Source Code for Module Biskit.ChainWriter

  1  ## ChainWriter: 
  2  ## 
  3  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  4  ## Copyright (C) 2004-2006 Raik Gruenberg & Johan Leckner 
  5  ## 
  6  ## This program is free software; you can redistribute it and/or 
  7  ## modify it under the terms of the GNU General Public License as 
  8  ## published by the Free Software Foundation; either version 2 of the 
  9  ## License, or any later version. 
 10  ## 
 11  ## This program is distributed in the hope that it will be useful, 
 12  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
 13  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
 14  ## General Public License for more details. 
 15  ## 
 16  ## You find a copy of the GNU General Public License in the file 
 17  ## license.txt along with this program; if not, write to the Free 
 18  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
 19  ## 
 20  ## $Version: $ 
 21  ## last $Date: 2007/03/05 10:28:21 $ 
 22  ## last $Author: graik $ 
 23   
 24  """ 
 25  Write cleaned peptide_chains as PDB for import into XPlor 
 26   
 27  This is vintage code. See L{Biskit.PDBCleaner} for a more recent 
 28  version. The writing of single chains could easily be done with PDBModel. 
 29   
 30  @todo: re-implement pdb2xplor with PDBCleaner / PDBModel 
 31  """ 
 32  from Scientific.IO.PDB import * 
 33  import commands 
 34  import os.path 
 35   
 36  import tools as T 
 37   
 38 -class ChainWriter: 
 39      """ 
 40      Take chain from chainCleaner; write single PDB with 
 41      unique segementID and no chainID 
 42      """ 
 43   
 44 -    def __init__(self, path): 
 45          """ 
 46          Take chains from ChainCleaner and write pdb files. 
 47          File names are created from segid of each chain + '_seg.pdb' 
 48           
 49          @param path: output path for PDB files 
 50          @type  path: string 
 51          """ 
 52          self.path = T.absfile( path ) 
 53   
 54   
 55 -    def _startPDB(self, chain, fname): 
 56          """ 
 57          Create pdb file and write header. 
 58           
 59          @param chain: Scientific.IO.PDB.PeptideChain object 
 60          @type  chain: chain object 
 61          @param fname: file name 
 62          @type  fname: string 
 63           
 64          @return: handle of open file 
 65          @rtype: PDBFile 
 66          """ 
 67          f = PDBFile(fname, 'w') 
 68          try: 
 69              for c in chain.comments:    # write comments, if any 
 70                  f.writeComment(c) 
 71          except: 
 72              pass 
 73          return f 
 74   
 75   
 76 -    def removeTER(self, fname): 
 77          """ 
 78          Remove TER record from PDB. 
 79           
 80          @param fname: name of existing file. 
 81          @type  fname: string 
 82          """ 
 83          try: 
 84              #command = 'egrep -v "^TER " ' + fname + '> temp.pdb' 
 85              path = os.path.dirname( fname ) 
 86              command = 'egrep -v "^TER " %s > %s/temp.pdb'%( fname, path ) 
 87              commands.getstatusoutput(command) 
 88              os.rename('%s/temp.pdb'%path, fname) 
 89          except (OSError): 
 90              T.errWriteln("Error removing 'TER' statement from %s: ") 
 91              T.errWriteln( T.lastError() ) 
 92   
 93   
 94 -    def writeChain(self, chain): 
 95          """ 
 96          Write single chain as PDB. File name will be segid + '_seg.pdb'. 
 97           
 98          @param chain: Scientific.IO.PDB.PeptideChain object 
 99          @type  chain: chain object 
100          """ 
101          if (chain <> None): 
102              try: 
103   
104                  fname = self.path + '/' + chain.segment_id + "_seg.PDB" 
105                  file = self._startPDB(chain, fname)     # include comments 
106                  chain.writeToFile(file)     # create PDB 
107                  file.close()                # make sure file is complete! 
108                  self.removeTER(file.file.file.name) #remove TER record from PDB 
109                  return 1        # write a chain 
110   
111              except (IOError): 
112                  T.errWriteln("Error writing chain to file %s:" % fname) 
113                  T.errWriteln( T.lastError() ) 
114   
115          return 0            # false, no more chains to write 
116   
117   
118  ############# 
119  ##  TESTING         
120  ############# 
121  import Biskit.test as BT 
122   
123 -class Test(BT.BiskitTest): 
124      """Test ChainWriter"""    
125   
126 -    def prepare(self): 
127          self.fname =   T.testRoot() + '/rec/1A2P_rec_original.pdb' 
128          self.outPath = T.tempDir() 
129   
130 -    def test_ChainWriter( self ): 
131          """ChainWriter test""" 
132   
133          from ChainCleaner import ChainCleaner 
134          from ChainSeparator import ChainSeparator 
135       
136          self.cleaner = ChainCleaner( ChainSeparator( self.fname, 
137                                                       self.outPath ) ) 
138   
139          self.writer = ChainWriter( self.outPath ) 
140           
141          all_msg = [] 
142          for i in range(3): 
143              msg = self.writer.writeChain( self.cleaner.next() ) 
144              if self.local: 
145                  print 'Writing separated, cleaned chain to disk...%i'%msg 
146              all_msg += [ msg ] 
147   
148          self.assertEquals( all_msg, [1, 0, 0] ) 
149           
150 -    def cleanUp(self): 
151          T.tryRemove( self.outPath + '/1A2P_waters.pdb' ) 
152          T.tryRemove( self.outPath + '/1A2A_seg.PDB' ) 
153                        
154       
155   
156  if __name__ == '__main__': 
157   
158      BT.localTest() 
159