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 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