refactor: unify buildgraph.py and build_graph functions for atom and residue level graphs
#1453
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The following actions uses node12 which is deprecated and will be forced to run on node16: styfle/cancel-workflow-action@0.4.0. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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