Tool box for determining whether a chain of atoms, i.e., a path, can be folded as to form a ring-closing bond that transforms the open chain in a ring. More...

Static Public Member Functions
static boolean	isCloseable (PathSubGraph subGraph, IAtomContainer mol, RingClosureParameters settings)
	Method to evaluate the closability of a single path in a graph. More...

Static Private Member Functions
static boolean	evaluateConstitutionalClosability (PathSubGraph subGraph, IAtomContainer iac, RingClosureParameters settings)
	Method to evaluate the closability of a single path considering only its constitution. More...

static boolean	evaluate3DPathClosability (PathSubGraph subGraph, IAtomContainer mol, RingClosureParameters settings)
	Method to evaluate the closability of a single path in a graph representing a molecule. More...

Detailed Description

Tool box for determining whether a chain of atoms, i.e., a path, can be folded as to form a ring-closing bond that transforms the open chain in a ring.

Author: Marco Foscato

Definition at line 70 of file PathClosabilityTools.java.

Member Function Documentation

◆ evaluate3DPathClosability()

static boolean denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability	(	PathSubGraph	subGraph,
		IAtomContainer	mol,
		RingClosureParameters	settings
	)

staticprivate

Method to evaluate the closability of a single path in a graph representing a molecule.

Since this is a computationally demanding task, this method makes use of serialized data that is updated on the fly.

Parameters

subGraph	the subgraph representing the path in the graph.
mol	the molecular representation of the system represented by the whole graph, not by the subgraph. This is only used to provide the molecular constitution and does not require 3D coordinates. This will not be altered.
settings	the parameters pertaining ring closures.

Returns: true is the path corresponds to a closable chain

Definition at line 306 of file PathClosabilityTools.java.

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

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◆ evaluateConstitutionalClosability()

static boolean denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability	(	PathSubGraph	subGraph,
		IAtomContainer	iac,
		RingClosureParameters	settings
	)

staticprivate

Method to evaluate the closability of a single path considering only its constitution.

Parameters

subGraph	the subgraph representing the path in the graph.
iac	the molecular representation. This is only used to provide the molecular constitution and does not require 3D coordinates. This will not be altered.
settings	the parameters pertaining ring closures.

Returns: true is the path is constitutionally closable

Definition at line 128 of file PathClosabilityTools.java.

References denoptim.graph.Edge.BondType.getCDKOrder(), denoptim.graph.rings.RingClosureParameters.getConstitutionalClosabilityConds(), denoptim.graph.rings.PathSubGraph.getEdgesPath(), denoptim.graph.rings.PathSubGraph.getHeadVertex(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.utils.ManySMARTSQuery.getNumMatchesOfQuery(), denoptim.graph.rings.RingClosureParameters.getRequiredRingElements(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.rings.PathSubGraph.getTailVertex(), denoptim.graph.rings.PathSubGraph.getVertecesPath(), denoptim.utils.MoleculeUtils.getVertexToAtomIdMap(), denoptim.graph.Edge.BondType.hasCDKAnalogue(), denoptim.utils.ManySMARTSQuery.hasProblems(), and denoptim.utils.MoleculeUtils.removeRCA().

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

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◆ isCloseable()

static boolean denoptim.graph.rings.PathClosabilityTools.isCloseable	(	PathSubGraph	subGraph,
		IAtomContainer	mol,
		RingClosureParameters	settings
	)

static

Method to evaluate the closability of a single path in a graph.

The criteria defining the closability condition are controlled by the given settings.

Parameters

subGraph	the subgraph representing the potentially closable path in the graph.
mol	the molecule corresponding to the graph. This is only used to provide the molecular constitution and does not require 3D coordinates.

Returns: true is the path corresponds to a closable chain

Definition at line 86 of file PathClosabilityTools.java.

References denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), and denoptim.graph.rings.RingClosureParameters.getClosabilityEvalMode().

Referenced by denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), and denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability().

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

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

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ evaluate3DPathClosability()

◆ evaluateConstitutionalClosability()

◆ isCloseable()