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

Class CeSymm

java.lang.Object
org.biojava.nbio.structure.symmetry.internal.CeSymm
public class CeSymm extends Object
Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.

Iterating over previous results and disabling the diagonal of the previous alignments can also be done with this implementation, which will generate a set of self-alignments (disabled, because none improvements were shown, but can be turn on manually).

Multiple levels of symmetry can be analyzed by finding symmetries in repeats of previous results. This feature allows to find multiple symmetry axes.

The alignment is then refined to obtain a consistent alignment among all residues of the structure and organized into different parts, called symmetric repeats.

After refinement of the initial alignment, an optimization step can be used to improve the overall score of the repeat multiple alignment.

Since:
4.1.1
Author:
Andreas Prlic, Spencer Bliven, Aleix Lafita

  • Field Details

    • version

      public static final String version
      Version History:

      • 1.0 - initial implementation of CE-Symm.
      • 1.1 - enable multiple CE-Symm runs to calculate all self-alignments.
      • 2.0 - refine the alignment for consistency of repeat definition.
      • 2.1 - optimize the alignment to improve the score.
      • 2.2 - run multiple symmetry levels recursively to find PG and hierarchical symmetries.