Class DSSPParser
java.lang.Object
org.biojava.nbio.structure.secstruc.DSSPParser
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 -
Method Summary
Modifier and TypeMethodDescriptionstatic List<SecStrucState>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 ofSecStrucStateobjects.static List<SecStrucState>Parse a DSSP output file and return the secondary structure annotation as a List ofSecStrucStateobjects.static List<SecStrucState>parseString(String dsspOut, Structure structure, boolean assign) Parse a DSSP format String and return the secondary structure annotation as a List ofSecStrucStateobjects.
-
Constructor Details
-
DSSPParser
public DSSPParser()
-
-
Method Details
-
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 ofSecStrucStateobjects.- 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:
StructureExceptionIOException
-
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 ofSecStrucStateobjects.- 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:
StructureExceptionIOException
-
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 ofSecStrucStateobjects.- 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:
StructureExceptionIOException
-