public class DSSPParser
extends java.lang.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 | Description |
---|---|
DSSPParser() |
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 of
SecStrucState 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 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. |
public static java.util.List<SecStrucState> parseFile(java.lang.String dsspPath, Structure structure, boolean assign) throws java.io.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 trueStructureException
java.io.IOException
public static java.util.List<SecStrucState> fetch(java.lang.String pdb, Structure structure, boolean assign) throws java.io.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 trueStructureException
java.io.IOException
public static java.util.List<SecStrucState> parseString(java.lang.String dsspOut, Structure structure, boolean assign) throws java.io.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 trueStructureException
java.io.IOException