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

Class ResidueGroup

java.lang.Object
org.biojava.nbio.structure.symmetry.internal.ResidueGroup
public class ResidueGroup extends Object
A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

This class provides an interface for comparing and combining them to refine self-Alignments into consistent MultipleAlignments of repeats.

Since:
4.2.0
Author:
Aleix Lafita

  • Constructor Details

    • ResidueGroup

      public ResidueGroup(Set<Integer> component)
      Create a ResidueGroup object from a maximally connected component.
      Parameters:
      component - set of residues connected

  • Method Details

    • order

      public int order()
      The order of symmetry of the group is the number of connected residues.
      Returns:
      size of residues List

    • isCompatible

      public boolean isCompatible(ResidueGroup other)
      Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion: 
       Two maximally connected components of the self-alignment Graph are
 compatible if they can be combined in a consistent multiple alignment
 of repeats, i.e.there exists one residue in c1 between each sorted
 pair of residues in c2.
      Compatibility is an intransitive relation, which means that for three ResidueGroups {A,B,C}, if A is compatible with B and B is compatible with C, then A is not necessarily compatible with C.
      Parameters:
      c2 - second maximally connected component
      Returns:
      true if compatible, false otherwise

    • combineWith

      public void combineWith(List<List<Integer>> alignRes)
      Combine the ResidueGroup with the alignment block.
      Parameters:
      alignRes - the alignment block, will be modified.