Extend TopologyProposal with convenience methods to retrieve atoms being deleted and atoms being created

[jchodera]

Perhaps we should make TopologyProposal a real class, since we could then define convenience methods that use new_to_old_atom_map along with old_topology and new_topology to return the lists of atoms being deleted or created. This would be helpful for creating alchemically modified systems without having to recompute these lists.

[pgrinaway]

I think this is a good idea. It might also make the proposal classes cleaner.

[jchodera]

Do you want to take a stab at this?

[pgrinaway]

Yep! Sounds good!

[pgrinaway]

I'll make this the next PR after fixing the test failures.

[pgrinaway]

Based on #22 and the discussion there, I've implemented a full class version of the TopologyProposal. I can open a PR now, though it will require a bit of a refactor to make the tests work (since the constructor is now different).

[jchodera]

Go for it!

[pgrinaway]

Implemented in #27