Esmfold

[a-r-j]

Description

Adds support for retrieving predicted structures from ESMFold.

Pull Request Checklist

• [ ] Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md file (if applicable)
• [x] Added appropriate unit test functions in the ./biopandas/*/tests directories (if applicable)
• [x] Modify documentation in the corresponding Jupyter Notebook under biopandas/docs/sources/ (if applicable)
• [x] Ran PYTHONPATH='.' pytest ./biopandas -sv and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv)
• [ ] Checked for style issues by running flake8 ./biopandas

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[rasbt]

@a-r-j It looks all good to me! Just added source='esmfold-v1' as a requirement if someone fetches a sequence. Just so that people now what they are fetching it from.

I noticed that the PDB jupyter notebook is corrupted though. Couldn't open it on my computer, and I also see that that it's the same for Gh rendering: https://github.com/rasbt/biopandas/blob/4515e39861a422c10a8aff7677ecd5aacb031508/docs/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb

Do you have a working version on your computer still? Othewise I will restore it from an earlier commit.

[a-r-j]

Oh gosh, let me see what I can do. Keeping notebooks under version control is always a nightmare.

[a-r-j]

Seems I hadn't resolved all the conflicts when merging. Should be fixed now :)

[rasbt]

Thanks, I will try to check that out today! I will also take care of the docs. But just if you are curious, there are a few notes here: https://biopandas.github.io/biopandas/CONTRIBUTING/#notes-for-the-developers

PS: I transferred the repo to a new BioPandas org. Looks like everything worked pretty smoothly so far

[rasbt]

I think you undid my commits where I added source='esmfold-v1' as a requirement including unit tests 😢

[a-r-j]

Oh gosh, my bad. Looks like I showed up to amateur hour :sweat:

I can't find your changes in the commit history - any chance you have a local copy?

[rasbt]

No worries, thinks happen. Unfortunately, I destroyed them when I pulled your recent branch ... arg