths in the given graph

Definition at line 153 of file CyclicGraphHandler.java.

References denoptim.constants.DENOPTIMConstants.BONDPROPROTATABLE, denoptim.graph.rings.RingClosureParameters.checkInterdependentChains(), denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.CyclicGraphHandler.fragSpace, denoptim.graph.rings.RingSizeManager.getCompatibilityOfPair(), denoptim.graph.Vertex.getProperty(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.rings.RingSizeManager.initialize(), denoptim.graph.rings.PathClosabilityTools.isCloseable(), denoptim.graph.rings.CyclicGraphHandler.logger, denoptim.graph.rings.CyclicGraphHandler.NL, and denoptim.graph.rings.CyclicGraphHandler.settings.

Referenced by denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), and denoptim.ga.EAUtils.setupRings().

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◆ getRandomCombinationOfRings()

List< Ring > denoptim.graph.rings.CyclicGraphHandler.getRandomCombinationOfRings	(	IAtomContainer	inMol,
		DGraph	molGraph,
		int	maxRingClosures
	)		throws DENOPTIMException

Identifies a random combination of ring closing paths and returns it as list of DENOPTIMRings ready to be appended to a DENOPTIMGraph.

Parameters

inMol	the molecule
molGraph	the molecular graph
maxRingClosures	maximum number of ring closures to perform.

Returns: the selected combination of closable paths

Definition at line 131 of file CyclicGraphHandler.java.

References denoptim.graph.rings.CyclicGraphHandler.fragSpace, denoptim.graph.rings.CyclicGraphHandler.logger, denoptim.graph.rings.RandomCombOfRingsIterator.next(), and denoptim.graph.rings.CyclicGraphHandler.settings.

Referenced by denoptim.ga.EAUtils.setupRings().

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◆ hasInterdependentPaths()

boolean denoptim.graph.rings.CyclicGraphHandler.hasInterdependentPaths	(	ArrayList< ObjectPair >	lstPairs,
		Map< IBond, List< PathSubGraph > >	interdepPaths
	)

private

Checks whether the combination of RCA's pairs leads to interdependent paths, that is, paths that share one or more bonds.

Definition at line 550 of file CyclicGraphHandler.java.

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

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Member Data Documentation

◆ fragSpace

FragmentSpace denoptim.graph.rings.CyclicGraphHandler.fragSpace

private

Fragment space definition.

Definition at line 91 of file CyclicGraphHandler.java.

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

◆ logger

Logger denoptim.graph.rings.CyclicGraphHandler.logger

private

Logger to use.

Definition at line 96 of file CyclicGraphHandler.java.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), and denoptim.graph.rings.CyclicGraphHandler.getRandomCombinationOfRings().

◆ maxLng

int denoptim.graph.rings.CyclicGraphHandler.maxLng = 0

private

Definition at line 81 of file CyclicGraphHandler.java.

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

◆ NL

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

staticprivate

New line character.

Definition at line 101 of file CyclicGraphHandler.java.

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

◆ recCount

int denoptim.graph.rings.CyclicGraphHandler.recCount = 0

private

variables needed by recursive methods

Definition at line 80 of file CyclicGraphHandler.java.

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

◆ settings

RingClosureParameters denoptim.graph.rings.CyclicGraphHandler.settings

private

Parameters.

Definition at line 86 of file CyclicGraphHandler.java.

Referenced by denoptim.graph.rings.CyclicGraphHandler.ClosableConf.canCoexistWith(), denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.CyclicGraphHandler.CyclicGraphHandler(), denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), and denoptim.graph.rings.CyclicGraphHandler.getRandomCombinationOfRings().

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

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CyclicGraphHandler()

Member Function Documentation

◆ checkChelatesGraph()

◆ checkClosabilityOfInterdependentPaths()

◆ combineCompatPathSubGraphs()

◆ getPossibleCombinationOfRings()

◆ getRandomCombinationOfRings()

◆ hasInterdependentPaths()

Member Data Documentation

◆ fragSpace

◆ logger

◆ maxLng

◆ NL

◆ recCount

◆ settings