CeSymmIterative

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.CeSymmIterative

public class CeSymmIterative extends Object

Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.

Works in the following way:

Run CeSymm on the original structure.
Calculate the symmetric unit boundaries.
Run CeSymm on one of the symmetric units to find further symmetries.
Repeat the last two steps until no more significant results are found.
Map back all residues in a multiple alignment of the repeats.

Since:: 4.1.1
Author:: Aleix Lafita

Constructor Summary

Constructors

Constructor

Description

CeSymmIterative(CESymmParameters param)

For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
Method Summary

Modifier and Type

Method

Description

CeSymmResult

execute(Atom[] atoms)

This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- CeSymmIterative
  
  public CeSymmIterative(CESymmParameters param)
  
  For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
  
  Parameters:
  
  param - CeSymm parameters, make sure they are cloned
Method Details
- execute
  
  public CeSymmResult execute(Atom[] atoms) throws StructureException
  
  This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
  
  Parameters:
  
  atoms - atoms
  
  Returns:
  
  CeSymmResult
  
  Throws:
  
  StructureException