Class EntityFinder

  • public class EntityFinder
    extends Object
    Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure. Entities 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/mmCIF files where possibly no SEQRES is given.
    Jose Duarte
    • Field Detail


        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

        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
    • Method Detail

      • findPolyEntities

        public static List<EntityInfofindPolyEntities​(List<List<Chain>> polyModels)
        Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor. To be used in case the information is missing in PDB/mmCIF file
      • createPurelyNonPolyEntities

        public static void createPurelyNonPolyEntities​(List<List<Chain>> nonPolyModels,
                                                       List<List<Chain>> waterModels,
                                                       List<EntityInfo> entities)
        Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them. The result is written back to the passed entities List.
        nonPolyModels -
        waterModels -
        entities -