Source Code for Module Biskit.PDBParsePickle

 1  ## 
 2  ## Biskit, a toolkit for the manipulation of macromolecular structures 
 3  ## Copyright (C) 2004-2005 Raik Gruenberg & Johan Leckner 
 4  ## 
 5  ## This program is free software; you can redistribute it and/or 
 6  ## modify it under the terms of the GNU General Public License as 
 7  ## published by the Free Software Foundation; either version 2 of the 
 8  ## License, or any later version. 
 9  ## 
10  ## This program is distributed in the hope that it will be useful, 
11  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
12  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
13  ## General Public License for more details. 
14  ## 
15  ## You find a copy of the GNU General Public License in the file 
16  ## license.txt along with this program; if not, write to the Free 
17  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
18  ## 
19  ## 
20  ## last $Author: graik $ 
21  ## last $Date: 2006/12/16 23:21:54 $ 
22  ## $Revision: 2.2 $ 
23  """ 
24  Parse a pickled PDBModel from disc into a new PDBModel instance  
25  """ 
26  import Biskit.tools as T 
27  import Biskit as B 
28   
29  from PDBParser import PDBParserError 
30  from PDBParseModel import PDBParseModel 
31   
32 -class PDBParsePickle( PDBParseModel ): 
33   
34      @staticmethod 
35 -    def supports( source ): 
36          """ 
37          The method is static and can thus be called directly with the parser 
38          class rather than with an instance:: 
39   
40          >>> if ParsePDBModel.supports( model ): 
41          >>>     ... 
42           
43          @return: True if the given source is supported by this parser 
44                   implementation (equivalent to isinstance( source, PDBModel) ) 
45          @rtype: bool 
46          """ 
47          return (type(source) is str) or isinstance(source, B.LocalPath) 
48   
49      @staticmethod 
50 -    def description(): 
51          """ 
52          The method is static and can thus be called directly with the parser 
53          class rather than with an instance:: 
54   
55          >>> if ParsePDBModel.description(): 
56          >>>     ... 
57   
58          @return: short free text description of the supported format 
59          @rtype: str 
60          """ 
61          return 'pickled PDBModel (file)' 
62           
63   
64 -    def update( self, model, source, skipRes=None, lookHarder=0 ): 
65          """ 
66          Update empty or missing fields of model from the source. The 
67          model will be connected to the source via model.source. 
68   
69          @param model: existing model 
70          @type  model: PDBModel 
71          @param source: source PDB file or pickled PDBModel or PDBModel object 
72          @type  source: str || file || PDBModel 
73          @param skipRes: list residue names that should not be parsed 
74          @type  skipRes: [ str ] 
75          """ 
76          try: 
77              if self.needsUpdate( model ): 
78   
79                  s = T.Load( source ) 
80   
81                  super( PDBParsePickle, self ).update( 
82                      model, s, skipRes=skipRes, lookHarder=lookHarder) 
83                                 
84          except Exception, why: 
85              raise PDBParserError, "Cannot unpickle source model from %s, "\ 
86                     % str(source) + "Reason:\n" + str(why) 
87   
88          model.setSource( source ) 
89