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