denoptim.fragmenter.TopoTemplateProducer Class Reference

Collaboration diagram for denoptim.fragmenter.TopoTemplateProducer:

Public Member Functions
	TopoTemplateProducer (IAtomContainer originalIAC)
	Constructor. More...
IAtomContainer	getTemplateWithBufferShell (int bufferShellSize)
	Produced a new IAtomContainer containing all the atoms needed to define the topology of the original graph plus all the atoms that are connected by the number of bonds fedined by the buffer shell size. More...

Package Attributes
Set< IAtom >	topoCriticalAtoms = new HashSet<>()
	topology-critical atoms More...
IAtomContainer	originalIAC
	The original IAtomContainer to produce a topology-critical template for. More...
boolean	produceHDepleted = false
	Flag recording whether we could only produce a H-depleted template. More...

Private Member Functions
void	initialize ()

Detailed Description

Definition at line 20 of file TopoTemplateProducer.java.

Constructor & Destructor Documentation

TopoTemplateProducer()

denoptim.fragmenter.TopoTemplateProducer.TopoTemplateProducer

(

IAtomContainer

originalIAC

)

Constructor.

Parameters

originalIAC

the original IAtomContainer to produce a topology-critical template for.

Definition at line 45 of file TopoTemplateProducer.java.

References denoptim.fragmenter.TopoTemplateProducer.initialize(), and denoptim.fragmenter.TopoTemplateProducer.originalIAC.

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Member Function Documentation

getTemplateWithBufferShell()

IAtomContainer denoptim.fragmenter.TopoTemplateProducer.getTemplateWithBufferShell

(

int

bufferShellSize

)

Produced a new IAtomContainer containing all the atoms needed to define the topology of the original graph plus all the atoms that are connected by the number of bonds fedined by the buffer shell size.

Parameters

bufferShellSize

the number of bonds to consider when defining the depth of the buffer shell around the topology-critical atoms.

Returns

a new IAtomContainer containing all the atoms needed to define the topology of the original graph plus all the atoms that are connected by the number of bonds fedined by the buffer shell size.

Definition at line 185 of file TopoTemplateProducer.java.

References denoptim.utils.MoleculeUtils.isElement(), denoptim.fragmenter.TopoTemplateProducer.originalIAC, and denoptim.fragmenter.TopoTemplateProducer.topoCriticalAtoms.

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation().

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initialize()

void denoptim.fragmenter.TopoTemplateProducer.initialize ( )

private

Definition at line 53 of file TopoTemplateProducer.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.MoleculeUtils.findShortestPath(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.fragmenter.TopoTemplateProducer.originalIAC, denoptim.fragmenter.TopoTemplateProducer.produceHDepleted, and denoptim.fragmenter.TopoTemplateProducer.topoCriticalAtoms.

Referenced by denoptim.fragmenter.TopoTemplateProducer.TopoTemplateProducer().

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Member Data Documentation

originalIAC

IAtomContainer denoptim.fragmenter.TopoTemplateProducer.originalIAC

package

The original IAtomContainer to produce a topology-critical template for.

Definition at line 31 of file TopoTemplateProducer.java.

Referenced by denoptim.fragmenter.TopoTemplateProducer.getTemplateWithBufferShell(), denoptim.fragmenter.TopoTemplateProducer.initialize(), and denoptim.fragmenter.TopoTemplateProducer.TopoTemplateProducer().

produceHDepleted

boolean denoptim.fragmenter.TopoTemplateProducer.produceHDepleted = false

package

Flag recording whether we could only produce a H-depleted template.

Definition at line 36 of file TopoTemplateProducer.java.

Referenced by denoptim.fragmenter.TopoTemplateProducer.initialize().

topoCriticalAtoms

Set<IAtom> denoptim.fragmenter.TopoTemplateProducer.topoCriticalAtoms = new HashSet<>()

package

topology-critical atoms

Definition at line 26 of file TopoTemplateProducer.java.

Referenced by denoptim.fragmenter.TopoTemplateProducer.getTemplateWithBufferShell(), and denoptim.fragmenter.TopoTemplateProducer.initialize().

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

• /github/workspace/src/main/java/denoptim/fragmenter/TopoTemplateProducer.java