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

source code

         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