Class Simulation

Set up a Simulation object.

:Keywords:
   *sim*
     Any object that contains the attributes *tpr*, *xtc*,
     and optionally *ndx*
     (e.g. :class:`gromacs.cbook.Transformer`). The individual keywrods such
     as *xtc* override the values in *sim*.
   *tpr*
     Gromacs tpr file (**required**)
   *xtc*
     Gromacs trajectory, can also be a trr (**required**)
   *edr*
     Gromacs energy file (only required for some plugins)
   *ndx*
     Gromacs index file
   *analysisdir*
     directory under which derived data are stored;
     defaults to the directory containing the tpr [None]
   *plugins* : list
     plugin instances or tuples (*plugin class*, *kwarg dict*) or tuples
     (*plugin_class_name*, *kwarg dict*) to be used; more can be
     added later with :meth:`Simulation.add_plugin`.

Overrides: object.__init__

Add a plugin to the registry.

- If *plugin* is a :class:`Plugin` instance then the
  instance is directly registered and any keyword arguments
  are ignored.

- If *plugin* is a :class:`Plugin` class object or a
  string that can be found in :mod:`gromacs.analysis.plugins`
  then first an instance is created with the given keyword
  arguments and then registered.

:Arguments:
    *plugin* : class or string, or instance
       If the parameter is a class then it should have been derived
       from :class:`Plugin`. If it is a string then it is taken as a
       plugin name in :mod:`gromacs.analysis.plugins` and the
       corresponding class is added. In both cases any parameters for
       initizlization should be provided.

       If *plugin* is already a :class:`Plugin` instance then the kwargs 
       will be ignored.
    *kwargs*
       The kwargs are specific for the plugin and should be
       described in its documentation.

Returns a path under self.analysis_dir, which is guaranteed to exist.

Raise :exc:`ValueError` if path does not exist. Uses *filetype* in message.

Set the plugin that should be used by default.

If no *plugin_name* is supplied to :meth:`run`, :meth:`analyze` etc. then
this will be used.

The currently active plugin (set with :meth:`Simulation.set_plugin`).

Decorators:

• @property

Plot all data for the selected plugin::

  plot(plugin_name, **kwargs)

:Arguments:
   *plugin_name*
      name of the plugin to plot data from
   *figure*
      - ``True``: plot to file with default name.
      - string: use this filename (+extension for format)
      - ``False``: only display
   *kwargs*
      arguments for plugin plot function (in many cases
      provided by :meth:`gromacs.formats.XVG.plot` and
      ultimately by :func:`pylab.plot`)

str(x)

Overrides: object.__str__

(inherited documentation)

repr(x)

Overrides: object.__repr__

(inherited documentation)

default_plugin_name

Use this plugin if none is explicitly specified. Typically set with :meth:`~Simulation.set_plugin`.