Class _ProteinOnly

Set up  ProteinOnly

: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:`_ProteinOnly.parameters.fit`).
  *keepalso*
     List of literal ``make_ndx`` selections that select additional
     groups of atoms that should also be kept in addition to the
     protein. For example *keepalso*=['"POPC"', 'resname DRUG'].

Overrides: object.__init__

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:`_ProteinOnly.parameters.fit`).
  *keepalso*
      List of ``make_ndx`` selections that should also be kept.

.. 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

Overrides: core.Worker.analyze

Overrides: core.Worker.plot