Source Code for Module gromacs.analysis.plugins.rmsd

  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  RMSD calculation 
  8  ================ 
  9   
 10  Calculation of the root mean square distance of a protein structure 
 11  over the course of a MD simulation. 
 12   
 13   
 14  Plugin class 
 15  ------------ 
 16   
 17  .. autoclass:: RMSD 
 18     :members: worker_class 
 19     :undoc-members: 
 20   
 21  Worker class 
 22  ------------ 
 23   
 24  The worker class performs the analysis. 
 25   
 26  .. autoclass:: _RMSD 
 27     :members: 
 28   
 29   
 30  """ 
 31  from __future__ import with_statement 
 32   
 33  __docformat__ = "restructuredtext en" 
 34   
 35  import os.path 
 36  import warnings 
 37   
 38  import gromacs 
 39  from gromacs.utilities import AttributeDict 
 40  from gromacs.analysis.core import Worker, Plugin 
 41   
 42  import logging 
 43  logger = logging.getLogger('gromacs.analysis.plugins.rmsd') 
 44   
 45  # Worker classes that are registered via Plugins (see below) 
 46  # ---------------------------------------------------------- 
 47  # These must be defined before the plugins. 
 48   
 49 -class _RMSD(Worker): 
 50      """RMSD worker class.""" 
 51   
 52 -    def __init__(self,**kwargs): 
 53          """Set up RMSD analysis. 
 54   
 55          This is the worker class; this is where all the real analysis is done. 
 56          """ 
 57          super(_RMSD, self).__init__(**kwargs) 
 58          if not self.simulation is None: 
 59              self._register_hook() 
 60   
 61 -    def _register_hook(self, **kwargs): 
 62          """Run when registering; requires simulation.""" 
 63   
 64          super(_RMSD, self)._register_hook(**kwargs) 
 65          assert not self.simulation is None 
 66   
 67          self.parameters.filenames = { 
 68              'RMSD': self.plugindir('rmsd.xvg'), 
 69              } 
 70          # default filename for the plot 
 71          self.parameters.figname = self.figdir('rmsd') 
 72   
 73 -    def run(self, force=False, group='C-alpha', **gmxargs): 
 74          """Analyze trajectory and write RMSD files. 
 75   
 76          Each frame is fit to the structure in the tpr, based on the 
 77          C-alpha atoms. The RMSd is alculated for the supplied index 
 78          group *group*. 
 79   
 80          :Arguments: 
 81            - *group*: index group for RMSD calculation (eg C-alpha or Protein) 
 82            - *force*: do analysis and overwrite existing files 
 83            - *gmxargs*: additional keyword arguments for :func:`gromacs.g_rms` (e.g. res=True) 
 84          """ 
 85          if not self.check_file_exists(self.parameters.filenames['RMSD'], resolve='warning') or force: 
 86              logger.info("Analyzing RMSD...") 
 87              gromacs.g_rms(s=self.simulation.tpr, f=self.simulation.xtc, fit="rot+trans",  
 88                            o=self.parameters.filenames['RMSD'], 
 89                            input=['C-alpha', group], **gmxargs) 
 90   
 91 -    def analyze(self,**kwargs): 
 92          """Collect output xvg files as :class:`gromacs.formats.XVG` objects. 
 93   
 94          :Returns:  a dictionary of the results and also sets ``self.results``. 
 95          """         
 96          from gromacs.formats import XVG 
 97   
 98          logger.info("Preparing RMSD graphs as XVG objects.") 
 99          results = AttributeDict(RMSD=XVG(self.parameters.filenames['RMSD'])) 
100          self.results = results 
101          return results 
102   
103 -    def plot(self, **kwargs): 
104          """Plot all results in one graph, labelled by the result keys. 
105   
106          :Keywords: 
107             figure 
108                 - ``True``: save figures in the given formats 
109                 - "name.ext": save figure under this filename (``ext`` -> format) 
110                 - ``False``: only show on screen 
111             formats : sequence 
112                 sequence of all formats that should be saved [('png', 'pdf')] 
113             plotargs     
114                 keyword arguments for pylab.plot() 
115          """ 
116   
117          import pylab 
118          figure = kwargs.pop('figure', False) 
119          extensions = kwargs.pop('formats', ('pdf','png')) 
120          for name,result in self.results.items(): 
121              kwargs['label'] = name 
122              try: 
123                  result.plot(**kwargs)      # This requires result classes with a plot() method!! 
124              except AttributeError: 
125                  warnings.warn("Sorry, plotting of result %(name)r is not implemented" % vars(), 
126                                category=UserWarning)                 
127          pylab.legend(loc='best') 
128          if figure is True: 
129              for ext in extensions: 
130                  self.savefig(ext=ext) 
131          elif figure: 
132              self.savefig(filename=figure) 
133   
134       
135   
136   
137  # Public classes that register the worker classes 
138  #------------------------------------------------ 
139   
140 -class RMSD(Plugin): 
141      """*RMSD* plugin. 
142       
143      Calculation of the root mean square distance (RMSD) of a protein 
144      structure over the course of a MD simulation. 
145   
146      The trajectory is always fitted to the reference structure in the 
147      tpr file. 
148   
149      .. class:: RMSD([name[, simulation]]) 
150       
151      :Arguments: 
152          *name* : string 
153              plugin name (used to access it) 
154          *simulation* : instance 
155              The :class:`gromacs.analysis.Simulation` instance that owns the plugin. 
156   
157      """ 
158      worker_class = _RMSD 
159