Class SeqRes2AtomAligner


  • public class SeqRes2AtomAligner
    extends java.lang.Object
    Aligns the SEQRES residues to the ATOM residues. The AminoAcids that can be matched between the two of them will be set in the SEQRES chains
    Author:
    Andreas Prlic
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean align​(java.util.List<Group> seqRes, java.util.List<Group> atomRes)
      aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).
      void align​(Structure s, java.util.List<Chain> seqResList)  
      java.lang.String getAlignmentString()  
      java.lang.String getFullAtomSequence​(java.util.List<Group> groups)
      returns the full sequence of the Atom records of a chain with X instead of HETATMSs.
      static SubstitutionMatrix getSubstitutionMatrix​(FiniteAlphabet alphabet)  
      boolean isDEBUG()  
      void setDEBUG​(boolean debug)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • SeqRes2AtomAligner

        public SeqRes2AtomAligner()
    • Method Detail

      • getAlignmentString

        public java.lang.String getAlignmentString()
      • isDEBUG

        public boolean isDEBUG()
      • setDEBUG

        public void setDEBUG​(boolean debug)
      • align

        public void align​(Structure s,
                          java.util.List<Chain> seqResList)
      • getFullAtomSequence

        public java.lang.String getFullAtomSequence​(java.util.List<Group> groups)
        returns the full sequence of the Atom records of a chain with X instead of HETATMSs. The advantage of this is that it allows us to also align HETATM groups back to the SEQRES.
        Parameters:
        groups - the list of groups in a chain
        Returns:
        string representations
      • align

        public boolean align​(java.util.List<Group> seqRes,
                             java.util.List<Group> atomRes)
                      throws StructureException
        aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information). This does the actual alignment and if a group can be mapped to a position in the SEQRES then the corresponding position is repplaced with the group that contains the atoms.
        Parameters:
        seqRes -
        atomRes -
        Returns:
        true if no match has bee found
        Throws:
        StructureException