Class CompoundFinder


  • public class CompoundFinder
    extends java.lang.Object
    Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. Compounds are the groups of sequence identical NCS-related polymer chains in the Structure. This is related to SeqRes2AtomAligner but it is intended for raw PDB files where possibly no SEQRES is given.
    Author:
    duarte_j
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static double GAP_COVERAGE_THRESHOLD
      Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
      static double IDENTITY_THRESHOLD
      Identity value for 2 chains to be considered part of same entity
      static double RATIO_GAPS_FOR_MISMATCH
      Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<Compound> findCompounds()
      Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file
      • Methods inherited from class java.lang.Object

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

      • RATIO_GAPS_FOR_MISMATCH

        public static final double RATIO_GAPS_FOR_MISMATCH
        Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it
        See Also:
        Constant Field Values
      • IDENTITY_THRESHOLD

        public static final double IDENTITY_THRESHOLD
        Identity value for 2 chains to be considered part of same entity
        See Also:
        Constant Field Values
      • GAP_COVERAGE_THRESHOLD

        public static final double GAP_COVERAGE_THRESHOLD
        Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
        See Also:
        Constant Field Values
    • Constructor Detail

      • CompoundFinder

        public CompoundFinder​(Structure s)
    • Method Detail

      • findCompounds

        public java.util.List<Compound> findCompounds()
        Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file
        Returns: