Cctk

Collected minor updates from the last 6 months; lots of bugfixes around ``GaussianFile`` parsing and quasiclassical initialization.

Added ability to specify ``molecule`` kwarg to ``GaussianFile.__init__()``.

Major updates:
- ``XYZFile`` now possesses an ``ensemble`` property, not a ``molecule`` property. (Calling ``xyzfile.molecule`` will give a ``DeprecationWarning`` but is permitted for now.)

Minor updates:
- Classical initialization has been added to ``cctk.quasiclassical``, along with the ability to perform mode-specific configuration.

Major updates:
- Added ability to Boltzmann-weight properties from conformational ensembles with ``ConformationalEnsemble.boltzmann_average("property", temp=450)``.
- Added ability to compute GFN2-xtb energies for static molecules with ``Molecule.compute_energy()``

Minor updates:
- Fixed ReadTheDocs bug which was breaking autogen of API. Sorry!
- Caught some *m/z* computation bugs.
- Added ``Molecule.coulomb_analysis()`` to calculate pairwise charge–charge interactions between fragments.

Happy Easter!

Major changes:
- A class ``SIFile`` has been added to enable automatic formatting of output files. This is a work in progress.
- ``cctk.Molecule.to_string()`` and ``cctk.Molecule.from_string(string)`` now permit storage of ``cctk.Molecule`` objects. Part of the string is yaml-formatted, but most is not very human-readable (compressed ``ndarray`` bytes).

Minor changes:
- velocities can now also be generated from ``cctk.quasiclassical`` to initialize quasiclassical MD trajectories.
- ``charge`` and ``multiplicity`` have been added to ``cctk.XYZFile``. Thanks to Gabe Gomes for pointing out this mistake.
- A new function ``compute_mass_spectrum`` has been added to ``cctk.helper_functions``, and the mass spec backend from ``cctk.Molecule`` has been moved there.
- A new function ``cctk.Molecule.equal()`` has been added to allow for comparison of molecules.
- A bug in ``cctk.optimize`` has been fixed. Thanks to Gabe Gomes for pointing out this mistake.

Minor changes:
- MP2, MP3, MP4, CI, and CC energies can now be read from Gaussian.
- Vibrational mode intensities and dipole vectors can now be read from Gaussian.
- cctk.Molecule now has a function ``atoms_moving_in_imaginary`` which returns a list of atomic numbers moving in the imaginary.
- Miscellaneous bugfixes to cctk.GaussianFile.read_file() have been applied.
- ``get_avg_mass()`` and ``get_z_from_mass()`` have been applied to cctk.helper_functions to convert between average elemental weight and atomic number.
- cctk.Molecule ``limit_solvent_shell()`` now lets you focus the solvation on a specific solute atom.
- cctk.XYZFile now has a function ``write_ensemble_to_file()`` which generates MOLDEN-compatible ``.xyz`` trajectories.

Fairly minor update comprised of several bug fixes. The only substantive new feature is the ability to read NMR shielding tensors from Gaussian.