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

always add dssp_version argument #403

Closed
edikedik opened this issue Jul 18, 2024 · 0 comments
Closed

always add dssp_version argument #403

edikedik opened this issue Jul 18, 2024 · 0 comments

Comments

@edikedik
Copy link

Hi,

I had a nasty bug, such that the DSSP features are silently omitted. This happens due to biopython returning an empty dictionary for newer DSSP versions, for which the old "dssp" format must be specified explicitly. As a result, the dssp_df becomes empty, and the required node features are not added, without throwing any errors (btw, at least checking that the "dssp_df" is not empty might be a good practice).

Anyway, taking this line (

graphein/graphein/protein/features/nodes/dssp.py

Line 113 in 27463a5

dssp_version = re.search(
) out of the if-else expression solves this issue.
a-r-j added a commit that referenced this issue Jul 24, 2024
@a-r-j
fix: improve support for newer dssp versions #403
94d832b
@a-r-j a-r-j mentioned this issue Jul 24, 2024
Merged
5 tasks
a-r-j added a commit that referenced this issue Aug 4, 2024
@a-r-j
fix: improve support for newer dssp versions #403 (#404)
2ebd211 
* fix: improve support for newer dssp versions #403

* docs: rename  arg to newer  arg in documentation notebooks #389

* feat: add decorators for checking python/external dependencies

* feat: add decorators to mol submodule

* feat: decorate pymol

* feat: decorate meshes

* fix: undo dssp tuple unpacking

---------

Co-authored-by: Arian Jamasb <arian.jamasb@roche.com>
@a-r-j a-r-j closed this as completed Sep 18, 2024
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

No branches or pull requests
2 participants
@edikedik @a-r-j