from propkatraj import PropkaTraj

pkatraj = PropkaTraj(atomgroup, select='protein', skip_failure=False)

   Runs :program:`propka` on the titrateable residues of the selected AtomGroup
   on each frame in the trajectory.
   
   Parameters
   ----------
   atomgroup : :class:`MDAnalysis.Universe` or :class:`MDAnalysis.AtomGroup`
       Group of atoms containing the residues for pKa analysis. Please note
       that :class:`MDAnalysis.UpdatingAtomGroup` are not supported and will
       be automatically converted to :class:`MDAnalysis.AtomGroup`.
   select : str
       Selection string to use for selecting a subsection of atoms to use
       from the input ``atomgroup``. Note: passing non-protein residues to
       :program:`propka` may lead to incorrect results (see notes). [`protein`]
   skip_failure : bool
       If set to ``True``, skip frames where :program:`propka` fails. A list
       of failed frames is made available in
       :attr:`PropkaTraj.failed_frames_log`. If ``False`` raise a
       RuntimeError exception on those frames. [`False`]


    Notes
    -----
    Currently only the default behaviour supplemented with the `--quiet` flag
    of :program:`propka` is used.

    Temporary :program:`propka` files are written in the current working
    directory. This will leave a ``current.pka`` and ``current.propka_input``
    file. These are the temporary files for the final frame and can be removed
    safely.

    Current known issues:

    1. Due to the current behaviour of the MDAnalysis PDBWriter, non-protein
       atoms are written to PDBs using `ATOM` records instead of `HETATM`.
       This is likely to lead to undefined behaviour in :program:`propka`,
       which will likely expect `HETATM` inputs. We recommend users to only
       pass protein atoms for now. See the following issue for more details:
       https://github.com/Becksteinlab/propkatraj/issues/24


pkatraj.run()

   Perform the calculation

   Parameters
   ----------
   start : int, optional
      start frame of analysis
   stop : int, optional
      stop frame of analysis
   step : int, optional
      number of frames to skip between each analysed frame
   verbose : bool, optional
      Turn on verbosity

pkatraj.results.pkas.describe()