Class performing the alignment of Fragments. More...

Collaboration diagram for denoptim.fragmenter.FragmentAlignement:

Public Member Functions
	FragmentAlignement (Fragment fragA, Fragment fragB) throws DENOPTIMException
	Constructor for an alignment of two fragments. More...

GraphMapping< FragIsomorphNode, FragIsomorphEdge >	getLowestRMSDMapping ()
	Returns the mapping leading to the lowest RMSD that could be found among all isomorphic mappings. More...

double	getMinimumRMSD ()
	Returns the lowest RMSD that could be found among all isomorphic mappings. More...

Private Attributes
double	minRMSD = Double.MAX_VALUE
	Lowest RMSD upon alignment. More...

GraphMapping< FragIsomorphNode, FragIsomorphEdge >	bestMapping = null
	Mapping of nodes leading to lowest RMSD upon alignment. More...

Detailed Description

Class performing the alignment of Fragments.

Author: marcof

Definition at line 21 of file FragmentAlignement.java.

Constructor & Destructor Documentation

◆ FragmentAlignement()

denoptim.fragmenter.FragmentAlignement.FragmentAlignement	(	Fragment	fragA,
		Fragment	fragB
	)		throws DENOPTIMException

Constructor for an alignment of two fragments.

Note we first have to find an ordering of the atoms/AP that is consistent. Thus we check for isomorphism between the fragments.

Parameters

fragA
fragB

Exceptions

DENOPTIMException if an isomorphism is not found.

Definition at line 43 of file FragmentAlignement.java.

References denoptim.fragmenter.FragmentAlignement.bestMapping, denoptim.graph.FragmentIsomorphismInspector.getMappings(), denoptim.graph.FragIsomorphNode.getPoint3d(), denoptim.graph.FragmentIsomorphismInspector.isomorphismExists(), and denoptim.fragmenter.FragmentAlignement.minRMSD.

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Member Function Documentation

◆ getLowestRMSDMapping()

GraphMapping< FragIsomorphNode, FragIsomorphEdge > denoptim.fragmenter.FragmentAlignement.getLowestRMSDMapping ( )

Returns the mapping leading to the lowest RMSD that could be found among all isomorphic mappings.

Returns

Definition at line 99 of file FragmentAlignement.java.

References denoptim.fragmenter.FragmentAlignement.bestMapping.

Referenced by denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments().

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◆ getMinimumRMSD()

double denoptim.fragmenter.FragmentAlignement.getMinimumRMSD ( )

Returns the lowest RMSD that could be found among all isomorphic mappings.

Returns

Definition at line 110 of file FragmentAlignement.java.

References denoptim.fragmenter.FragmentAlignement.minRMSD.

Referenced by denoptim.fragmenter.FragmentAlignementTest.testGetMinimumRMSD().

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Member Data Documentation

◆ bestMapping

GraphMapping<FragIsomorphNode, FragIsomorphEdge> denoptim.fragmenter.FragmentAlignement.bestMapping = null

private

Mapping of nodes leading to lowest RMSD upon alignment.

Definition at line 31 of file FragmentAlignement.java.

Referenced by denoptim.fragmenter.FragmentAlignement.FragmentAlignement(), and denoptim.fragmenter.FragmentAlignement.getLowestRMSDMapping().

◆ minRMSD

double denoptim.fragmenter.FragmentAlignement.minRMSD = Double.MAX_VALUE

private

Lowest RMSD upon alignment.

Definition at line 26 of file FragmentAlignement.java.

Referenced by denoptim.fragmenter.FragmentAlignement.FragmentAlignement(), and denoptim.fragmenter.FragmentAlignement.getMinimumRMSD().

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

/github/workspace/src/main/java/denoptim/fragmenter/FragmentAlignement.java

Public Member Functions

Private Attributes