Source Code for Module Biskit.Mod.ModelSlave

  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  ## Contributions: Olivier PERIN, Raik Gruenberg 
 20  ## last $Author: graik $ 
 21  ## last $Date: 2006/12/22 14:27:30 $ 
 22  ## $Revision: 2.3 $ 
 23  """ 
 24  Parallelize Modeller runs 
 25  """ 
 26   
 27  from Biskit.PVM import JobSlave 
 28  import Biskit.tools as T 
 29   
 30  from Biskit.Mod import Modeller as M 
 31   
 32  from Biskit import LogFile 
 33  import os 
 34  import subprocess 
 35  import settings 
 36  import socket 
 37   
 38   
 39 -class ModelSlave(JobSlave): 
 40   
 41 -    def initialize(self, params): 
 42          """ 
 43          Initialize AlignerSlave. 
 44   
 45          @param params: dictionary with init parameters 
 46          @type  params: {param:value}           
 47          """ 
 48          self.__dict__.update( params ) 
 49          self.params = params 
 50   
 51          self.errorLog = LogFile( self.ferror, mode='a' ) 
 52   
 53   
 54   
 55 -    def reportError(self, msg, d ): 
 56          """ 
 57          Report error. 
 58   
 59          @param msg: error message 
 60          @type  msg: str 
 61          @param d: error data 
 62          @type  d: any 
 63          """ 
 64          try: 
 65              s = '%s on %s, job %r\n' % (msg, os.uname()[1], d) 
 66              s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n' 
 67   
 68              self.errorLog.add( s ) 
 69   
 70              try: 
 71                  print msg 
 72              except: 
 73                  pass 
 74          except Exception, why: 
 75              f = open('ErrorReportError_XRefineSlave','a') 
 76              f.write( str(why) ) 
 77              try: 
 78                  f.write( t.lastErrorTrace() ) 
 79              except: 
 80                  pass 
 81              f.close() 
 82   
 83   
 84 -    def go(self, dict): 
 85          """ 
 86          Run Modeller job. 
 87   
 88          @param dict: dictionary with run parameters 
 89          @type  dict: {param:value}  
 90          """ 
 91          d = {} 
 92          val = None 
 93   
 94          try: 
 95   
 96              T.flushPrint( self.params['progress_str'] ) 
 97              for id, val in dict.items(): 
 98   
 99                  modeller_log = LogFile( '%s/Modeller.log' %val["outFolder"] )      
100   
101                  d[id] = val 
102   
103   
104                  m = M( outFolder= val["outFolder"], 
105                         log=modeller_log, 
106                         fasta_target=val["fastaTarget"], 
107                         f_pir=val["f_pir"], 
108                         template_folder=val["template_folder"], 
109                         starting_model=val["starting_model"], 
110                         ending_model=val["ending_model"] ) 
111                   
112                  m.run() 
113   
114   
115          except Exception, why: 
116              self.reportError( 'ERROR '+str(why), val ) 
117   
118          print "Done." 
119   
120          return d 
121   
122   
123  if __name__ == '__main__': 
124   
125      slave = ModelSlave() 
126      slave.start() 
127