code: def _define_canned_commands():
      
      global trj_compact, rmsd_backbone, trj_fitted, trj_xyfitted
  
      trj_compact = tools.Trjconv(ur='compact', center=True, boxcenter='tric', pbc='mol',
                                  input=('protein','system'),
                                  doc="""
  Writes a compact representation of the system centered on the protein""")
  
      rmsd_backbone = tools.G_rms(what='rmsd', fit='rot+trans',
                                  input=('Backbone','Backbone'),
                                  doc="""
  Computes RMSD of backbone after fitting to the backbone.""")
  
      trj_fitted = tools.Trjconv(fit='rot+trans',
                                 input=('backbone', 'system'),
                                 doc="""
  Writes a trajectory fitted to the protein backbone.
  
  Note that this does *not* center; if center is required, the *input*
  selection should have the group to be centered on in second position,
  e.g. ``input = ('backbone', 'Protein', System')``.
  """)
  
  
      # Gromacs 4.x
      trj_xyfitted = tools.Trjconv(fit='rotxy+transxy',
                                   input=('backbone', 'protein','system'),
                                   doc="""
  Writes a trajectory fitted to the protein in the XY-plane only.
  
  This is useful for membrane proteins. The system *must* be oriented so
  that the membrane is in the XY plane. The protein backbone is used
  for the least square fit, centering is done for the whole protein.
  
  Note that centering together with fitting does not always work well
  and that one sometimes need two runs of trjconv: one to center and
  one to fit.
  
  .. Note:: Gromacs 4.x only""")
docs: Define functions for the top level name space.
  
      Definitions are collected here so that they can all be wrapped in
      a try-except block that avoids code failing when the Gromacs tools
      are not available --- in some cases they are not necessary to use
      parts of GromacsWrapper.
  
      .. Note:: Any function defined here **must be listed in ``global``**!