Logo Search packages:      
Sourcecode: python-biopython version File versions  Download package

# Copyright 2000 by Jeffrey Chang.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

# Gavin E. Crooks 2001-11-07:
#     Interface and comments modified to reflect changes to the SCOP
#     module, and to SCOP itself.

""" Handle the SCOP DOMain file.

The DOM file has been officially deprecated. For more information see
the SCOP"release notes.":http://scop.berkeley.edu/release-notes-1.55.html 
The DOM files for older releases can be found 
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/

from Residues import Residues

00021 class Record(object):
    """Holds information for one SCOP domain.

    sid -- The SCOP ID of the entry, e.g. d1anu1

    residues -- The domain definition as a Residues object

    hierarchy -- A string specifying where this domain is in the hierarchy.
    def __init__(self, line=None):
        self.sid = ''
        self.residues = []
        self.hierarchy = ''
        if line:

00037     def _process(self, line):
        """Parses DOM records.
        Records consist of 4 tab deliminated fields;
        sid, pdbid, residues, hierarchy
        #For example ::
        #d1sctg_ 1sct    g:
        #d1scth_ 1sct    h:
        #d1flp__ 1flp    -
        #d1moh__ 1moh    -

        line = line.rstrip()  # no trailing whitespace
        columns = line.split("\t")  # separate the tab-delineated cols
        if len(columns) != 4:
            raise ValueError("I don't understand the format of %s" % line)
        self.sid, pdbid, res, self.hierarchy = columns
        self.residues = Residues(res)
        self.residues.pdbid =pdbid

    def __str__(self):
        s = []
        s.append(str(self.residues).replace(" ","\t") )
        return "\t".join(s) + "\n"

def parse(handle):
    """Iterates over a DOM file, returning a Dom record for each line
    in the file.

        handle -- file-like object.
    for line in handle:
        if line.startswith('#'):
        yield Record(line)

Generated by  Doxygen 1.6.0   Back to index