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google-deepmind / alphafold

Open source code for AlphaFold.
Apache License 2.0
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Fix deprecation warning / error from BioPython #954

Open edawson opened 1 week ago

edawson commented 1 week ago

Hi,

Here is a small PR to fix a deprecation issue related to BioPython. It would be great if y'all could run this through CI to make sure it doesn't have any side effects, but BioPython seems to promise it's a safe change.

Description:

This PR swaps the BioPython.SCOPData module import in the mmcif_parsing module for BioPython.PDBData.

Related issue:

See https://github.com/biopython/biopython/blob/master/DEPRECATED.rst#biodatascopdata for information about the SCOPData deprecation.

Motivation:

SCOPData was removed in version 1.82 of BioPython, so its usage throws an error when imported. This change allows upgrading BioPython beyond version 1.79, which brings improvements in security and stability. I had been trying to use AlphaFold2 with an updated BioPython but kept receiving deprecation warnings / errors depending on which version I was using.

Verification

[X] Package still installs after change [X] run_alphafold_test.py returns ok after this change.

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