Package gromacs :: Package analysis :: Package plugins :: Module stripwater :: Class _StripWater
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Class _StripWater

source code

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

StripWater worker class.
Instance Methods [hide private]
 
__init__(self, **kwargs)
Set up StripWater
source code
 
_register_hook(self, **kwargs)
Run when registering; requires simulation.
source code
 
run(self, **kwargs)
Write new trajectory with water index group stripped.
source code
 
analyze(self, **kwargs)
No postprocessing.
source code
 
plot(self, **kwargs)
No plotting.
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  StripWater

:Arguments:
  *force*
     ``True`` will always regenerate trajectories even if they 
     already exist, ``False`` raises an exception, ``None``
     does the sensible thing in most cases (i.e. notify and
     then move on).
  *dt* : float or list of floats
     only write every dt timestep (in ps); if a list of floats is 
     supplied, write multiple trajectories, one for each dt.             
  *compact* : bool
     write a compact representation
  *fit*          
     Create an additional trajectory from the stripped one in which
     the Protein group is rms-fitted to the initial structure. See
     :meth:`gromacs.cbook.Transformer.fit` for details. Useful 
     values:
       - "xy" : perform a rot+trans fit in the x-y plane
       - "all": rot+trans
       - ``None``: no fitting
     If *fit* is not supplied then the constructore-default is used
     (:attr:`_StripWater.parameters.fit`).
  *resn*
     name of the residues that are stripped (typically it is
     safe to leave this at the default 'SOL')

Overrides: object.__init__

_register_hook(self, **kwargs)

source code 
Run when registering; requires simulation.
Overrides: core.Worker._register_hook

run(self, **kwargs)

source code 
Write new trajectory with water index group stripped.

kwargs are passed to
:meth:`gromacs.cbook.Transformer.strip_water`. Important
parameters:

:Keywords:
  *force*
     ``True`` will always regenerate trajectories even if they 
     already exist, ``False`` raises an exception, ``None``
     does the sensible thing in most cases (i.e. notify and
     then move on).
  *dt* : float or list of floats
     only write every dt timestep (in ps); if a list of floats is 
     supplied, write multiple trajectories, one for each dt.             
  *compact* : bool
     write a compact representation
  *fit*          
     Create an additional trajectory from the stripped one in which
     the Protein group is rms-fitted to the initial structure. See
     :meth:`gromacs.cbook.Transformer.fit` for details. Useful 
     values:
       - "xy" : perform a rot+trans fit in the x-y plane
       - "all": rot+trans
       - ``None``: no fitting
     If *fit* is not supplied then the constructore-default is used
     (:attr:`_StripWater.parameters.fit`).
  *resn*
     name of the residues that are stripped (typically it is
     safe to leave this at the default 'SOL')

.. Note:: If set, *dt* is only applied to a fit step; the
          no-water trajectory is always generated for all time
          steps of the input.

Overrides: core.Worker.run

analyze(self, **kwargs)

source code 
No postprocessing.
Overrides: core.Worker.analyze

plot(self, **kwargs)

source code 
No plotting.
Overrides: core.Worker.plot