denoptim.graph.rings.RandomCombOfRingsIterator Class Reference

A class for iterating over sets of ring combinations generated by considering any constrain and setting defined in the fragment space and ring-closure settings and by randomly picking candidates when no criterion can be used to take an informed decision. More...

Inheritance diagram for denoptim.graph.rings.RandomCombOfRingsIterator:

Collaboration diagram for denoptim.graph.rings.RandomCombOfRingsIterator:

Public Member Functions
	RandomCombOfRingsIterator (IAtomContainer iac, DGraph molGraph, int maxRingClosures, FragmentSpace fragSpace, RingClosureParameters rcParams) throws DENOPTIMException
	Constructs an iterator. More...
boolean	hasNext ()
	Always returns true because we allow duplicates. More...
List< Ring >	next ()

Private Attributes
IAtomContainer	originalMol
	Chemical representation of the system we work with. More...
DGraph	molGraph
	Graph representation of the system we work with. More...
int	maxRingClosures = -1
	Max number of ring closures to consider in a valid combination of rings. More...
FragmentSpace	fragSpace
	Space of building blocks. More...
RingClosureParameters	settings
	Parameters related to rings. More...

Detailed Description

A class for iterating over sets of ring combinations generated by considering any constrain and setting defined in the fragment space and ring-closure settings and by randomly picking candidates when no criterion can be used to take an informed decision.

Note this iterator loops infinitely, i.e., hasNext() returns always true.

Definition at line 26 of file RandomCombOfRingsIterator.java.

Constructor & Destructor Documentation

RandomCombOfRingsIterator()

denoptim.graph.rings.RandomCombOfRingsIterator.RandomCombOfRingsIterator	(	IAtomContainer	iac,
		DGraph	molGraph,
		int	maxRingClosures,
		FragmentSpace	fragSpace,
		RingClosureParameters	rcParams
	)		throws DENOPTIMException

Constructs an iterator.

Parameters

inMol
molGraph
maxRingClosures

Exceptions

DENOPTIMException

Definition at line 63 of file RandomCombOfRingsIterator.java.

References denoptim.graph.rings.RandomCombOfRingsIterator.fragSpace, denoptim.graph.rings.RandomCombOfRingsIterator.maxRingClosures, and denoptim.graph.rings.RandomCombOfRingsIterator.molGraph.

Member Function Documentation

hasNext()

boolean denoptim.graph.rings.RandomCombOfRingsIterator.hasNext

(

)

Always returns true because we allow duplicates.

Definition at line 80 of file RandomCombOfRingsIterator.java.

next()

List< Ring > denoptim.graph.rings.RandomCombOfRingsIterator.next

(

)

Definition at line 88 of file RandomCombOfRingsIterator.java.

References denoptim.graph.rings.RingSizeManager.addRingClosingBond(), denoptim.graph.rings.RandomCombOfRingsIterator.fragSpace, denoptim.graph.Edge.getBondType(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), denoptim.graph.rings.PathSubGraph.getVertecesPath(), denoptim.graph.rings.RingSizeManager.initialize(), denoptim.graph.rings.PathClosabilityTools.isCloseable(), denoptim.graph.rings.RandomCombOfRingsIterator.maxRingClosures, denoptim.graph.rings.RandomCombOfRingsIterator.molGraph, denoptim.utils.Randomizer.nextInt(), denoptim.graph.rings.RandomCombOfRingsIterator.originalMol, denoptim.graph.Ring.setBondType(), denoptim.graph.rings.RandomCombOfRingsIterator.settings, and denoptim.graph.rings.RingSizeManager.setVertexAsDone().

Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.graph.rings.CyclicGraphHandler.getRandomCombinationOfRings(), and denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability().

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Member Data Documentation

fragSpace

FragmentSpace denoptim.graph.rings.RandomCombOfRingsIterator.fragSpace

private

Space of building blocks.

Definition at line 46 of file RandomCombOfRingsIterator.java.

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

maxRingClosures

int denoptim.graph.rings.RandomCombOfRingsIterator.maxRingClosures = -1

private

Max number of ring closures to consider in a valid combination of rings.

Definition at line 41 of file RandomCombOfRingsIterator.java.

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

molGraph

DGraph denoptim.graph.rings.RandomCombOfRingsIterator.molGraph

private

Graph representation of the system we work with.

Definition at line 36 of file RandomCombOfRingsIterator.java.

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

originalMol

IAtomContainer denoptim.graph.rings.RandomCombOfRingsIterator.originalMol

private

Chemical representation of the system we work with.

Definition at line 31 of file RandomCombOfRingsIterator.java.

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

settings

RingClosureParameters denoptim.graph.rings.RandomCombOfRingsIterator.settings

private

Parameters related to rings.

Definition at line 51 of file RandomCombOfRingsIterator.java.

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

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

• /github/workspace/src/main/java/denoptim/graph/rings/RandomCombOfRingsIterator.java