Source Code for Module Biskit.PDBParseModel

  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 00:00:25 $ 
 22  ## $Revision: 2.3 $ 
 23  """ 
 24  Parse a in-memory PDBModel instance into a new PDBModel 
 25   
 26  @see L{PDBModel} 
 27  @see L{PDBParserFactory} 
 28  """ 
 29  import Numeric as N 
 30   
 31  import Biskit.tools as T 
 32  import Biskit as B 
 33  from PDBParser import PDBParser, PDBParserError 
 34   
 35   
 36 -class PDBParseModel( PDBParser ): 
 37   
 38      @staticmethod 
 39 -    def supports( source ): 
 40          """ 
 41          The method is static and can thus be called directly with the parser 
 42          class rather than with an instance:: 
 43   
 44          >>> if ParsePDBModel.supports( model ): 
 45          >>>     ... 
 46           
 47          @return: True if the given source is supported by this parser 
 48                   implementation (equivalent to isinstance( source, PDBModel) ) 
 49          @rtype: bool 
 50          """ 
 51          return isinstance( source, B.PDBModel ) 
 52   
 53      @staticmethod 
 54 -    def description(): 
 55          """ 
 56          The method is static and can thus be called directly with the parser 
 57          class rather than with an instance:: 
 58   
 59          >>> if ParsePDBModel.description(): 
 60          >>>     ... 
 61   
 62          @return: short free text description of the supported format 
 63          @rtype: str 
 64          """ 
 65          return 'in-memory instances of PDBModel' 
 66           
 67   
 68 -    def update( self, model, source, skipRes=None, lookHarder=0 ): 
 69          """ 
 70          Update empty or missing fields of model from the source. The 
 71          model will be connected to the source via model.source. 
 72          Override! 
 73          @param model: existing model 
 74          @type  model: PDBModel 
 75          @param source: PDBModel object 
 76          @type  source: str | file | PDBModel 
 77          @param skipRes: list residue names that should not be parsed 
 78          @type  skipRes: [ str ] 
 79          """ 
 80          try: 
 81              ## atoms and/or coordinates need to be updated from PDB 
 82              if self.needsUpdate( model ): 
 83   
 84                  s = source 
 85   
 86                  model.fileName = model.fileName or s.fileName 
 87   
 88                  model.pdbCode  = model.pdbCode or s.pdbCode 
 89   
 90                  model.atoms = model.atoms or s.getAtoms() 
 91   
 92                  model.xyz = model.xyz or s.getXyz() 
 93   
 94                  model.__terAtoms = getattr(model, '_PDBModel__terAtoms',[])or \ 
 95                                     getattr(s,'_PDBModel__terAtoms',[]) 
 96   
 97                  model.rProfiles.updateMissing( s.rProfiles, 
 98                                                 copyMissing=lookHarder) 
 99                  model.aProfiles.updateMissing( s.aProfiles, 
100                                                 copyMissing=lookHarder) 
101   
102                  if skipRes: 
103                      model.removeRes( skipRes ) 
104                                  
105          except B.ProfileError, why: 
106              EHandler.warning("Cannot read/update profiles from source: %r"\ 
107                               %why) 
108   
109          model.setSource( source ) 
110   
111 -class Test: 
112      """ 
113      Test class 
114      """ 
115   
116 -    def run( self, local=0 ): 
117          """ 
118          run function test 
119           
120          @param local: transfer local variables to global and perform 
121                        other tasks only when run locally 
122          @type  local: 1|0 
123           
124          @return: coordinates of center of mass 
125          @rtype:  array 
126          """ 
127   
128          ## loading output file from X-plor 
129          if local: 
130              print 'Loading pdb file ..' 
131   
132          p = PDBParseModel() 
133          m = p.parse2new( B.PDBModel(T.testRoot()+'/rec/1A2P.pdb') ) 
134   
135          if local: 
136              globals().update( locals() ) 
137   
138          return N.sum( m.centerOfMass() ) 
139   
140   
141 -    def expected_result( self ): 
142          """ 
143          Precalculated result to check for consistent performance. 
144   
145          @return: coordinates of center of mass 
146          @rtype:  array 
147          """ 
148          return N.sum( N.array([ 29.53385022,  46.39655482,  37.75218589])) 
149           
150   
151  if __name__ == '__main__': 
152   
153      test = Test() 
154   
155      assert abs( test.run( local=1 ) - test.expected_result() ) < 1e-8 
156