Handling partial occupancy (e.g CIF, PDB)

[ghutchis]

Avogadro needs better support for partial occupancy, e.g., #2437. I'm not sure the best way to handle this (e.g., generating multiple possible coordinate sets?) but the current approach isn't great since all sites will get 100% occupancy.

[ghutchis]

There are a few libraries we could use for native CIF support:

• gemmi https://gemmi.readthedocs.io/en/stable/cif.html
• readCIF https://github.com/RBVI/readcif?tab=readme-ov-file#license
• cctbx https://cctbx.github.io/
• CIFPARSE https://mmcif.wwpdb.org/docs/sw-examples/cpp/html/index.html