Add ESMFold #19977
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Add ESMFold #19977
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The documentation is not available anymore as the PR was closed or merged. |
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Merging for now, there are still a few improvements needed (example in a docstring for instance) but they can go in their own PRs :-) |
amyeroberts
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Nov 1, 2022
* initial commit * First draft that gets outputs without crashing! * Add all the ported openfold dependencies * testing * Restructure config files for ESMFold * Debugging to find output discrepancies * Mainly style * Make model runnable without extra deps * Remove utils and merge them to the modeling file * Use correct gelu and remove some debug prints * More cleanup * Update esm docs * Update conversion script to support ESMFold properly * Port some top-level changes from ESMFold repo * Expand EsmFold docstrings * Make attention_mask optional (default to all 1s) * Add inference test for ESMFold * Use config and not n kwargs * Add modeling output class * Remove einops * Remove chunking in ESM FFN * Update tests for ESMFold * Quality * REpo consistency * Remove tree dependency from ESMFold * make fixup * Add an error in case my structure map function breaks later * Remove needless code * Stop auto-casting the LM to float16 so CPU tests pass * Stop auto-casting the LM to float16 so CPU tests pass * Final test updates * Split test file * Copyright and quality * Unpin PyTorch to see built doc * Fix config file to_dict() method * Add some docstrings to the output * Skip TF checkpoint tests for ESM until we reupload those * make fixup * More docstrings * Unpin to get even with main * Flag example to write Co-authored-by: Sylvain Gugger <Sylvain.gugger@gmail.com>
amyeroberts
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Nov 3, 2022
* initial commit * First draft that gets outputs without crashing! * Add all the ported openfold dependencies * testing * Restructure config files for ESMFold * Debugging to find output discrepancies * Mainly style * Make model runnable without extra deps * Remove utils and merge them to the modeling file * Use correct gelu and remove some debug prints * More cleanup * Update esm docs * Update conversion script to support ESMFold properly * Port some top-level changes from ESMFold repo * Expand EsmFold docstrings * Make attention_mask optional (default to all 1s) * Add inference test for ESMFold * Use config and not n kwargs * Add modeling output class * Remove einops * Remove chunking in ESM FFN * Update tests for ESMFold * Quality * REpo consistency * Remove tree dependency from ESMFold * make fixup * Add an error in case my structure map function breaks later * Remove needless code * Stop auto-casting the LM to float16 so CPU tests pass * Stop auto-casting the LM to float16 so CPU tests pass * Final test updates * Split test file * Copyright and quality * Unpin PyTorch to see built doc * Fix config file to_dict() method * Add some docstrings to the output * Skip TF checkpoint tests for ESM until we reupload those * make fixup * More docstrings * Unpin to get even with main * Flag example to write Co-authored-by: Sylvain Gugger <Sylvain.gugger@gmail.com>
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cc @sgugger @LysandreJik @tomsercu @rmrao @nikitos9000
Opening a draft PR because deadlines are getting tight and I'd like to get everyone on the same page!
What's done:
openfoldEsmForProteinFoldingTODO:
transformersrootAdd an auto class for protein folding?openfoldfunctions/methods that aren't being calledopenfoldport into a single dir/fileopenfoldcode is correctly licencedAdd auxiliary method(s) to convert the outputs into bio file formats likepdb