Source Code for Module Biskit.StructureSlave

  1  ## Convert PDB files to a pickled PDBModel object. 
  2  ## 
  3  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  4  ## Copyright (C) 2004-2005 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  ## 
 21  ## $Revision: 2.4 $ 
 22  ## last $Date: 2006/12/22 14:27:30 $ 
 23  ## last $Author: graik $ 
 24  ## 
 25  ## required by pdbs2struct.py 
 26   
 27  """ 
 28  Convert a PDB file to a pickled PDBModel object. 
 29  """ 
 30       
 31  from PDBModel import PDBModel 
 32  import tools as T 
 33   
 34  ## PVM imports 
 35  from Biskit.PVM import JobSlave 
 36   
 37   
 38 -class StructureSlave(JobSlave): 
 39      """ 
 40      Convert a PDB file to a pickled PDBModel object. 
 41      """ 
 42   
 43 -    def initialize(self, params): 
 44          """ 
 45          Copy the parameters that Master is passing in as dict into 
 46          fields of this class. 
 47           
 48          @param params: defined in Master 
 49          @type  params: dict 
 50          """ 
 51          self.params = params 
 52   
 53   
 54 -    def renameAmberRes( self, model ): 
 55          """ 
 56          Rename special residues (from Amber) back into standard 
 57          names (i.e CYX S{->} CYS). 
 58           
 59          @param model: model 
 60          @type  model: PDBModel 
 61          """ 
 62          for a in model.getAtoms(): 
 63              if a['residue_name'] == 'CYX': 
 64                  a['residue_name'] = 'CYS' 
 65              if a['residue_name'] in ['HIE','HID','HIP']: 
 66                  a['residue_name'] = 'HIS' 
 67   
 68   
 69 -    def renameToAmberAtoms( self, model ): 
 70          """ 
 71          ptraj puts last letter/number of 4-letter atom names first. Undo. 
 72           
 73          @param model: model 
 74          @type  model: PDBModel 
 75           
 76          @note: could be avoided if ptraj would be told: 
 77                 trajout |file| pdb nowrap 
 78          """ 
 79          numbers = map( str, range(10) ) 
 80   
 81          for a in model.getAtoms(): 
 82              if len(a['name'])==4 and a['name'][0] in numbers: 
 83                  a['name'] = a['name'][1:] + a['name'][0] 
 84   
 85   
 86 -    def go(self, dict): 
 87          """ 
 88          Calculate rmsd values for trajectory and plot them. 
 89   
 90          @param dict: dictionary with path to pdb files as keys 
 91          @type  dict: dict 
 92   
 93          @return: dictionary mapping input:output names 
 94          @rtype: dict         
 95          """ 
 96          d = {} 
 97   
 98          print "working on :", 
 99          for pdbIn, out in dict.items(): 
100   
101              print T.stripFilename( pdbIn ) 
102   
103              ## set file name for pickled Structure object 
104              dir = os.path.dirname( pdbIn ) 
105              if self.params['out'] <> None: 
106                  dir = self.params['out'] 
107   
108              out = dir + '/' + T.stripFilename( pdbIn) + '.model' 
109   
110              try: 
111                  m = PDBModel( pdbIn, skipRes=self.params['skipRes'] ) 
112   
113                  if self.params['amber']: 
114                      self.renameAmberRes( m ) 
115                      self.renameToAmberAtoms( m ) 
116   
117                  if self.params['sort']: 
118                      m = m.sort() 
119   
120                  m.saveAs( out ) 
121   
122              except: 
123                  if self.params.has_key('report') and self.params['report']: 
124                      f = open( out[:-6] + '.error', 'w' ) 
125                      f.write( T.lastError() ) 
126                      f.close() 
127                  else: 
128                      T.errWriteln("Error" + T.lastError()  ) 
129   
130   
131                  out = '' 
132   
133              d[pdbIn] = out 
134   
135          print "Done." 
136          return d 
137   
138  if __name__ == '__main__': 
139   
140      import os, sys 
141   
142      if len(sys.argv) == 2: 
143   
144          niceness = int(sys.argv[1]) 
145          os.nice(niceness) 
146   
147      slave = StructureSlave() 
148      slave.start() 
149