Class Transformer

Set up Transformer with structure and trajectory.

Supply *n* = tpr, *f* = xtc (and *n* = ndx) relative to dirname.

:Keywords:
   *s* 
      tpr file (or similar); note that this should not contain
      position restraints if it is to be used with a reduced
      system (see :meth:`~Transformer.strip_water`)
   *f*
      trajectory (xtc, trr, ...)
   *n*
      index file (it is typically safe to leave this as ``None``; in
      cases where a trajectory needs to be centered on non-standard
      groups this should contain those groups)
   *force*
      Set the default behaviour for handling existing files:
        - ``True``: overwrite existing trajectories
        - ``False``: throw a IOError exception
        - ``None``: skip existing and log a warning [default]

Overrides: object.__init__

Return canonical path to file under dirname with components args

If args form an absolute path then just return it as the absolute path.

Write compact xtc that is fitted to the tpr reference structure.

See :func:gromacs.cbook.trj_fitandcenter` for details and description of kwargs. The most important ones are listed here but in most cases the defaults should work.

Returns:

dictionary with keys tpr, xtc, which are the names of the the new files

Write xtc that is fitted to the tpr reference structure.

See :func:`gromacs.cbook.trj_xyfitted` for details and
description of *kwargs*. The most important ones are listed
here but in most cases the defaults should work.

:Keywords:
   *s*
     Input structure (typically the default tpr file but can be set to
     some other file with a different conformation for fitting)
   *n*
     Alternative index file.           
   *o*
     Name of the output trajectory. A default name is created. 
     If e.g. *dt* = 100  is one of the *kwargs* then the default name includes
     "_dt100ps".
  *xy* : boolean
     If ``True`` then only do a rot+trans fit in the xy plane
     (good for membrane simulations); default is ``False``.
  *force*
    ``True``: overwrite existing trajectories
    ``False``: throw a IOError exception
    ``None``: skip existing and log a warning [default]
  *kwargs*
     kwargs are passed to :func:`~gromacs.cbook.trj_xyfitted`           

:Returns: 
      dictionary with keys *tpr*, *xtc*, which are the names of the
      the new files              

Write xtc and tpr with water (by resname) removed.

:Keywords:
   *os*
      Name of the output tpr file; by default use the original but
      insert "nowater" before suffix.
   *o*
      Name of the output trajectory; by default use the original name but
      insert "nowater" before suffix.
   *on*
      Name of a new index file (without water).
   *compact*
      ``True``: write a compact and centered trajectory
      ``False``: use trajectory as it is [``False``]
   *resn*
      Residue name of the water molecules; all these residues are excluded.
   *groupname*
      Name of the group that is generated by subtracting all waters
      from the system.
   *force* : Boolean
     - ``True``: overwrite existing trajectories
     - ``False``: throw a IOError exception
     - ``None``: skip existing and log a warning [default]           
   *kwargs* 
      are passed on to :func:`gromacs.cbook.trj_compact` (unless the
      values have to be set to certain values such as s, f, n, o
      keywords). The *input* keyword is always mangled: Only the first
      entry (the group to centre the trajectory on) is kept, and as a
      second group (the output group) *groupname* is used.

:Returns: 
      dictionary with keys *tpr*, *xtc*, *ndx* which are the names of the
      the new files
      
.. warning:: The input tpr file should *not* have *any position restraints*;
             otherwise Gromacs will throw a hissy-fit and say 

             *Software inconsistency error: Position restraint coordinates are
             missing*

             (This appears to be a bug in Gromacs 4.x.)

Write xtc and tpr only containing the protein.

:Keywords:
   *os*
      Name of the output tpr file; by default use the original but
      insert "proteinonly" before suffix.
   *o*
      Name of the output trajectory; by default use the original name but
      insert "proteinonly" before suffix.
   *on*
      Name of a new index file.
   *compact*
      ``True``: write a compact and centered trajectory
      ``False``: use trajectory as it is [``False``]
   *groupname*
      Name of the protein-only group.
   *keepalso*
      List of literal make_ndx selections of additional groups that should 
      be kept, e.g. ['resname DRUG', 'atom 6789'].
   *force* : Boolean
     - ``True``: overwrite existing trajectories
     - ``False``: throw a IOError exception
     - ``None``: skip existing and log a warning [default]           
   *kwargs* 
      are passed on to :func:`gromacs.cbook.trj_compact` (unless the
      values have to be set to certain values such as s, f, n, o
      keywords). The *input* keyword is always mangled: Only the first
      entry (the group to centre the trajectory on) is kept, and as a
      second group (the output group) *groupname* is used.

:Returns: 
      dictionary with keys *tpr*, *xtc*, *ndx* which are the names of the
      the new files
      
.. warning:: The input tpr file should *not* have *any position restraints*;
             otherwise Gromacs will throw a hissy-fit and say 

             *Software inconsistency error: Position restraint coordinates are
             missing*

             (This appears to be a bug in Gromacs 4.x.)