Source Code for Module Biskit.PDBParser

  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: 2006/12/17 00:30:05 $ 
 22  ## $Revision: 2.2 $ 
 23  """ 
 24  Parse a certain file / memory object into a PDBModel. 
 25   
 26  This module provides helper classes for L{Biskit.PDBModel}. In most 
 27  cases, it should not be necessary to use it directly. 
 28   
 29  @see L{Biskit.PDBModel} 
 30  @see L{Biskit.PDBParserFactory} 
 31  @see L{Biskit.PDBParseFile} 
 32  @see L{Biskit.PDBParseModel} 
 33  @see L{Biskit.PDBParsePickle} 
 34  """ 
 35  from Biskit import StdLog, ErrLog 
 36  import Biskit as B 
 37   
 38 -class PDBParserError( Exception ): 
 39      """Error while parsing a structure file or object""" 
 40      pass 
 41   
 42 -class PDBParser(object): 
 43      """ 
 44      **Abstract** base class for parsers that generate PDBModel objects from 
 45      different source formats. 
 46      """ 
 47   
 48 -    def __init__( self, log=None ): 
 49          """ 
 50          @param log: Log for warnings [default log to STDERR] 
 51          @type  log: Biskit.LogFile.LogFile 
 52           
 53          Override if needed. Call parent method in overriding class! 
 54          """ 
 55          self.log = log or ErrLog() 
 56   
 57   
 58      @staticmethod 
 59 -    def supports( source ): 
 60          """ 
 61          Override! 
 62           
 63          The method is static and can thus be called directly with the parser 
 64          class rather than with an instance:: 
 65   
 66          >>> if PDBParser.supports('myfile.pdb'): 
 67          >>>     ... 
 68           
 69          @return: True if the given source is supported by this parser 
 70                   implementation 
 71          @rtype: bool 
 72          """ 
 73          raise NotImplementedError, 'issupported() is not implemented.' 
 74   
 75   
 76      @staticmethod 
 77 -    def description(): 
 78          """ 
 79          Override! 
 80   
 81          The method is static and can thus be called directly with the parser 
 82          class rather than with an instance:: 
 83   
 84          >>> if PDBParser.description('myfile.pdb'): 
 85          >>>     ... 
 86   
 87          @return: short free text description of the supported format 
 88          @rtype: str 
 89          """ 
 90          raise NotImplementedError, 'description() is not implemented.' 
 91           
 92   
 93 -    def update( self, model, source, skipRes=None, lookHarder=0 ): 
 94          """ 
 95          Update empty or missing fields of model from the source. The 
 96          model will be connected to the source via model.source. 
 97          Override! 
 98           
 99          @param model: existing model 
100          @type  model: PDBModel 
101          @param source: source PDB file or pickled PDBModel or PDBModel object 
102          @type  source: str || file || PDBModel 
103          @param skipRes: list residue names that should not be parsed 
104          @type  skipRes: [ str ] 
105          @param lookHarder: check source for additional profiles that are not 
106                             yet known for the model [False] 
107          @type  lookHarder: 1 || 0 
108          """ 
109          raise NotImplementedError, 'update() is not implemented.' 
110   
111   
112 -    def needsUpdate( self, model ): 
113          """ 
114          This function is called by update() to decide whether or not to open 
115          the source. 
116          Override if needed. 
117   
118          @param model: model 
119          @type  model: PDBModel 
120          @return: true, if the model needs to be updated from its source 
121          @rtype: bool 
122          """ 
123          return (model.atoms is None or model.xyz is None) 
124   
125   
126 -    def parse2new( self, source, disconnect=False, skipRes=None ): 
127          """ 
128          Create a new PDBModel from the source. 
129   
130          @param source: source PDB file or pickled PDBModel or PDBModel object 
131          @type  source: str || file || PDBModel 
132          @param disconnect: do *not* associate new model with the source [False] 
133          @type  disconnect: bool 
134          @param skipRes: list residues that should not be parsed 
135          @type  skipRes: [ str ] 
136   
137          @return: new model (always of type PDBModel, regardless of source type) 
138          @rtype: PDBModel 
139          """ 
140          m = B.PDBModel() 
141          self.update( m, source, skipRes=skipRes) 
142   
143          if disconnect: m.disconnect() 
144   
145          return m 
146