Source Code for Module gromacs.analysis.plugins.rmsf

  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  RMSF calculation 
  8  ================ 
  9   
 10  Calculation of the root mean square fluctuations from a trajectory. 
 11   
 12  Plugin class 
 13  ------------ 
 14   
 15  .. autoclass:: RMSF 
 16     :members: worker_class 
 17     :undoc-members: 
 18   
 19  Worker class 
 20  ------------ 
 21   
 22  The worker class performs the analysis. 
 23   
 24  .. autoclass:: _RMSF 
 25     :members: 
 26   
 27   
 28  """ 
 29  from __future__ import with_statement 
 30   
 31  __docformat__ = "restructuredtext en" 
 32   
 33  import os.path 
 34  import warnings 
 35   
 36  import gromacs 
 37  from gromacs.utilities import AttributeDict 
 38  from gromacs.analysis.core import Worker, Plugin 
 39   
 40  import logging 
 41  logger = logging.getLogger('gromacs.analysis.plugins.rmsf') 
 42   
 43  # Worker classes that are registered via Plugins (see below) 
 44  # ---------------------------------------------------------- 
 45  # These must be defined before the plugins. 
 46   
 47 -class _RMSF(Worker): 
 48      """RMSF worker class.""" 
 49   
 50 -    def __init__(self,**kwargs): 
 51          """Set up RMSF analysis. 
 52   
 53          This is the worker class; this is where all the real analysis is done. 
 54   
 55          """ 
 56          super(_RMSF, self).__init__(**kwargs) 
 57          if not self.simulation is None: 
 58              self._register_hook() 
 59   
 60 -    def _register_hook(self, **kwargs): 
 61          """Run when registering; requires simulation.""" 
 62   
 63          super(_RMSF, self)._register_hook(**kwargs) 
 64          assert not self.simulation is None 
 65   
 66          self.parameters.filenames = { 
 67              'RMSF': self.plugindir('rmsf.xvg'), 
 68              'RMSD': self.plugindir('rmsdev.xvg'), 
 69              } 
 70          # default filename for the plot 
 71          self.parameters.figname = self.figdir('rmsf') 
 72   
 73 -    def run(self, force=False, group='C-alpha', **gmxargs): 
 74          """Analyze trajectory and write RMSF files. 
 75   
 76          The run method typically processes trajectories and writes data files. 
 77   
 78          :Arguments: 
 79            - *group*: index group (eg C-alpha or Protein) 
 80            - *force*: do analysis and overwrite existing files 
 81            - *gmxargs*: additional keyword arguments for :func:`gromacs.g_rmsf` (e.g. res=True) 
 82          """ 
 83          if not self.check_file_exists(self.parameters.filenames['RMSF'], resolve='warning') or force: 
 84              logger.info("Analyzing RMSF...") 
 85              gromacs.g_rmsf(s=self.simulation.tpr, f=self.simulation.xtc, fit=True,  
 86                             o=self.parameters.filenames['RMSF'], 
 87                             od=self.parameters.filenames['RMSD'],  
 88                             input=[group], **gmxargs) 
 89   
 90 -    def analyze(self,**kwargs): 
 91          """Collect output xvg files as :class:`gromacs.formats.XVG` objects. 
 92   
 93          :Returns:  a dictionary of the results and also sets ``self.results``. 
 94          """         
 95          from gromacs.formats import XVG 
 96   
 97          logger.info("Preparing RMSF graphs as XVG objects.") 
 98          results = AttributeDict(RMSF=XVG(self.parameters.filenames['RMSF']), 
 99                                  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 RMSF(Plugin): 
141      """*RMSF* plugin. 
142       
143      Compute the root mean square fluctuations (RMSF) of the C-alpha 
144      atoms. The trajectory is always fitted to the reference structure 
145      in the tpr file. 
146   
147      .. class:: RMSF([name[, simulation]]) 
148       
149      :Arguments: 
150          *name* : string 
151              plugin name (used to access it) 
152          *simulation* : instance 
153              The :class:`gromacs.analysis.Simulation` instance that owns the plugin. 
154   
155      """ 
156      worker_class = _RMSF 
157