Code

Alphafold3 backend#470

Code

Merged

DimaMolod merged 22 commits intomainKosinskiLab/AlphaPulldown:mainfrom alphafold3_backendKosinskiLab/AlphaPulldown:alphafold3_backendCopy head branch name to clipboardDec 13, 2024

+711-84

Commits

Commits on Dec 2, 2024

• Add alphafold3 submodule

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  10c99ac

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• Add AF3 without dependencies

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• New

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Commits on Dec 3, 2024

• Update alphafold3

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• ap object to folding_input.input converter

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• parse templates from feature dict

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Commits on Dec 4, 2024

• Inherit from FoldingBackend

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Commits on Dec 5, 2024

• Create templates hits using templates.py

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• Works but slow. Use native alphafold3.data.templates.hits instead?

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• Direct transfer of Templates. Dies at:af3.structure.parsing.py:L1576

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Commits on Dec 6, 2024

• Works for monomers. TODO: Compare with native AF3

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  e882e5a

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• Typo

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Commits on Dec 9, 2024

• Fix pdb_code parser

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Commits on Dec 10, 2024

• Small clean up

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  afc99fa

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Commits on Dec 11, 2024

• Added AF3 flags

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  5250afd

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• Fixed jax issue. Works for monomers

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Commits on Dec 12, 2024

• Code refactored. Removed data pipeline

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  cbb7983

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• Added support for multimers

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• Added mamba root prefix env var

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• Use RUNNER_TEMP env var

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• Create AP env locally with prefix

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• use conda-incubator

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