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

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 Details
- 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