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object --+ | Simulation
Class that represents one simulation. Analysis capabilities are added via plugins. 1. Set the *active plugin* with the :meth:`Simulation.set_plugin` method. 2. Analyze the trajectory with the active plugin by calling the :meth:`Simulation.run` method. 3. Analyze the output from :meth:`run` with :meth:`Simulation.analyze`; results are stored in the plugin's :attr:`~Worker.results` dictionary. 4. Plot results with :meth:`Simulation.plot`.
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Inherited from |
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plugins Registry for plugins: This dict is central. |
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default_plugin_name Use this plugin if none is explicitly specified. |
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Inherited from |
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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`.
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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. Note Parent dirs are created if necessary. |
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`).
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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)
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repr(x)
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default_plugin_nameUse this plugin if none is explicitly specified. Typically set with :meth:`~Simulation.set_plugin`. |
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