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Merged
merged 117 commits into from
Sep 30, 2024
Merged

v0.5.0 - Add results with AlphaFold 3 predicted structures and for Chai-1 #7

merged 117 commits into from
Sep 30, 2024

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amorehead
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@amorehead amorehead commented Sep 30, 2024 •
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What does this PR do?

Introduces PoseBench 0.5.0

Additions:

  • Adds results with AlphaFold 3 predicted structures (now the default)
  • Adds results for the new Chai-1 model from Chai Discovery
  • Adds a new inference sweep pipeline for HPC clusters to allow users to quickly run an exhaustive sweep of all baseline methods, datasets, and tasks e.g., using generated batch scripts and a SLURM scheduler

Updates:

  • Updates all Zenodo links to point to the latest version of the project's Zenodo record, which now includes the above-mentioned AlphaFold 3 predicted structures and baseline method results using them
  • Updates documentation project-wide according to the additions listed above

Fixes:

  • Fixes some CI testing issues

Before submitting

  • Did you make sure title is self-explanatory and the description concisely explains the PR?
  • Did you make sure your PR does only one thing, instead of bundling different changes together?
  • Did you list all the breaking changes introduced by this pull request?
  • Did you run pre-commit hooks with pre-commit run -a command?

Did you have fun?

Make sure you had fun coding 🙃

amorehead added 30 commits August 13, 2024 10:56
@amorehead
Generify ESMFold references en masse
b7b0858
@amorehead
Update paths to CASP15 predicted structures
b569c63
@amorehead
Begin adding sweep config
df94ae1
@amorehead
Finish implementation of inference script builder
2580c5d
@amorehead
Clean up inference script builder for Vina
c23b888
@amorehead
Fix small bugs
457a09d
@amorehead
Inform user
9e16717
@amorehead
Update .gitignore
a12bcc1
@amorehead
Activate env during runs
bbb967a
@amorehead
Specify runs' CUDA device index
1e03264
@amorehead
Adjust outputs for Conda
b519e7b
@amorehead
Remove PWD
56202cf
@amorehead
Update README and docs
7be0aa0
@amorehead
Reference Conda env prefix for PoseBench HPC environment
ad64779
@amorehead
Reduce min jaxtyping version
deeb6d2
@amorehead
Undo last commit
83c9628
@amorehead
Make posebench pip package compatible with Python 3.7 and up
d2da9c8
@amorehead
Merge branch 'main' of https://github.com/BioinfoMachineLearning/Pose…
7560dd7 
…Bench into af
@amorehead
Add missing packages to pyproject.yaml
5c879d9
@amorehead
Merge branch 'main' of https://github.com/BioinfoMachineLearning/Pose…
4ce797b 
…Bench into af
@amorehead
Document prefix
7886b3c
@amorehead
Add missing argument
f06888d
@amorehead
Correct Bash header
66188f9
@amorehead
Clean out local pre-commit cache to fix notebook formatting, and upgr…
4233a69 
…ade workflow extensions
@amorehead
Document DiffDock-L and DynamicBind's occasional numerical instabilit…
215d2a6 
…ies for the CASP15 dataset
@amorehead
Handle Astex Diverse inputs parsing more elegantly
a7d2503
@amorehead
Rename no_pretraining to no_ilcl
a374ea3
@amorehead
Add ability to sweep pocket-only baselines on PoseBusters Benchmark set
1dc7895
@amorehead
Make printout more verbose
522c090
@amorehead
Differentiate with relax_protein=true
ae7fd8c
amorehead and others added 24 commits August 29, 2024 18:10
@amorehead amorehead changed the title Add results with AlphaFold 3 predicted structures (now the default) and for Chai-1 v0.5.0 - Add results with AlphaFold 3 predicted structures and for Chai-1 Sep 30, 2024
@amorehead amorehead merged commit 4ac71fd into main Sep 30, 2024
4 checks passed
@amorehead amorehead deleted the af branch September 30, 2024 16:18
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