Source Code for Module Biskit.StructureMaster

  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 the convertion of PDB files into pickled PDBModel objects. 
 27  """ 
 28   
 29  import Biskit.hosts as hosts 
 30  import Biskit.tools as T 
 31  ## from Biskit.PVM.TrackingJobMaster import TrackingJobMaster 
 32  from Biskit.PVM import TrackingJobMaster 
 33   
 34   
 35 -class StructMaster(TrackingJobMaster): 
 36   
 37 -    def __init__(self, dat, chunk, hosts, outFolder, skipWat=0, amber=0, 
 38                   sort=0, add_hosts=1, **kw): 
 39          """ 
 40          @param dat: data dictionary 
 41          @type  dat: dict 
 42          @param chunk: chunk size passed to slave 
 43          @type  chunk: int 
 44          @param hosts: list of host-names 
 45          @type  hosts: [str] 
 46          @param outFolder: alternative output folder 
 47          @type  outFolder: str 
 48          """ 
 49          niceness = {'default': 0} 
 50          slave_script = T.projectRoot() + '/Biskit/StructureSlave.py' 
 51   
 52          TrackingJobMaster.__init__(self, dat, chunk, hosts, niceness, 
 53                             slave_script, **kw) 
 54   
 55          self.options = {} 
 56          self.options['out'] = outFolder 
 57   
 58          self.options['skipRes'] = None 
 59          if skipWat: 
 60              self.options['skipRes'] = ['WAT','TIP3','H2O','WWW','Na+','Cl-'] 
 61           
 62          if kw.has_key('show_output'): 
 63              self.options['report'] = not kw['show_output'] 
 64   
 65          self.options['amber'] = amber 
 66   
 67          self.options['sort'] = sort 
 68   
 69   
 70 -    def getInitParameters(self, slave_tid): 
 71          """ 
 72          hand over parameters to slave once. 
 73   
 74          @param slave_tid: slave task id 
 75          @type  slave_tid: int 
 76   
 77          @return: dictionary with init parameters 
 78          @rtype: {param:value} 
 79          """ 
 80          return self.options 
 81   
 82   
 83 -    def done(self): 
 84   
 85          self.exit() 
 86   
 87   
 88   
 89  ############# 
 90  ##  TESTING         
 91  ############# 
 92           
 93 -class Test: 
 94      """ 
 95      Test class 
 96      """ 
 97       
 98 -    def run( self, local=0 ): 
 99          """ 
100          run function test 
101           
102          @param local: transfer local variables to global and perform 
103                        other tasks only when run locally 
104          @type  local: 1|0 
105           
106          @return: 1 
107          @rtype: int 
108          """ 
109          import tempfile 
110          out_folder = tempfile.mkdtemp( '_test_StructureMaster' ) 
111           
112          pdbs = {T.testRoot() + '/lig/1A19.pdb':'', 
113                  T.testRoot() + '/rec/1A2P.pdb':'', 
114                  T.testRoot() + '/com/1BGS.pdb':''} 
115   
116          master = StructMaster( pdbs, 
117                                 2, 
118                                 hosts=hosts.cpus_all, 
119                                 outFolder=out_folder, 
120                                 show_output=local, 
121                                 verbose=local, 
122                                 add_hosts=1 ) 
123   
124          ## run and wait for result 
125          r = master.calculateResult() 
126   
127          if local: 
128              print 'The converted pdb files has been written to %s'%out_folder 
129              globals().update( locals() ) 
130   
131          ## cleanup 
132          T.tryRemove( out_folder, tree=1 ) 
133   
134          return 1 
135   
136   
137 -    def expected_result( self ): 
138          """ 
139          Precalculated result to check for consistent performance. 
140   
141          @return: 1 
142          @rtype:  int 
143          """ 
144          return 1 
145       
146           
147  if __name__ == '__main__': 
148   
149      test = Test() 
150   
151      assert test.run( local=1 ) == test.expected_result() 
152