charite.christo.protein
Class DSSP_Parser

java.lang.Object
  charite.christo.protein.DSSP_Parser

All Implemented Interfaces:

ProteinParser

public class DSSP_Parser
extends java.lang.Object
implements ProteinParser

HELP DSSP-files are calculated from PDB-files with the program DSSP by Kabsh and Sander which is freely available in the Web (see WIKI:DSSP_(protein)).

 SECONDARY STRUCTURE DEFINITION BY THE PROGRAM DSSP, VERSION OCT. 1985 **** MONTH=12 DAY=24 YEAR=2001

#  RESIDUE AA STRUCTURE BP1 BP2  ACC   N-H-->O  O-->H-N  N-H-->O  O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA
  1   -9 H L              0   0  117    0, 0.0   2,-0.1   0, 0.0 101,-0.1   0.000 360.0 360.0 360.0 125.0   40.8 -139.0   51.3
  2   -8 H K    >   -     0   0  118    1,-0.1   3,-1.5   2, 0.0   2,-0.2  -0.349 360.0 -86.7 -69.0 147.8   43.1 -138.1   48.4
  3   -7 H K  T 3  S-     0   0  205    1,-0.2  -1,-0.1  -2,-0.1   0, 0.0  -0.321 106.3  -4.6 -59.3 118.2   45.4 -140.7   46.9
  4   -6 H G  T 3  S+     0   0   68    1,-0.2  -1,-0.2  -2,-0.2  -2, 0.0   0.372  92.0 135.9  84.1  -4.0   48.7 -140.7   48.9

Field Summary

Fields inherited from interface charite.christo.protein.ProteinParser

IGNORE_SEQRES, SEQUENCE_FEATURES, SIDE_CHAIN_ATOMS

Constructor Summary

DSSP_Parser()

Method Summary

boolean

parse(Protein prot, long options, BA byteArray)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DSSP_Parser

public DSSP_Parser()

Method Detail

parse

public boolean parse(Protein prot,
                     long options,
                     BA byteArray)

Specified by:

parse in interface ProteinParser

byteArray - the entire file contents It is a byte array and not a String Object for performance reasons.

Returns:

true: success, false: inappropriate file format