SymmetryRefiner (biojava 6.1.0 API)

All Known Implementing Classes:

GraphComponentRefiner, SequenceFunctionRefiner
```
public interface SymmetryRefiner
```
Interface for all symmetry refinement implementations.

Since:

4.2.0

Author:

Aleix Lafita

Method Summary

All Methods Instance Methods Abstract Methods
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 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