Package Bio :: Package SCOP :: Module Dom
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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 Attribues: 25 26 - sid - The SCOP ID of the entry, e.g. d1anu1 27 - residues - The domain definition as a Residues object 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 as a Dom record for each line. 68 69 Arguments: 70 71 - handle -- file-like object. 72 """ 73 for line in handle: 74 if line.startswith('#'): 75 continue 76 yield Record(line)
77