Class GraphComponentRefiner
java.lang.Object
org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
- All Implemented Interfaces:
SymmetryRefiner
The GraphRefiner transforms the self-alignment into a Graph and extracts its
maximally connected Components. It then refines the alignment by combining
the compatible Components with the following heuristic:
Given a set of components and their pairwise compatibilities, iteratively add the most compatible component, which is compatible to all the components already added, to the final alignment.
- Author:
- Aleix Lafita
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionReturns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
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Constructor Details
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GraphComponentRefiner
public GraphComponentRefiner()
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Method Details
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refine
public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) throws StructureException, RefinerFailedException Description copied from interface:SymmetryRefinerReturns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.- Specified by:
refinein interfaceSymmetryRefiner- Parameters:
selfAlignment- optimal self-alignment calculated by CeSymmatoms- coordinates of the structureorder- order of symmetry to use- Returns:
- MultipleAlignment refined symmetry alignment
- Throws:
StructureExceptionRefinerFailedException
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