[codex] Reuse existing monomer features in default TrueMultimer mode#609
Merged
[codex] Reuse existing monomer features in default TrueMultimer mode#609
Conversation
![chatgpt-codex-connector[bot]](https://avatars.githubusercontent.com/in/1144995?s=60&v=4){kind=small}
There was a problem hiding this comment.
💡 Codex Review
Here are some automated review suggestions for this pull request.
Reviewed commit: 55af0f777f
ℹ️ About Codex in GitHub
Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you
- Open a pull request for review
- Mark a draft as ready
- Comment "@codex review".
If Codex has suggestions, it will comment; otherwise it will react with 👍.
Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".
…timer-existing-msa # Conflicts: # alphapulldown/scripts/create_individual_features.py
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
This PR fixes the default non-clustered TrueMultimer path so it can reuse precomputed monomer feature pickles instead of requiring fresh MSAs.
Closes #465.
Root Cause
process_multimeric_features()always created a freshMonomericObjectand ran the full AF2 feature pipeline, even when a monomer feature pickle for the original FASTA entry already existed in the output directory. As a result, default TrueMultimer still required the original MSA inputs and database access just to replace template features.What Changed
<output_dir>/<protein>.pklor<output_dir>/<protein>.pkl.xzwhen availableextract_multimeric_template_features_for_single_chain.pkland.pkl.xzsource picklesValidation
PYTHONPATH=/tmp/ap_pyshim:$PYTHONPATH conda run -n AlphaPulldown python -m pytest -q test/integration/test_create_individual_features.py -k 'reuses_existing_source_pickle or process_multimeric_features or create_and_save_monomer_objects'PYTHONPATH=/tmp/ap_pyshim:$PYTHONPATH conda run -n AlphaPulldown python -m pytest -q test/integration/test_create_individual_features.pyNote: the temporary
PYTHONPATHshim was only needed on this workstation to work around local AlphaFold/Biopython version mismatches during test collection. It is not part of the repo changes.