Class DSSPParser


  • public class DSSPParser
    extends java.lang.Object
    Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.

    This class has been ported from the OWL Java library for Structural Bioinformatics (https://github.com/eppic-team/owl).

    As of September 2015, the DSSP source code and executables can be downloaded from http://swift.cmbi.ru.nl/gv/dssp/.

    Since:
    4.1.1
    Author:
    Aleix Lafita
    • Constructor Summary

      Constructors 
      Constructor Description
      DSSPParser()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.List<SecStrucState> fetch​(java.lang.String pdb, Structure structure, boolean assign)
      Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
      static java.util.List<SecStrucState> parseFile​(java.lang.String dsspPath, Structure structure, boolean assign)
      Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
      static java.util.List<SecStrucState> parseString​(java.lang.String dsspOut, Structure structure, boolean assign)
      Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.
      • Methods inherited from class java.lang.Object

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

      • DSSPParser

        public DSSPParser()
    • Method Detail

      • parseFile

        public static java.util.List<SecStrucState> parseFile​(java.lang.String dsspPath,
                                                              Structure structure,
                                                              boolean assign)
                                                       throws java.io.IOException,
                                                              StructureException
        Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
        Parameters:
        dsspPath - path to the DSSP file to parse
        structure - Structure object associated to the dssp
        assign - assigns the SS to the structure if true
        Returns:
        a List of SS annotation objects
        Throws:
        StructureException
        java.io.IOException
      • fetch

        public static java.util.List<SecStrucState> fetch​(java.lang.String pdb,
                                                          Structure structure,
                                                          boolean assign)
                                                   throws java.io.IOException,
                                                          StructureException
        Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
        Parameters:
        pdb - path to the DSSP file to parse
        structure - Structure object associated to the dssp
        assign - assigns the SS to the structure if true
        Returns:
        a List of SS annotation objects
        Throws:
        StructureException
        java.io.IOException
      • parseString

        public static java.util.List<SecStrucState> parseString​(java.lang.String dsspOut,
                                                                Structure structure,
                                                                boolean assign)
                                                         throws java.io.IOException,
                                                                StructureException
        Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.
        Parameters:
        dsspOut - String with the DSSP output to parse
        structure - Structure object associated to the dssp
        assign - assigns the SS to the structure if true
        Returns:
        a List of SS annotation objects
        Throws:
        StructureException
        java.io.IOException