Improved support for hierarchy schemes from OpenMM and PDBs

[Yoshanuikabundi]

This adds residue and chain hierarchy scheme support to Molecule.from_pdb_and_smiles and Topology.from_openmm.

This is based on #1400 to avoid conflicts, so that should be merged first.

Fixes #1386.

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

[codecov]

Codecov Report

Merging #1404 (1f52f1a) into main (4a7a16c) will increase coverage by 0.01%.
The diff coverage is 100.00%.

Additional details and impacted files

[j-wags]

Looking great - I think this is the right direction to go in. Adding hierarchy schemes in code paths where users are loading from PDB seems helpful at best and harmless at worst!

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[Yoshanuikabundi]

OK, I've added tests for the new behavior, updated the toolkit showcase to no longer use ensure_unique_atomnames=False, and fixed the broken JSON serialization of tuples in hierarchy schemes that was causing the examples to fail. I also noticed that the showcase still had widget states saved, even though the output had been cleared, so I cleaned that up too.

I think this is ready to go - tests are passing locally but I'll check later tonight that CI is happy! And I'm happy for this to be merged while I'm asleep, or I can merge it tomorrow.

[j-wags]

Looks good, @Yoshanuikabundi. The tuple thing is a good improvement but I was a bit confused seeing it without context - In the future it may be good to keep urgent PRs minimal to reduce overhead on review :-)

[j-wags]

(not blocking) I don't understand the purpose of this - Is it checking that there are no Nones in any of the HierarchyElements? Or no (None, None, None, None) HierarchyElements? If the iterators weren't exposed at all this wouldn't need an assert since it would cause an AttributeError. This could use a comment explaining it.