Implemented the chemical fragmentation based on Van der Waals radii

[mcocdawc]

Implemented chemically motivated fragmentation

• uses van der Waals radii (relies on chemcoord)
• separate fragmentation from the assignment of AO indices
• Is very fast. On the big molecule of @lweisburn and @mscho527 (342 atoms) the BE3 fragmentation takes on my notebook 17 ms.¹ ²

Nice properties:

• Explicit assumptions about the indices are encoded in the type system. This means that there is a clear distinction in the type between a center index, an edge index or the index of an atomic orbital. At runtime they are of course plain old integers.
• All data structures are immutable.
• Nearly everything is just a concatenation of pure, side-effect free functions and/or dictionary comprehensions. Makes it very easy to parallelize, if performance would ever become an issue.
• Fully generalized to arbitrary n-BE >= 1. Also strange input such as nBE == 20 for an octane just works and produces one fragment.
• Fully generalized the motif concept such that one can decide if hydrogens are also centers. This means that the hydrogen chain is just a special case of the code which requires no adaptations. This means that any nBE >= 1 for hydrogen chains is also possible.
• In-code documentation of the terms that are also nicely typeset in the user documentation, see the attached screenshot.

Still to do:

• The assignment of AO indices is still missing. Is done separately to not have a huge single PR.
• The types such as AtomIdx are probably useful for other code as well and should be moved to shared.typing.

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¹ For comparison:

• autogen takes 312 ms.
• graphgen with cutoff=70 takes 35 s.

Note that this is not a fair comparison, because both autogen and graphgen also create the AO indices per fragment.

² The first execution might take longer, because perfomance-relevant code is jitted.

[mcocdawc]

Since this is a long PR I would add @ShaunWeatherly and one of you (@lweisburn or @mscho527 ) as reviewers.

[mscho527]

Great, nice work!

[mscho527]

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