Package gromacs :: Package analysis :: Package plugins :: Module rmsd :: Class _RMSD

Class _RMSD

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

RMSD worker class.

Instance Methods

[hide private]

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

source code

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

source code

run(self, force=False, group='C-alpha', **gmxargs)
Analyze trajectory and write RMSD files.

source code

analyze(self, **kwargs)
Collect output xvg files as :class:`gromacs.formats.XVG` objects.

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 RMSD analysis.

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

Overrides: object.__init__

_register_hook(self, **kwargs)

source code

Run when registering; requires simulation.

Overrides: core.Worker._register_hook

run(self, force=False, group='C-alpha', **gmxargs)

source code

Analyze trajectory and write RMSD files.

Each frame is fit to the structure in the tpr, based on the
C-alpha atoms. The RMSd is alculated for the supplied index
group *group*.

:Arguments:
  - *group*: index group for RMSD calculation (eg C-alpha or Protein)
  - *force*: do analysis and overwrite existing files
  - *gmxargs*: additional keyword arguments for :func:`gromacs.g_rms` (e.g. res=True)

Overrides: core.Worker.run

analyze(self, **kwargs)

source code

Collect output xvg files as :class:`gromacs.formats.XVG` objects.

:Returns:  a dictionary of the results and also sets ``self.results``.

Overrides: core.Worker.analyze

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 _RMSD

__init__(self, **kwargs) (Constructor)

_register_hook(self, **kwargs)

run(self, force=False, group='C-alpha', **gmxargs)

analyze(self, **kwargs)

plot(self, **kwargs)

init(self, **kwargs)
(Constructor)