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# 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
class Record(object):
"""Holds information for one SCOP domain.
Attribues:
- 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:
self._process(line)
def _process(self, line):
"""Parses DOM records.
Records consist of 4 tab deliminated fields;
sid, pdbid, residues, hierarchy
"""
# For example ::
#
# d1sctg_ 1sct g: 1.001.001.001.001.001
# d1scth_ 1sct h: 1.001.001.001.001.001
# d1flp__ 1flp - 1.001.001.001.001.002
# d1moh__ 1moh - 1.001.001.001.001.002
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(self.sid)
s.append(str(self.residues).replace(" ", "\t"))
s.append(self.hierarchy)
return "\t".join(s) + "\n"
def parse(handle):
"""Iterates over a DOM file as a Dom record for each line.
Arguments:
- handle -- file-like object.
"""
for line in handle:
if line.startswith('#'):
continue
yield Record(line)
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