Class 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
    Andreas Prlic, Jose Duarte
    • Method Detail

      • getMatchingAtomRes

        public static Chain getMatchingAtomRes​(Chain seqRes,
                                               List<Chain> atomList,
                                               boolean useChainId)
        seqRes -
        atomList -
        useChainId - if true chainId (Chain.getId) is used for matching, if false chainName (Chain.getName) is used
      • 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.
        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.
        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'
        string representations
      • storeUnAlignedSeqRes

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