org.biojava.nbio.structure.symmetry.internal

Class GraphComponentRefiner

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner

All Implemented Interfaces:

SymmetryRefiner

public class GraphComponentRefiner
extends Object
implements 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

Constructor Summary

Constructors

Constructor and Description
GraphComponentRefiner()

Method Summary

Modifier and Type	Method and Description
MultipleAlignment	refine(AFPChain selfAlignment, Atom[] atoms, int order) Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GraphComponentRefiner

public GraphComponentRefiner()

Method Detail

refine

public MultipleAlignment refine(AFPChain selfAlignment,
                                Atom[] atoms,
                                int order)
                         throws StructureException,
                                RefinerFailedException

Description copied from interface: SymmetryRefiner

Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

Specified by:

refine in interface SymmetryRefiner

Parameters:

selfAlignment - optimal self-alignment calculated by CeSymm

atoms - coordinates of the structure

order - order of symmetry to use

Returns:

MultipleAlignment refined symmetry alignment

Throws:

StructureException

RefinerFailedException