-
Notifications
You must be signed in to change notification settings - Fork 181
Open
Conversation
jamesmkrieger
commented
May 8, 2025
Contributor
Author
probably we need more tests for this
jamesmkrieger
marked this pull request as draft
May 8, 2025 13:53
jamesmkrieger
force-pushed
the
fix_fetchPDB_cif
branch
from
August 20, 2025 09:39
cf351ad to
d3c007e
Compare
jamesmkrieger
marked this pull request as ready for review
August 20, 2025 10:03
jamesmkrieger
commented
Aug 20, 2025
Contributor
Author
This won't fix the pfam gzip error, but it will at least make things slightly less cryptic
AnthonyBogetti
commented
Dec 4, 2025
Member
@anupam-banerjee Does any of this conflict with your PR #2165 ?
jamesmkrieger
commented
Dec 4, 2025
Contributor
Author
It shouldn't do because it barely touches the actually parsing functions and it's a different one that is touched
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Bug 1: parseMMCIF was taking .pdb files if they were found. This is solved by adding the format to the second run of findPDBFiles in fetchPDB.
Bug 2: non-pdb files couldn't be retrieved from the PDBe as the extension replacement wasn't being done. This is fixed by making the replacement from .ent as well as .pdb