Class LocalProteinDomainParser


  • public class LocalProteinDomainParser
    extends java.lang.Object
    Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. Since domains in proteins are difficult to define, results detected by automated algorithms have to be taken with a grain of salt. see
    J Mol Biol. 2004 Jun 4;339(3):647-78.
    
    Toward consistent assignment of structural domains in proteins.
    
    Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN.
    
    This implementation is based on a Java port of the PDP algorithm, as described in:
    Since:
    3.0.2
    Author:
    Andreas Prlic
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.List<Domain> suggestDomains​(Atom[] ca)
      Suggest domains for a set of Calpha atoms
      static java.util.List<Domain> suggestDomains​(Structure s)
      Suggest domains for a protein structure
      • Methods inherited from class java.lang.Object

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

      • suggestDomains

        public static java.util.List<Domain> suggestDomains​(Atom[] ca)
                                                     throws StructureException
        Suggest domains for a set of Calpha atoms
        Parameters:
        ca - an array of Calpha atoms
        Returns:
        a list of possible domains
        Throws:
        StructureException