Source Code for Module gromacs.analysis.plugins.trajectories

  1  # $Id$ 
  2  # Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com> 
  3  # Released under the GNU Public License 3 (or higher, your choice) 
  4  # See the file COPYING for details. 
  5   
  6  """ 
  7  Trajectories 
  8  ============ 
  9   
 10  Write centered trajectories. Trajectories will be stored under the 
 11  base dir / trj.   
 12   
 13  - full fitxy  
 14  - fitxy at 100 ps intervals 
 15   
 16   
 17  Plugin class 
 18  ------------ 
 19   
 20  .. autoclass:: Trajectories 
 21     :members: worker_class 
 22     :undoc-members: 
 23   
 24  Worker class 
 25  ------------ 
 26   
 27  The worker class performs the analysis. 
 28   
 29  .. autoclass:: _Trajectories 
 30     :members: 
 31   
 32   
 33  """ 
 34  from __future__ import with_statement 
 35   
 36  __docformat__ = "restructuredtext en" 
 37   
 38  import os 
 39  import errno 
 40  import warnings 
 41   
 42  import gromacs 
 43  from gromacs.utilities import AttributeDict 
 44  from gromacs.analysis.core import Worker, Plugin 
 45   
 46  import logging 
 47  logger = logging.getLogger('gromacs.analysis.plugins.trajectories') 
 48   
 49  # Worker classes that are registered via Plugins (see below) 
 50  # ---------------------------------------------------------- 
 51  # These must be defined before the plugins. 
 52   
 53 -class _Trajectories(Worker): 
 54      """Trajctories worker class.""" 
 55   
 56 -    def __init__(self,**kwargs): 
 57          """Set up  Trajectories 
 58   
 59          :Arguments: 
 60             None at the moment, everything is hard coded. 
 61          """ 
 62          # specific arguments: take them before calling the super class that 
 63          # does not know what to do with them 
 64          dt = kwargs.pop('dt', 100)   # reduced xtc: write steps every dt ps 
 65   
 66          # super class init: do this before doing anything else 
 67          # (also sets up self.parameters and self.results) 
 68          super(_Trajectories, self).__init__(**kwargs) 
 69   
 70          # process specific parameters now and set instance variables 
 71          self.parameters.dt = dt 
 72   
 73          # self.simulation might have been set by the super class 
 74          # already; just leave this snippet at the end. Do all 
 75          # initialization that requires the simulation class in the 
 76          # _register_hook() method. 
 77          if not self.simulation is None: 
 78              self._register_hook() 
 79   
 80 -    def _register_hook(self, **kwargs): 
 81          """Run when registering; requires simulation.""" 
 82   
 83          super(_Trajectories, self)._register_hook(**kwargs) 
 84          assert not self.simulation is None         
 85   
 86          xtcdir,xtcname = os.path.split(self.simulation.xtc) 
 87          xtcbasename, xtcext = os.path.splitext(xtcname) 
 88          trjdir = os.path.join(xtcdir, 'trj') 
 89          fitxy_gro = os.path.join(trjdir, xtcbasename+'_fitxy'+'.gro') 
 90          fitxy_pdb = os.path.join(trjdir, xtcbasename+'_fitxy'+'.pdb') 
 91          fitxy_xtc = os.path.join(trjdir, xtcbasename+'_fitxy'+xtcext) 
 92          fitxydt_xtc = os.path.join(trjdir, (xtcbasename+'_fitxy_dt%dps'+xtcext) % self.parameters.dt) 
 93   
 94          # make sure trjdir exists 
 95          try: 
 96              os.makedirs(trjdir) 
 97          except OSError, err: 
 98              if err.errno == errno.EEXIST: 
 99                  pass 
100   
101          self.parameters.trjdir = trjdir         
102          self.parameters.filenames = { 
103              'gro': fitxy_gro, 
104              'pdb': fitxy_pdb, 
105              'fitxy': fitxy_xtc, 
106              'fitxydt': fitxydt_xtc, 
107              } 
108   
109      # override 'API' methods of base class 
110           
111 -    def run(self, force=False, **gmxargs): 
112          """Write new trajectories""" 
113   
114          filename = self.parameters.filenames['gro'] 
115          if not self.check_file_exists(filename, resolve='warning') or force: 
116              logger.info("Writing fitted GRO file...") 
117              gromacs.cbook.trj_fitandcenter(xy=True, s=self.simulation.tpr, f=self.simulation.xtc,  
118                                             o=filename, dump=0) 
119   
120          filename = self.parameters.filenames['pdb'] 
121          if not self.check_file_exists(filename, resolve='warning') or force: 
122              logger.info("Writing fitted PDB file...") 
123              gromacs.cbook.trj_fitandcenter(xy=True, s=self.simulation.tpr, f=self.simulation.xtc,  
124                                             o=filename, dump=0) 
125   
126          filename = self.parameters.filenames['fitxydt'] 
127          if not self.check_file_exists(filename, resolve='warning') or force: 
128              logger.info("Writing fitted xtc file (frame every %d ps)..." % self.parameters.dt) 
129              gromacs.cbook.trj_fitandcenter(xy=True, s=self.simulation.tpr, f=self.simulation.xtc,  
130                                             o=filename, dt=self.parameters.dt) 
131   
132          filename = self.parameters.filenames['fitxy'] 
133          if not self.check_file_exists(filename, resolve='warning') or force: 
134              logger.info("Writing fitted xtc file (all frames)...") 
135              gromacs.cbook.trj_fitandcenter(xy=True, s=self.simulation.tpr, f=self.simulation.xtc,  
136                                             o=filename) 
137   
138          logger.info("New trajectories can be found in %r." % self.parameters.trjdir) 
139   
140 -    def analyze(self,**kwargs): 
141          """No postprocessing."""         
142          pass 
143   
144   
145 -    def plot(self, **kwargs): 
146          """No plotting.""" 
147          pass 
148   
149   
150  # Public classes that register the worker classes 
151  #------------------------------------------------ 
152   
153 -class Trajectories(Plugin): 
154      """*Trajectories* plugin. 
155   
156      Write new xy-fitted trajectories (see :func:`gromacs.cbook.trj_fitandcenter`), 
157   
158      .. class:: Trajectories([name[, simulation]]) 
159       
160      :Arguments: 
161          *name* : string 
162              plugin name (used to access it) 
163          *simulation* : instance 
164              The :class:`gromacs.analysis.Simulation` instance that owns the plugin. 
165   
166      """ 
167      worker_class = _Trajectories 
168