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

Class SequenceFunctionRefiner

java.lang.Object
org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner
All Implemented Interfaces:
SymmetryRefiner
public class SequenceFunctionRefiner extends Object implements SymmetryRefiner
Creates a refined alignment with the CE-Symm alternative self-alignment. Needs the order of symmetry and assumes that the last repeat aligns with the first, being thus a CLOSE symmetry.
Since:
4.2.0
Author:
Spencer Bliven, Aleix Lafita

  • Constructor Details

    • SequenceFunctionRefiner

      public SequenceFunctionRefiner()

  • Method Details

    • refine

      public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) throws RefinerFailedException, StructureException
      Description copied from interface: SymmetryRefiner
      Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
      Specified by:
      refine in interface SymmetryRefiner
      Parameters:
      selfAlignment - optimal self-alignment calculated by CeSymm
      atoms - coordinates of the structure
      order - order of symmetry to use
      Returns:
      MultipleAlignment refined symmetry alignment
      Throws:
      RefinerFailedException
      StructureException

    • refineSymmetry

      public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) throws StructureException, RefinerFailedException
      Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.
      Parameters:
      afpChain - Input alignment from CE-Symm
      k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
      Returns:
      The refined alignment
      Throws:
      StructureException
      RefinerFailedException

    • refineSymmetry

      public static Map<Integer,Integer> refineSymmetry(Map<Integer,Integer> alignment, int k) throws StructureException
      Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.
      Parameters:
      alignment - The input alignment, as a map. This will be modified.
      k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
      Returns:
      A modified map with the refined alignment
      Throws:
      StructureException