Package org.biojava.nbio.structure.io

Class CompoundFinder

java.lang.Object
org.biojava.nbio.structure.io.CompoundFinder
public class CompoundFinder extends 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 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
    static final double
    IDENTITY_THRESHOLD
    Identity value for 2 chains to be considered part of same entity
    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

  • Constructor Summary

    Constructors
    Constructor
    Description
    CompoundFinder(Structure s)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    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 Details

    • 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:

    • IDENTITY_THRESHOLD

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

    • 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:

  • Constructor Details

    • CompoundFinder

      public CompoundFinder(Structure s)

  • Method Details

    • findCompounds

      public 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: