add kwarg to MoleculeGraph method and fix PackmolSet bug

[orionarcher]

Summary

The get_disconnected_fragments method returns a new graph with reordered indices but provides no way to get the mapping from new to original indices. This PR reconstructs that map and adds an optional keyword argument to return it. This will not affect current functionality.

Additionally, I found an error in the pymatgen.io.packmol code where a non-abstract class had an abstract method, preventing it from being instantiated. This slipped under the radar because the tests are skipped due to a difficult dependency (packmol). The tests are now passing locally for me.

A downstream code I am working on requires this addition.

• a new return_index_map kwarg for MoleculeGraph.get_disconnected_fragments
• remove abc.abstractmethod decorator from PackmolBoxGen.get_input_set()

Checklist

• Doc strings have been added in the Google docstring format. Run pydocstyle on your code.
• Type annotations are highly encouraged. Run mypy path/to/file.py to type check your code.
• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.

[janosh]

Thanks @orionarcher! 👍

[orionarcher]

Thank you @janosh!