Add tests and custom exceptions for index lookups in Topology

[mattwthompson]

While working on #1276, I found that Topology.molecule_index was only ever used in the machinery that checks which molecules had charges assigned to them. I added a couple of unit tests, custom exceptions, and updated some docstrings.

I noticed there are a lot of bits in the Topology API that deal with particles, i.e.

    @property
    def particles(self):
        for molecule in self.molecules:
            for atom in molecule.atoms:
                yield atom

@j-wags would you accept a PR that removes or deprecates the concept of a "particle" since virtual sites are no longer a part of Molecule objects?

• Tag issue being addressed
• Add tests
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog

[codecov]

Codecov Report

Merging #1302 (55c5e15) into topology-biopolymer-refactor (6001482) will increase coverage by 0.53%.
The diff coverage is 100.00%.

[j-wags]

@j-wags would you accept a PR that removes or deprecates the concept of a "particle" since virtual sites are no longer a part of Molecule objects?

Oh, good question. Yes, I think that the 0.11.0 release would be a good time to give particles the same treatment as topology_atoms - Have the particles API points instead redirect to atoms and issue a deprecation warning that they'll be completely gone in 0.12.

[j-wags]

Looks good to me!

[mattwthompson]

Thanks!