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# Copyright 2001 by Gavin E. Crooks. 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.berkeley.edu/release-notes-1.55.html
The latest CLA file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
"Release 1.55":http://scop.berkeley.edu/parse/dir.cla.scop.txt_1.55 (July 2001)
"""
from types import *
from Residues import *
from FileIndex import FileIndex
class Record:
"""Holds information for one SCOP domain
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 sequence of tuples (nodetype, sunid) describing the
location of this domain in the SCOP hierarchy.
See the Scop module for a description of nodetypes.
"""
def __init__(self):
self.sid = ''
self.residues = None
self.sccs = ''
self.sunid =''
self.hierarchy = []
def __str__(self):
s = []
s.append(self.sid)
s += str(self.residues).split(" ")
s.append(self.sccs)
s.append(self.sunid)
h=[]
for ht in self.hierarchy:
h.append("=".join(map(str,ht)))
s.append(",".join(h))
return "\t".join(map(str,s)) + "\n"
class Iterator:
"""Iterates over a CLA file.
"""
def __init__(self, handle, parser=None):
"""Create an object that iterates over a DES file.
handle -- file-like object.
parser -- an optional Parser object to chang the results into
another form. If set to None, then the raw contents
of the file will be returned.
"""
if type(handle) is not FileType and type(handle) is not InstanceType:
raise TypeError, "I expected a file handle or file-like object"
self._handle = handle
self._parser = parser
def next(self):
"""Retrieve the next CLA record."""
while 1:
line = self._handle.readline()
if not line: return None
if line[0] !='#': break # Not a comment line
if self._parser is not None :
return self._parser.parse(line)
return line
def __iter__(self):
return iter(self.next, None)
class Parser:
"""Parses tab-deliminated CLA records.
"""
def parse(self, entry):
"""Returns a Cla Record """
entry = entry.rstrip() # no trailing whitespace
columns = entry.split('\t') # separate the tab-delineated cols
if len(columns) != 6:
raise SyntaxError, "I don't understand the format of %s" % entry
rec = Record()
rec.sid, pdbid, residues, rec.sccs, rec.sunid, hierarchy = columns
rec.residues = Residues(residues)
rec.residues.pdbid = pdbid
rec.sunid = int(rec.sunid)
h = []
for ht in hierarchy.split(",") :
h.append( ht.split('='))
for ht in h:
ht[1] = int(ht[1])
rec.hierarchy = h
return rec
class Index(FileIndex):
"""A CLA file indexed by SCOP identifiers."""
def __init__(self, filename, ) :
iterator = lambda f : Iterator(f, Parser())
key_gen = lambda rec : rec.sid
FileIndex.__init__(self, filename, iterator, key_gen)
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