public class DSSPParser extends Object
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/.
| Constructor and Description |
|---|
DSSPParser() |
| Modifier and Type | Method and 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. |
public DSSPParser()
public static List<SecStrucState> parseInputStream(InputStream dsspIs, Structure structure, boolean assign) throws IOException, StructureException
SecStrucState objects.dsspIs - an InputStream to a DSSP filestructure - Structure object associated to the dsspassign - assigns the SS to the structure if trueStructureExceptionIOExceptionpublic static List<SecStrucState> parseFile(String dsspPath, Structure structure, boolean assign) throws IOException, StructureException
SecStrucState objects.dsspPath - path to the DSSP file to parsestructure - Structure object associated to the dsspassign - assigns the SS to the structure if trueStructureExceptionIOExceptionpublic static List<SecStrucState> fetch(String pdb, Structure structure, boolean assign) throws IOException, StructureException
SecStrucState objects.pdb - path to the DSSP file to parsestructure - Structure object associated to the dsspassign - assigns the SS to the structure if trueStructureExceptionIOExceptionpublic static List<SecStrucState> parseString(String dsspOut, Structure structure, boolean assign) throws IOException, StructureException
SecStrucState objects.dsspOut - String with the DSSP output to parsestructure - Structure object associated to the dsspassign - assigns the SS to the structure if trueStructureExceptionIOExceptionCopyright © 2000–2018 BioJava. All rights reserved.