Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Closed
anton-bushuiev opened this issue Apr 15, 2023 · 2 comments · Fixed by #305
Closed

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

anton-bushuiev opened this issue Apr 15, 2023 · 2 comments · Fixed by #305

Comments

@anton-bushuiev
Copy link
Contributor

Hi 👋!

Is remove_insertions here on purpose or just a legacy part from the times when insertion codes were always removed?

graphein/graphein/protein/graphs.py

Line 540 in 649a490

rgroup_df=compute_rgroup_dataframe(remove_insertions(raw_pdb_df)),

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
Copy link
Owner

a-r-j commented Apr 15, 2023

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
Copy link
Contributor Author

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

@anton-bushuiev anton-bushuiev mentioned this issue Apr 16, 2023
Merged
5 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Fix and enhance geometric node features anton-bushuiev/graphein
2 participants
@a-r-j @anton-bushuiev