Source Code for Module Biskit.QualSlave

  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  ## $Revision: 2.3 $ 
 21  ## last $Date: 2006/12/22 14:27:30 $ 
 22  ## last $Author: graik $ 
 23   
 24  """ 
 25  Plot RMSD, Energy of ensemble trajectory. 
 26  """ 
 27       
 28  from os.path import dirname 
 29   
 30  import tools as T 
 31  from Biskit import Trajectory, EHandler 
 32  from Biskit.EnsembleTraj import traj2ensemble, EnsembleTraj 
 33   
 34  from PVM import JobSlave 
 35   
 36 -class QualSlave(JobSlave): 
 37      """ 
 38      Plot RMSD, Energy of ensemble trajectory. 
 39      """ 
 40   
 41 -    def initialize(self, params): 
 42          """ 
 43          Copy the parameters that Master is passing in as dict into 
 44          fields of this class. 
 45           
 46          @param params: defined in Master 
 47          @type  params: dict 
 48          """ 
 49          pass 
 50   
 51   
 52 -    def go( self, dict ): 
 53          """ 
 54          Calculate rmsd values for trajectory and plot them. 
 55   
 56          @param dict: dictionary with path to trajectories as values 
 57          @type  dict: dict 
 58   
 59          @return: dictionary with path to trajectories as values 
 60          @rtype: dict 
 61          """ 
 62          for k, f in dict.items(): 
 63   
 64              fout = dirname( f )+'/'+'%s'+ T.stripFilename(f)+'.eps' 
 65              fshort = dirname( f )[-15:] 
 66   
 67              print fshort 
 68   
 69              t = self.loadTraj( f ) 
 70   
 71              self.calcRmsd( t ) 
 72   
 73              p = self.plotRmsdRef(t, fshort ) 
 74              p.write_eps( fout % 'rms_', width="18cm", height="29cm" ) 
 75   
 76              print "Done" 
 77   
 78          return dict 
 79   
 80   
 81 -    def loadTraj( self, ftraj ): 
 82          """ 
 83          Load trajectories from disc. 
 84           
 85          @param ftraj: path to trajectory 
 86          @type  ftraj: str 
 87   
 88          @return: ensemble trajectory object 
 89          @rtype: EnsembleTraj 
 90          """ 
 91          t = T.Load( T.absfile( ftraj ) ) 
 92          return traj2ensemble( t ) 
 93   
 94   
 95 -    def calcRmsd( self, t ): 
 96          """ 
 97          Calculate the rmsd to the reference, the CA rmsd to the average 
 98          member and the CA rmsd to last member frame. Add the results 
 99          into a profile. 
100           
101          @param t: ensemble trajectory object 
102          @type  t:  EnsembleTraj 
103          """ 
104          mCA = t.ref.maskCA() 
105   
106          t.fit( ref=t.ref, prof='rms_all_ref', comment='all heavy') 
107   
108          t.fitMembers( mask=mCA, prof='rms_CA_av', comment='CA to member avg') 
109   
110          t.fitMembers( refIndex=-1, mask=mCA, prof='rms_CA_last', 
111                        comment='all CA to last member frame') 
112   
113   
114 -    def plotRmsdRef( self, t, title ): 
115          """ 
116          Plot the rmsd profiles calculated in L{ calcRmsd }. 
117           
118          @param t: ensemble trajectory object 
119          @type  t:  EnsembleTraj 
120          @param title: plot title 
121          @type  title: str 
122   
123          @return: biggles plot object 
124          @rtype: biggles.FramedPlot 
125          """ 
126          p = t.plotMemberProfiles('rms_all_ref', 'rms_CA_av', 'rms_CA_last') 
127          p.title = title 
128          p.xlabel= 'frame #' 
129          p.ylabel= 'RMSD [A]' 
130          return p 
131   
132   
133  if __name__ == '__main__': 
134   
135      import os, sys 
136   
137      if len(sys.argv) == 2: 
138   
139          niceness = int(sys.argv[1]) 
140          os.nice(niceness) 
141   
142      slave = QualSlave() 
143      slave.start() 
144