Package org.biojava.nbio.structure.secstruc

Class DSSPParser

java.lang.Object

org.biojava.nbio.structure.secstruc.DSSPParser

public class DSSPParser
extends 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

Modifier and Type	Method	Description
static List<SecStrucState>	fetch(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 List<SecStrucState>	parseFile(String dsspPath, Structure structure, boolean assign)	Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
static List<SecStrucState>	parseInputStream(InputStream dsspIs, Structure structure, boolean assign)	Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
static List<SecStrucState>	parseString(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 List<SecStrucState> parseInputStream(InputStream dsspIs,
                                                   Structure structure,
                                                   boolean assign)
                                            throws 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

IOException

parseFile

public static List<SecStrucState> parseFile(String dsspPath,
                                            Structure structure,
                                            boolean assign)
                                     throws 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

IOException

fetch

public static List<SecStrucState> fetch(String pdb,
                                        Structure structure,
                                        boolean assign)
                                 throws 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

IOException

parseString

public static List<SecStrucState> parseString(String dsspOut,
                                              Structure structure,
                                              boolean assign)
                                       throws 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

IOException