Cctk

Major changes:

- Speed updates to ``GaussianFile`` and ``Mol2File`` reading (several orders of magnitude for large files).
- New functions ``epimerize()`` and ``renumber_to_match()`` have been added to ``Molecule``, as well as additional functions to detect chirality.
- Quasiharmonic free energy calculations employing Grimme's correction are now calculated by default and stored in ``Ensemble`` ``properties`` as ``quasiharmonic_gibbs_free_energy``.

Minor changes:

- Bugs pertaining to incomplete files and hanging filestreams from internal static data have been ironed out.
- ``analyze.py`` has been given a significant cosmetic upgrade (colors!).
- Elapsed time, temperature, gradient, max force/displacement, and internal forces/displacement can now be read from Gaussian ``.out`` files.

Major changes:

Documentation and theme completely overhauled. Many updates still needed.
`Ensemble` access API redesigned.
Code to calculate RMSD, align structures, and eliminate redundant conformations.
NMR shieldings can be extracted, symmetry-corrected, and linearly scaled.
Charges can be read.

Minor changes:

Many docstring and bugfixes.

Major changes:
- The underlying data structure of ``Ensemble`` has been changed from a list of ``Molecules`` to a dictionary of {``Molecule``: property}, where properties is itself a dictionary containing information from the job. The indexing of ``Ensemble`` has been changed such that most list-like behavior still behave like they used to.
- NMR shifts, charges, forces, and dipole moments can now be read from Gaussian files, and NMR scaling can be applied.
- ``Ensemble`` alignment and removal of redundant molecules has been refactored.

Major changes:
- Rolling back last release, ``GaussianFile`` now only composes ``ConformationalEnsemble``. To handle the case where multiple unrelated molecules have been combined in the same Link1-based output file, ``GaussianFile.read_file()`` can now return a list of ``GaussianFile`` objects.
- Link 0 Gaussian commands are now stored in ``GaussianFile.link0`` as a dictionary and are automatically read/written to files (both input and output).
- To prevent ambiguity, ``GaussianFile.header`` is now called ``GaussianFile.route_card``.
- NMR isotropic shifts are now read automatically from NMR jobs in Gaussian.
- ``.mol2`` files can now be written.

Minor changes:
- Formatting on ``.gjf`` file writing has been changed, and there's an option to use atomic symbols instead of atomic numbers.
- Varying capitalization for atomic symbols is now tolerated throughout the program.
- There is now a method to combine multiple molecules into one molecule object (``Molecule.combine_molecules``).

Major changes:
- ``GaussianFile``'s ``molecules`` attribute can now be either ``Ensemble`` or ``ConformationalEnsemble``, depending on if the individual molecules are compatible or not.
- Multiple structures can now be written to the same file using Link1 syntax with the ``GaussianFile.write_ensemble_to_file()`` command.
- ``Molecule`` ``atomic_numbers`` and ``geometries`` are now indexed from 1 **internally** using a custom subclass of ``numpy.ndarray`` called ``cctk.OneIndexedArray``.

Minor changes:
- Two new tutorials have been added.
- More preloaded groups have been added (Cl, Br, F, I, SF5, SO3H).

A bug preventing proper alignment of `ConformationalEnsemble` objects has been identified and fixed, and appropriate tests added.