Package org.biojava.nbio.structure.symmetry.internal

Class 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 Detail

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 Detail

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