org.biojava.nbio.structure.symmetry.internal

Interface SymmetryRefiner

All Known Implementing Classes:

GraphComponentRefiner, SequenceFunctionRefiner

public interface SymmetryRefiner

Interface for all symmetry refinement implementations.

Since:

4.2.0

Author:

Aleix Lafita

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.

Method Detail

refine

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

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

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:

RefinerFailedException

StructureException