test modification of intermediate structural representations

[stephprince]

Motivation

These changes add analysis scripts and methods to test how alphafold outputs change when manipulating the intermediate structural representations during the recycling process.

See related PR changes in lbl-cbg/alphafold#1 and lbl-cbg/ColabFold#1 to run.

How to test the behavior?

0. Pull related PRs from lbl-cbg ColabFold/alphafold repos.
1. Add conformer pair data to metfish/data folder.
2. Run preprocess_conformer_pairs.py to generate pdb, fasta, and pickle files to use as inputs to AF.
3. Run colabfold_batch with the following arguments to modify the intermediate structural representations.

colabfold_batch --save-all --save-recycles --num-recycle=5 --modification_method="replace_structure" ${INPUT} ${OUTPUT_DIR}

4. Visualize results using the scripts/plot_conformer_pair_outcomes.ipynb notebook

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
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• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

❌ Patch coverage is 23.59551% with 68 lines in your changes missing coverage. Please review.
✅ Project coverage is 46.62%. Comparing base (aab0700) to head (3a64fa6).
⚠️ Report is 11 commits behind head on main.

Files with missing lines	Patch %	Lines
src/metfish/utils.py	23.59%	68 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main       #3       +/-   ##
===========================================
- Coverage   80.95%   46.62%   -34.34%     
===========================================
  Files           2        2               
  Lines          63      148       +85     
===========================================
+ Hits           51       69       +18     
- Misses         12       79       +67     

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[smallfishabc]

I think we should use SeqIO in the BioPython to extract sequences. And I think we should avoid using Biopandas if BioPython can do the job to keep the simplicity of the dependency.