Molecule de-duplication lost in Topology roundtrips

[mattwthompson]

Describe the bug

Molecule de-duplication is needed to make several API points useful but can be very slow, so its results are cached after the first call. This cache, however, does not survive several roundtrips.

For better or worse, duplicating a Topology object using its constructor is a support feature and commonly-used downstream. Losing this cache forces its re-building and removes some of the benefit of caching it in the first place.

To Reproduce

>>> from openff.toolkit import Topology, Molecule
>>> topology = Topology.from_molecules([Molecule.from_smiles(n * "C") for n in range(1, 10)])
>>> _ = topology.identical_molecule_groups
>>> topology._cached_chemically_identical_molecules is None
False
>>> Topology(topology)._cached_chemically_identical_molecules is None
True

Additional context

One could

>>> new_topology = Topology(topology)
>>> new_topology._cached_chemically_identical_molecules = topology._cached_chemically_identical_molecules

but this is unstable