[ENH] Replace PFOA with 5NU7 and 1BRQ #198
Open
Conversation
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
fkiraly
requested changes
Nov 25, 2025
Contributor
There was a problem hiding this comment.
I think you can already see by the fact that so many locations are affected that something isn't quite right.
- can you add loaders
load_5nu7andload_1brqto be used in example code? - Why are you just deleting the 1GNH and PFOA loaders? I see no reason for that, add them back please.
- the function
structure_loaderfeels unnecessary. It just aliasesPDBParser.get_structure. Youcan also see that it was a bad idea since you need to use unnevessarylambdaexpressions to make current code work. I suggest: remove. - the function
mol_loaderfeels unnecssary. It just aliasesMoleculeLoader.__init__. It would be useful of allpdbstrings could be used, but currently only two can? I suggest: remove.
satvshr
changed the title
fkiraly
reviewed
Nov 30, 2025
| "load_aptacom_x_y", | ||
| "load_csv_dataset", | ||
| "load_hf_dataset", | ||
| "load_pfoa", |
Contributor
There was a problem hiding this comment.
seems like some exports get deleted - why?
Contributor
|
as discussed. Please do not delete the code for PFOA. |
Collaborator
Author
We had discussed in a meeting (where you were not present) where I asked everyone if PFOA is useful given it has no SEQRES or ATOM records and everyone said that we had no use for it given we cannot extract a sequence from it, hence it was removed. |
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Outdated suggestions cannot be applied.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.
Fixes #197.
from the issue description: As discussed in the weekly on 20/11/2025 we will be replacing PFOA with 5NU7 and 1BRQ, given that is what is mostly used by the corporation partners of ecoSPECS. I am going to directly add them to the library as they are about 200kb in size.