More static typing

[speleo3]

• Parameters typing
• Options typing
• vector_algebra tests and refactoring
• Raise NotImplementedError from unused functions (of which some are broken if you try to run them)

[codecov[bot]]

Codecov Report

Attention: 56 lines in your changes are missing coverage. Please review.

Comparison is base (9d4b59c) 74.05% compared to head (abd3d05) 74.82%.

Files	Patch %	Lines
propka/hydrogens.py	0.00%	15 Missing :warning:
propka/output.py	57.14%	15 Missing :warning:
propka/ligand_pka_values.py	58.33%	5 Missing :warning:
propka/group.py	75.00%	3 Missing :warning:
propka/lib.py	93.18%	3 Missing :warning:
propka/vector_algebra.py	91.66%	3 Missing :warning:
propka/atom.py	94.73%	2 Missing :warning:
propka/bonds.py	0.00%	2 Missing :warning:
propka/parameters.py	97.89%	2 Missing :warning:
propka/conformation_container.py	93.33%	1 Missing :warning:
... and 5 more

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #177 +/- ## ========================================== + Coverage 74.05% 74.82% +0.77% ========================================== Files 25 25 Lines 3943 4116 +173 ========================================== + Hits 2920 3080 +160 - Misses 1023 1036 +13 ```

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