Source Code for Module Biskit.AmberCrdEntropist

  1  ## 
  2  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  3  ## Copyright (C) 2004-2006 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  ## last $Author: graik $ 
 21  ## last $Date: 2006/12/30 19:27:24 $ 
 22  ## $Revision: 2.5 $ 
 23   
 24  """ 
 25  Run ptraj entropy analysis on existing amber trajectory (.crd) and 
 26  topology (.parm7) file. 
 27  """ 
 28       
 29  import os.path as osp 
 30  import re 
 31  import tempfile 
 32   
 33  import Biskit.tools as T 
 34  ## import Biskit.settings as settings 
 35  from Biskit.Errors import BiskitError 
 36  from Biskit.Executor import Executor 
 37   
 38 -class EntropistError( BiskitError ): 
 39      pass 
 40   
 41 -class AmberCrdEntropist( Executor ): 
 42      """ 
 43      Run ptraj entropy analysis on existing amber trajectory (.crd) and 
 44      topology (.parm7) file. 
 45      """ 
 46   
 47      ## template for ptraj input script 
 48      ptraj_script = """ 
 49      trajin %(f_crd)s %(start)i %(stop)i %(step)i 
 50      matrix mwcovar name mwc 
 51      analyze matrix mwc vecs 0 thermo 
 52      """ 
 53   
 54 -    def __init__( self, f_parm, f_crd, f_template=None, 
 55                    s=0, e=None, step=1, **kw ): 
 56          """ 
 57          @param f_parm: path to amber topology file 
 58          @type  f_parm: str 
 59          @param f_crd: path to amber trajectory file 
 60          @type  f_crd: str 
 61          @param f_template: alternative ptraj input template (default: None) 
 62          @type  f_template: str  
 63          @param s: start frame (default: 0, first) 
 64          @type  s: int 
 65          @param e: end frame (default: None, last) 
 66          @type  e: int 
 67          @param step: frame offset (default: 1, no offset ) 
 68          @type  step: int 
 69   
 70          @param kw: additional key=value parameters for Executor: 
 71          @type  kw: key=value pairs 
 72          :: 
 73            debug    - 0|1, keep all temporary files (default: 0) 
 74            verbose  - 0|1, print progress messages to log (log != STDOUT) 
 75            node     - str, host for calculation (None->local) NOT TESTED 
 76                            (default: None) 
 77            nice     - int, nice level (default: 0) 
 78            log      - Biskit.LogFile, program log (None->STOUT) (default: None) 
 79          """ 
 80          template = f_template or self.ptraj_script 
 81   
 82          Executor.__init__( self, 'ptraj', template=template, push_inp=0, **kw ) 
 83   
 84          self.f_parm = T.absfile( f_parm ) 
 85          self.f_crd  = T.absfile( f_crd ) 
 86   
 87          self.start = s 
 88          self.stop  = e or 10000000 
 89          self.step  = step 
 90   
 91          ## default result 
 92          self.result = { 'T':None, 'mass':None, 'vibes':None, 
 93                          'S_total':None, 'S_trans':None, 'S_rot':None, 
 94                          'S_vibes':None, 
 95                          'contributions':None, 'nframes':None, 
 96                          'version':self.version(), 'node':self.node } 
 97   
 98   
 99 -    def version( self ): 
100          """ 
101          Version of class. 
102           
103          @return: version 
104          @rtype: str 
105          """ 
106          return 'AmberCrdEntropist $Revision: 2.5 $' 
107   
108   
109 -    def command( self ): 
110          """ 
111          Build the command string. 
112           
113          @return: command 
114          @rtype: str 
115          """         
116          return "%s %s %s" % (self.exe.bin, self.f_parm, self.f_in) 
117   
118   
119   
120 -    def __tryMatch( self, regex, str, integer=0 ): 
121          m = regex.search( str ) 
122          if m: 
123              return round( float( m.groups()[0] ), 3 ) 
124          return None 
125   
126   
127 -    def finish( self ): 
128          """ 
129          Overrides Executor method 
130          """ 
131          self.result = self.parsePtrajResult( self.f_out ) 
132   
133   
134 -    def isFailed( self ): 
135          """ 
136          Detect whether external program failed, override! 
137          """ 
138          if not osp.exists( self.f_out ): 
139              return 1 
140   
141          return 0 
142   
143   
144 -    def parsePtrajResult( self, f_out ): 
145          """ 
146          Extract results from ptraj. 
147           
148          @param f_out: result of ptraj run 
149          @type  f_out: str 
150   
151          @return: extracted prtaj result 
152          @rtype: dict 
153   
154          @raise EntropistError: if unexpected end of ptraj output file 
155          """ 
156          ## regular expressions for parsing of ptraj output 
157          re_thermo= re.compile('- Thermochemistry -') 
158          re_T     = re.compile('^\s*temperature\s*(\d+\.\d+)\s*kelvin') 
159          re_mass  = re.compile('^\s*molecular mass\D*(\d+\.\d+)\s*amu') 
160          re_vibes = re.compile('^\s*Warning--\s*(\d+)\s*vibrations have low') 
161          re_table = re.compile('^-{80}$') 
162          re_value = re.compile('(-*\d+\.\d+)$') 
163          re_nsets = re.compile('Successfully read in (\d+) sets') 
164   
165          r = self.result 
166   
167          try: 
168              lines = open( f_out, 'r' ).readlines() 
169              lines.reverse() 
170              l = lines.pop() 
171   
172              while not re_thermo.search(l): 
173                  l = lines.pop() 
174   
175              while not re_table.search(l): 
176                  r['T']    = r['T']     or self.__tryMatch( re_T, l ) 
177                  r['mass'] = r['mass']  or self.__tryMatch( re_mass, l ) 
178                  r['vibes']= r['vibes'] or self.__tryMatch( re_vibes,l ) 
179                  l = lines.pop() 
180   
181              l = lines.pop() 
182              v = [] 
183              while l != '\n': 
184                  v += [ self.__tryMatch( re_value, l ) ] 
185                  l = lines.pop() 
186   
187              r['S_total'], r['S_trans'], r['S_rot'], r['S_vibes'] = tuple(v[:4]) 
188              r['contributions'] = v[4:] 
189   
190              while len( lines ) > 0: 
191                  r['nframes'] = r['nframes'] or self.__tryMatch( re_nsets, l ) 
192                  l = lines.pop() 
193   
194          except IndexError: 
195              raise EntropistError, 'unexpected end of ptraj output file.' 
196   
197          return r 
198   
199  if __name__ == '__main__': 
200   
201      print "Setting up" 
202   
203      f = T.testRoot() + '/Amber/AmberCrdEntropist/'  
204   
205      e = AmberCrdEntropist( f + 'lig_traj.parm', 
206                             f + 'lig_traj.crd', debug=0, verbose=1) 
207   
208      print "Running" 
209   
210      e.run() 
211