# 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 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, line=None): self.sid = '' self.residues = [] self.hierarchy = '' if line: self._process(line) def _process(self, line): """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 line = line.rstrip() # no trailing whitespace columns = line.split("\t") # separate the tab-delineated cols if len(columns) != 4: raise ValueError("I don't understand the format of %s" % line) self.sid, pdbid, res, self.hierarchy = columns self.residues = Residues(res) self.residues.pdbid =pdbid def __str__(self): s = [] s.append(self.sid) s.append(str(self.residues).replace(" ","\t") ) s.append(self.hierarchy) return "\t".join(s) + "\n" def parse(handle): """Iterates over a DOM file, returning a Dom record for each line in the file. Arguments: handle -- file-like object. """ for line in handle: if line.startswith('#'): continue yield Record(line) 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. """ import warnings warnings.warn("Bio.SCOP.Dom.Iterator is deprecated. Please use Bio.SCOP.Dom.parse() instead.", DeprecationWarning) from types import FileType, InstanceType 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 line.startswith('#'): return self.next() if self._parser is not None: return self._parser.parse(line) return line