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Extend Molecular Graph Implementation for Proteins

Chance Brandtrequested to merge
connectivity into main

Creates a new set of classes to define the MolecularGraphs and ProteinGraphs in the 'connectivity' sub-package of the conformer packageand all relevant tests. Also include some updates to the systems code to accommodate functionality desired for MolecularGraphs.

Pre-merge checklist

  • All files are properly formatted. Check with ruff check ..
  • All files have license headers. Check with python deploy/check_license.py.
  • All unit tests run successfully. Check with python -m unittest discover

Merge request reports