Class DSSPParser
- java.lang.Object
-
- org.biojava.nbio.structure.secstruc.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 ofSecStrucState
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 ofSecStrucState
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 ofSecStrucState
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 ofSecStrucState
objects.
-
-
-
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 ofSecStrucState
objects.- Parameters:
dsspIs
- an InputStream to a DSSP filestructure
- Structure object associated to the dsspassign
- 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 ofSecStrucState
objects.- Parameters:
dsspPath
- path to the DSSP file to parsestructure
- Structure object associated to the dsspassign
- 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 ofSecStrucState
objects.- Parameters:
pdb
- path to the DSSP file to parsestructure
- Structure object associated to the dsspassign
- 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 ofSecStrucState
objects.- Parameters:
dsspOut
- String with the DSSP output to parsestructure
- Structure object associated to the dsspassign
- assigns the SS to the structure if true- Returns:
- a List of SS annotation objects
- Throws:
StructureException
java.io.IOException
-
-