Source Code for Module Biskit.PCRModel

  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  ## $Revision: 2.4 $ 
 21  ## last $Author: leckner $ 
 22  ## last $Date: 2006/09/12 06:34:36 $ 
 23   
 24  """ 
 25  PDBModel with attached Xplor topology (PSF). 
 26  """ 
 27   
 28  ## PCRModel: 
 29  ## collect and manage information about a ligand or receptor conformation 
 30  ## generated by (PCR)MD 
 31   
 32  import os.path 
 33   
 34  import tools as t 
 35  from PDBModel import PDBModel 
 36   
 37   
 38 -class PCRModel( PDBModel ): 
 39      """ 
 40      PDBModel with attached Xplor topology (PSF). 
 41      Creates more problems than it solves... 
 42      """ 
 43   
 44 -    def __init__(self, fPsf=None, source=None, pdbCode=None, **params): 
 45          """ 
 46          @param fPsf: file name of psf 
 47          @type  fPsf: str 
 48          @param source: file name of pdb OR PDBModel instance 
 49          @type  source: str | PDBModel 
 50          @param pdbCode: if None, first 4 letters of filename will be used 
 51          @type  pdbCode: str 
 52          """ 
 53          PDBModel.__init__( self, source=source, pdbCode=pdbCode, **params ) 
 54   
 55          if fPsf: fPsf = t.absfile( fPsf ) 
 56   
 57          ## in case given fPDB is already a PCRModel, keep psfFileName 
 58          self.psfFileName = fPsf or getattr( source, 'psfFileName', None) 
 59   
 60          ## version as of creation of this object 
 61          self.initVersion = self.version() 
 62   
 63   
 64 -    def version( self ): 
 65          return PDBModel.version(self) + '; PCRModel $Revision: 2.4 $' 
 66   
 67   
 68 -    def getPsfFile(self): 
 69          """ 
 70          @return: file name 
 71          @rtype: str 
 72          """ 
 73          return self.psfFileName 
 74   
 75   
 76 -    def take(self, i, deepcopy=0 ): 
 77          r = PDBModel.take( self, i, deepcopy ) 
 78          r.psfFileName = self.psfFileName 
 79          r.initVersion = self.initVersion 
 80          return r 
 81   
 82   
 83 -    def concat(self, *models ): 
 84          r = PDBModel.concat( self, *models ) 
 85          r.psfFileName = self.psfFileName 
 86          r.initVersion = self.initVersion 
 87          return r 
 88   
 89   
 90  ############# 
 91  ##  TESTING         
 92  ############# 
 93           
 94 -class Test: 
 95      """ 
 96      Test class 
 97      """ 
 98       
 99   
100 -    def run( self, local=0 ): 
101          """ 
102          run function test 
103           
104          @param local: transfer local variables to global and perform 
105                        other tasks only when run locally 
106          @type  local: 1|0 
107           
108          @return: rmsd value 
109          @rtype:  float 
110          """ 
111          ## Loading PDB... 
112          m_com = PCRModel( t.testRoot() + "/com/1BGS.psf", 
113                            t.testRoot() + "/com/1BGS.pdb" ) 
114   
115          m_rec = PCRModel( t.testRoot() + "/rec/1A2P.psf", 
116                            t.testRoot() + "/rec/1A2P.pdb" ) 
117   
118          ## remove waters 
119          m_com = m_com.compress( m_com.maskProtein() ) 
120          m_rec = m_rec.compress( m_rec.maskProtein() ) 
121   
122          ## fit the complex structure to the free receptor 
123          m_com_fit = m_com.magicFit( m_rec ) 
124   
125          ## calculate the rmsd between the original complex and the 
126          ## one fitted to the free receptor 
127          rms = m_com_fit.rms(m_com, fit=0) 
128           
129          if local: 
130              print 'Rmsd between the two complex structures: %.2f Angstrom'%rms 
131              globals().update( locals() ) 
132           
133          return rms 
134   
135   
136 -    def expected_result( self ): 
137          """ 
138          Precalculated result to check for consistent performance. 
139   
140          @return: rmsd value 
141          @rtype:  float 
142          """ 
143          return 58.784401345508634 
144       
145           
146  if __name__ == '__main__': 
147   
148      test = Test() 
149   
150      assert abs( test.run( local=1 ) - test.expected_result() ) < 1e-8 
151