Package org.biojava.nbio.structure.secstruc

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> 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> parseInputStream​(java.io.InputStream dsspIs, 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

      • parseInputStream

        public static java.util.List<SecStrucState> parseInputStream​(java.io.InputStream dsspIs,
                                                             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:
        dsspIs - an InputStream to a DSSP file
        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

      • 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

      • 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