Copy alphafold from colabfold #1
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…es to be removed - change Protein.to_pdb back to default implementation
important for batch compute that uses masking
* fix memory leaks * use bfloat16 for representations * move confidence compute inside module.py * move multimer key splitting to model.py
* fix memory leaks various edits to fix memory leaks memory leak fix * v2.3.4 - fix memory leaks another attempt to fix memory leaks! * Update config.py * bugfix - num-ensemble
Update OpenMM imports to work with new OpenMM API
msa_activation is (N,L,256) in colabfold v1.5.2 we return msa_activation[0] as our single representation vector looks like there is one extra linear layer to convert msa_activations[0] to single_activation:  If anything the (L,256) representation might be better, as you might be losing some information by doing the extra transformation at the end. But since people are asking, I'm adding the transformation back so that the output is (L,386). typo
oruebel
approved these changes
Dec 19, 2023
stephprince
approved these changes
Dec 19, 2023
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This PR merges the version of alphafold used for ColabFold. I am copying their version over so we can work on a version of alphafold that will work with ColabFold.
When you install ColabFold locally, it will install alphafold from this PyPI package, which I believe is just a fork of DeepMind's alphafold repository that they've modified to work with the rest of the ColabFold code base.
Since we've decided to work with ColabFold, I thought it would be good to have their modifications in our codebase to build on top of.