Package org.biojava.nbio.structure.io

Class SeqRes2AtomAligner

java.lang.Object
org.biojava.nbio.structure.io.SeqRes2AtomAligner
public class SeqRes2AtomAligner extends 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, Jose Duarte

  • Constructor Details

    • SeqRes2AtomAligner

      public SeqRes2AtomAligner()

  • Method Details

    • getAlignmentString

      public String getAlignmentString()

    • getMatchingAtomRes

      public static Chain getMatchingAtomRes(Chain seqRes, List<Chain> atomList)

    • align

      public void align(Structure s, List<Chain> seqResList)

    • mapSeqresRecords

      public void mapSeqresRecords(Chain atomRes, Chain seqRes)
      Map the seqRes groups to the atomRes chain. Updates the atomRes chain object with the mapped data The seqRes chain should not be needed after this and atomRes should be further used.
      Parameters:
      atomRes - the chain containing ATOM groups (in atomGroups slot). This chain is modified to contain in its seqresGroups slot the mapped atom groups
      seqRes - the chain containing SEQRES groups (in atomGroups slot). This chain is not modified

    • getFullAtomSequence

      public static String getFullAtomSequence(List<Group> groups, Map<Integer,Integer> positionIndex, boolean isNucleotideChain)
      Returns the full sequence of the Atom records of a parent 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 parent
      positionIndex - a Map to keep track of which group is at which sequence position
      isNucleotideChain - whether the atom groups are predominantly nucleotides (the groups represent a nucleotide chain), if true non-standard nucleotides will be represented with ambiguous letter 'N' instead of 'X', if false all non-standard residues will be 'X'
      Returns:
      string representations

    • storeUnAlignedSeqRes

      public static void storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly)
      Storing unaligned SEQRES groups in a Structure.
      Parameters:
      structure -
      seqResChains -