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   
 19  from Residues import Residues 
 20   
21 -class Record:
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
59 - def __str__(self):
60 s = [] 61 s.append(self.sid) 62 s.append(str(self.residues).replace(" ","\t") ) 63 s.append(self.hierarchy) 64 return "\t".join(s) + "\n"
65 66
67 -def parse(handle):
68 """Iterates over a DOM file, returning a Dom record for each line 69 in the file. 70 71 Arguments: 72 73 handle -- file-like object. 74 """ 75 for line in handle: 76 yield Record(line)
77 78
79 -class Iterator:
80 """Iterates over a DOM file. 81 """
82 - def __init__(self, handle, parser=None):
83 """Create an object that iterates over a DES file. 84 85 handle -- file-like object. 86 87 parser -- an optional Parser object to change the results into 88 another form. If set to None, then the raw contents 89 of the file will be returned. 90 91 """ 92 from types import FileType, InstanceType 93 if type(handle) is not FileType and type(handle) is not InstanceType: 94 raise ValueError, "I expected a file handle or file-like object" 95 self._handle = handle 96 self._parser = parser
97
98 - def next(self):
99 line = self._handle.readline() 100 if not line: 101 return None 102 if self._parser is not None: 103 return self._parser.parse(line) 104 return line
105
106 -class Parser:
107 - def parse(self, entry):
108 """Returns a Dom.Record """ 109 import warnings 110 warnings.warn("""Bio.SCOP.Dom.Parser is deprecated. 111 Instead of 112 113 parser = Dom.Parser() 114 record = parser.parse(entry) 115 116 please use 117 118 record = Dom.Record(entry) 119 """) 120 return Record(entry)
121