On `rgroup_df=compute_rgroup_dataframe(remove_insertions(raw_pdb_df))`

a-r-j / graphein

Protein Graph Library

https://graphein.ai/

MIT License

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On `rgroup_df=compute_rgroup_dataframe(remove_insertions(raw_pdb_df))` #304

Closed anton-bushuiev closed 1 year ago

anton-bushuiev commented 1 year ago

Hi 👋!

Is remove_insertions here on purpose or just a legacy part from the times when insertion codes were always removed? https://github.com/a-r-j/graphein/blob/649a490505740a266b26976807e7f303c2a32ff0/graphein/protein/graphs.py#L540

Now it leads to an error, when running add_beta_carbon_vector(g) on any g with underlying insertions because rgroup_df does not contain beta carbons of inserted residues when the difference vectors are computed.

a-r-j commented 1 year ago

Good spot! Yep, this should be removed. I think now that insertion codes are part of residue IDs this shouldn't create any downstream problems.

anton-bushuiev commented 1 year ago

I found another related bug, so I'll make a PR