Source Code for Module gromacs.analysis.plugins.ls

  1  # GromacsWrapper plugin: ls.py 
  2  # Copyright (c) 2010 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  ls plugin 
  8  ========= 
  9   
 10  This simply lists the files on disk. It is useful for testing the 
 11  plugin architecture. 
 12   
 13   
 14  Plugin class 
 15  ------------ 
 16   
 17  .. autoclass:: Ls 
 18     :members: worker_class 
 19     :undoc-members: 
 20   
 21  Worker class 
 22  ------------ 
 23   
 24  The worker class performs the analysis. 
 25   
 26  .. autoclass:: _Ls 
 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.ls') 
 44   
 45  # Worker classes that are registered via Plugins (see below) 
 46  # ---------------------------------------------------------- 
 47  # These must be defined before the plugins. 
 48   
 49 -class _Ls(Worker): 
 50      """ls worker class.""" 
 51   
 52 -    def __init__(self,**kwargs): 
 53          """ 
 54          :Arguments: 
 55            *kwargs* 
 56               same as ls ?? 
 57          """ 
 58          # super class init: do this before doing anything else 
 59          # (also sets up self.parameters and self.results) 
 60          super(_Ls, self).__init__(**kwargs) 
 61   
 62          # process specific parameters now and set instance variables 
 63          # .... 
 64          # self.parameters.filenames = { 'xxx': 'yyy', ....} 
 65          # .... 
 66   
 67          # self.simulation might have been set by the super class 
 68          # already; just leave this snippet at the end. Do all 
 69          # initialization that requires the simulation class in the 
 70          # _register_hook() method. 
 71          if not self.simulation is None: 
 72              self._register_hook() 
 73   
 74 -    def _register_hook(self, **kwargs): 
 75          """Run when registering; requires simulation.""" 
 76   
 77          super(_Ls, self)._register_hook(**kwargs) 
 78          assert not self.simulation is None 
 79   
 80   
 81      # override 'API' methods of base class 
 82           
 83 -    def run(self, *args, **kwargs): 
 84          """List the contents of the simulation directory. 
 85          """ 
 86   
 87          from subprocess import call 
 88          lscmd = ['ls', '-la'] + list(args) 
 89          cmd = lscmd + [self.simulation.tpr, self.simulation.xtc] 
 90          with rulify("TPR and XTC"): 
 91              rc = call(cmd)   # just print to screen 
 92   
 93          adir = self.simulation.analysis_dir 
 94          cmd = lscmd + [adir] 
 95          with rulify("Analysis dir %(adir)s" % vars()): 
 96              rc = call(cmd)   # just print to screen 
 97           
 98 -    def analyze(self,**kwargs): 
 99          pass 
100   
101 -    def plot(self, **kwargs): 
102          pass 
103   
104  from contextlib import contextmanager 
105   
106  @contextmanager 
107 -def rulify(header, ncol=79): 
108      toprule = ncol * '=' 
109      midrule = ncol * '-' 
110      botrule = toprule 
111      print toprule 
112      print header 
113      print midrule 
114      try: 
115          yield None 
116      finally: 
117          print botrule 
118          print 
119   
120  # Public classes that register the worker classes 
121  #------------------------------------------------ 
122   
123 -class Ls(Plugin): 
124      """*ls* plugin. 
125       
126      This simply lists the files on disk. It is useful for testing the 
127      plugin architecture. 
128   
129      .. class:: Ls([name[, simulation]]) 
130       
131      :Arguments: 
132          *name* : string 
133              plugin name (used to access it) 
134          *simulation* : instance 
135              The :class:`gromacs.analysis.Simulation` instance that owns the plugin. 
136   
137      """ 
138      worker_class = _Ls 
139