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# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. 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.
""" Handle the SCOP CLAssification file, which describes SCOP domains.
The file format is described in the scop
"release notes.":http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html
The latest CLA file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
"Release 1.73": http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.73
(July 2008)
"""
from . import Residues
class Record(object):
"""Holds information for one SCOP domain.
Attributes:
- sid - SCOP identifier. e.g. d1danl2
- residues - The domain definition as a Residues object
- sccs - SCOP concise classification strings. e.g. b.1.2.1
- sunid - SCOP unique identifier for this domain
- hierarchy - A dictionary, keys are nodetype, values are sunid,
describing the location of this domain in the SCOP hierarchy. See
the Scop module for a description of nodetypes. This used to be a
list of (key,value) tuples in older versions of Biopython (see
Bug 3109).
"""
def __init__(self, line=None):
self.sid = ''
self.residues = None
self.sccs = ''
self.sunid = ''
self.hierarchy = {}
if line:
self._process(line)
def _process(self, line):
line = line.rstrip() # no trailing whitespace
columns = line.split('\t') # separate the tab-delineated cols
if len(columns) != 6:
raise ValueError("I don't understand the format of %s" % line)
self.sid, pdbid, residues, self.sccs, self.sunid, hierarchy = columns
self.residues = Residues.Residues(residues)
self.residues.pdbid = pdbid
self.sunid = int(self.sunid)
for ht in hierarchy.split(","):
key, value = ht.split('=')
self.hierarchy[key] = int(value)
def __str__(self):
s = []
s.append(self.sid)
s += str(self.residues).split(" ")
s.append(self.sccs)
s.append(self.sunid)
s.append(','.join('='.join((key, str(value))) for key, value
in self.hierarchy.items()))
return "\t".join(map(str, s)) + "\n"
def parse(handle):
"""Iterates over a CLA file as Cla records for each line.
Arguments:
- handle - file-like object.
"""
for line in handle:
if line.startswith('#'):
continue
yield Record(line)
class Index(dict):
"""A CLA file indexed by SCOP identifiers for rapid random access."""
def __init__(self, filename):
"""Create CLA index.
Arguments:
- filename - The file to index
"""
dict.__init__(self)
self.filename = filename
with open(self.filename, "rU") as f:
position = 0
while True:
line = f.readline()
if not line:
break
if line.startswith('#'):
continue
record = Record(line)
key = record.sid
if key is not None:
self[key] = position
position = f.tell()
def __getitem__(self, key):
"""Return an item from the indexed file."""
position = dict.__getitem__(self, key)
with open(self.filename, "rU") as f:
f.seek(position)
line = f.readline()
record = Record(line)
return record
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