1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
|
# 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 types import *
from Residues import Residues
class Record:
"""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):
self.sid = ''
self.residues = []
self.hierarchy = ''
def __str__(self):
s = []
s.append(self.sid)
s.append(str(self.residues).replace(" ","\t") )
s.append(self.hierarchy)
return "\t".join(s) + "\n"
class Iterator:
"""Iterates over a DOM 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 change 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 ValueError, "I expected a file handle or file-like object"
self._handle = handle
self._parser = parser
def next(self):
line = self._handle.readline()
if not line:
return None
if self._parser is not None:
return self._parser.parse(line)
return line
class Parser:
"""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
def parse(self, entry):
"""Returns a Dom.Record """
entry = entry.rstrip() # no trailing whitespace
columns = entry.split("\t") # separate the tab-delineated cols
if len(columns) != 4:
raise SyntaxError, "I don't understand the format of %s" % entry
dom = Record()
dom.sid, pdbid, res, dom.hierarchy = columns
dom.residues = Residues(res)
dom.residues.pdbid =pdbid
return dom
|
