Source Code for Module Biskit.QualMaster

  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  ## 
 21  ## last $Author: leckner $ 
 22  ## last $Date: 2006/12/21 09:33:09 $ 
 23  ## $Revision: 1.5 $ 
 24   
 25  """ 
 26  Parallizes calculation and plotting of ensemble trajectory RMSDs 
 27  """ 
 28   
 29  from Biskit.hosts import cpus_all, nice_dic, nodes_all 
 30  import Biskit.tools as T 
 31  ## from Biskit.PVM.TrackingJobMaster import TrackingJobMaster 
 32  from Biskit.PVM import TrackingJobMaster 
 33   
 34   
 35 -class QualMaster(TrackingJobMaster): 
 36   
 37 -    def __init__(self, trajFiles, n_hosts=20, **kw): 
 38          """ 
 39          @param trajFiles: list of trajectory filed 
 40          @type  trajFiles: [ str ] 
 41          @param n_hosts: number of hosts to use 
 42          @type  n_hosts: int 
 43          """ 
 44          dat = {} 
 45          i = 0 
 46          for f in trajFiles: 
 47              dat[i] = T.absfile( f ) 
 48              i += 1 
 49   
 50          niceness = nice_dic 
 51          hosts = nodes_all[ :n_hosts ] 
 52   
 53          slave_script = T.projectRoot() +'/Biskit/QualSlave.py' 
 54   
 55          TrackingJobMaster.__init__(self, dat, 1, hosts, niceness, 
 56                                     slave_script, **kw) 
 57   
 58   
 59 -    def getInitParameters(self, slave_tid): 
 60          """ 
 61          hand over parameters to slave once. 
 62   
 63          @param slave_tid: slave task id 
 64          @type  slave_tid: int 
 65   
 66          @return: dictionary with init parameters 
 67          @rtype: {param:value} 
 68          """ 
 69          return 1 
 70   
 71   
 72 -    def done(self): 
 73          self.exit() 
 74   
 75   
 76  ############# 
 77  ##  TESTING         
 78  ############# 
 79           
 80 -class Test: 
 81      """ 
 82      Test class 
 83      """ 
 84       
 85 -    def run( self, local=0 ): 
 86          """ 
 87          run function test 
 88           
 89          @param local: transfer local variables to global and perform 
 90                        other tasks only when run locally 
 91          @type  local: 1|0 
 92           
 93          @return: 1 
 94          @rtype: int 
 95          """ 
 96          import os.path 
 97           
 98          ## a minimal list of trajectories 
 99          traj_list = [ T.testRoot() + '/lig_pcr_00/traj.dat' ] 
100   
101          master = QualMaster( traj_list, 
102                               show_output=local, 
103                               verbose=local ) 
104   
105          ## run and wait for result 
106          r = master.calculateResult() 
107          #master.start() 
108   
109          f_plot = '%s/rms_traj.eps'%os.path.dirname(r[0]) 
110           
111          if local: 
112              print 'A RMSD plot is writen to: %s'%f_plot 
113              globals().update( locals() ) 
114               
115          ## cleanup 
116          T.tryRemove( f_plot ) 
117           
118          return 1 
119   
120   
121 -    def expected_result( self ): 
122          """ 
123          Precalculated result to check for consistent performance. 
124   
125          @return: 1 
126          @rtype:  int 
127          """ 
128          return 1 
129       
130           
131  if __name__ == '__main__': 
132   
133      test = Test() 
134   
135      assert test.run( local=1 ) == test.expected_result() 
136