Package gromacs :: Package analysis :: Package plugins :: Module template_plugin :: Class _TEMPLATEplugin

Class _TEMPLATEplugin

         object --+        
                  |        
utilities.FileUtils --+    
                      |    
            core.Worker --+
                          |
                         _TEMPLATEplugin

TEMPLATE worker class.

Instance Methods

[hide private]

__init__(self, **kwargs)
Set up TEMPLATE analysis.

source code

_register_hook(self, **kwargs)
Run when registering; requires simulation.

source code

run(self, cutoff=None, force=False, **gmxargs)
Short description of what is performed.

source code

analyze(self, **kwargs)
Short description of postprocessing.

source code

plot(self, **kwargs)
Plot all results in one graph, labelled by the result keys.

source code

Inherited from core.Worker: figdir, plugindir, savefig, store_xvg, topdir

Inherited from utilities.FileUtils: __repr__, check_file_exists, filename, infix_filename

Inherited from utilities.FileUtils (private): _init_filename

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__

Class Variables

[hide private]

Inherited from utilities.FileUtils: default_extension

Instance Variables

[hide private]

Inherited from core.Worker: plugin, plugin_name

Inherited from utilities.FileUtils: real_filename

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, **kwargs)
(Constructor)

source code

Set up TEMPLATE analysis.

This is the worker class; this is where all the real analysis is done.

Overrides: object.__init__

Arguments:

keyword_1: description
keyword_2: description

_register_hook(self, **kwargs)

source code

Run when registering; requires simulation.

Overrides: core.Worker._register_hook

run(self, cutoff=None, force=False, **gmxargs)

source code

Short description of what is performed.

The run method typically processes trajectories and writes data files.

Overrides: core.Worker.run

analyze(self, **kwargs)

source code

Short description of postprocessing.

The analyze method typically postprocesses the data files generated by run. Splitting the complete analysis task into two parts (run and analyze) is advantageous because in this way parameters of postprocessing steps can be easily changed without having to rerun the time consuming trajectory analysis.

Returns:: a dictionary of the results and also sets self.results.
Overrides: core.Worker.analyze

Keywords:

kw1: description

plot(self, **kwargs)

source code

Plot all results in one graph, labelled by the result keys.

Parameters:

figure -
- True: save figures in the given formats
- "name.ext": save figure under this filename (ext -> format)
- False: only show on screen
formats (sequence) - sequence of all formats that should be saved [('png', 'pdf')]
plotargs - keyword arguments for pylab.plot()

Overrides: core.Worker.plot

Class _TEMPLATEplugin

__init__(self, **kwargs) (Constructor)

_register_hook(self, **kwargs)

run(self, cutoff=None, force=False, **gmxargs)

analyze(self, **kwargs)

plot(self, **kwargs)

init(self, **kwargs)
(Constructor)