Class ProteinOnly

source code

 object --+    
          |    
core.Plugin --+
              |
             ProteinOnly

*ProteinOnly* plugin.

Write a new trajectory which has the water index group removed. 

.. class:: ProteinOnly([selection[, name[, simulation[, ...]]]])

:Arguments:
    *selection*
        optional selection for the water instead of "SOL"
    *name* : string
        plugin name (used to access it)
    *simulation* : instance
        The :class:`gromacs.analysis.Simulation` instance that owns the plugin.
    *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'].