Source Code for Module Bio.SCOP.Dom

 1  # Copyright 2000 by Jeffrey Chang.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  # Gavin E. Crooks 2001-11-07: 
 7  #     Interface and comments modified to reflect changes to the SCOP 
 8  #     module, and to SCOP itself. 
 9   
10  """ Handle the SCOP DOMain file. 
11   
12  The DOM file has been officially deprecated. For more information see 
13  the SCOP"release notes.":http://scop.berkeley.edu/release-notes-1.55.html 
14  The DOM files for older releases can be found 
15  "elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ 
16  """ 
17   
18  from Residues import Residues 
19   
20   
21 -class Record(object): 
22      """Holds information for one SCOP domain. 
23   
24      sid -- The SCOP ID of the entry, e.g. d1anu1 
25   
26      residues -- The domain definition as a Residues object 
27   
28      hierarchy -- A string specifying where this domain is in the hierarchy. 
29      """ 
30 -    def __init__(self, line=None): 
31          self.sid = '' 
32          self.residues = [] 
33          self.hierarchy = '' 
34          if line: 
35              self._process(line) 
36   
37 -    def _process(self, line): 
38          """Parses DOM records. 
39   
40          Records consist of 4 tab deliminated fields; 
41          sid, pdbid, residues, hierarchy 
42          """ 
43          #For example :: 
44          # 
45          #d1sctg_ 1sct    g:      1.001.001.001.001.001 
46          #d1scth_ 1sct    h:      1.001.001.001.001.001 
47          #d1flp__ 1flp    -       1.001.001.001.001.002 
48          #d1moh__ 1moh    -       1.001.001.001.001.002 
49   
50          line = line.rstrip()  # no trailing whitespace 
51          columns = line.split("\t")  # separate the tab-delineated cols 
52          if len(columns) != 4: 
53              raise ValueError("I don't understand the format of %s" % line) 
54          self.sid, pdbid, res, self.hierarchy = columns 
55          self.residues = Residues(res) 
56          self.residues.pdbid =pdbid 
57   
58 -    def __str__(self): 
59          s = [] 
60          s.append(self.sid) 
61          s.append(str(self.residues).replace(" ","\t") ) 
62          s.append(self.hierarchy) 
63          return "\t".join(s) + "\n" 
64   
65   
66 -def parse(handle): 
67      """Iterates over a DOM file, returning a Dom record for each line 
68      in the file. 
69   
70      Arguments: 
71   
72          handle -- file-like object. 
73      """ 
74      for line in handle: 
75          if line.startswith('#'): 
76              continue 
77          yield Record(line) 
78