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Commits on Jan 9, 2025

• Use true chain type for paired_msa creation

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  andycowie

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• Fix RASA calculation to work with arbitrary chain IDs

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  Augustin-Zidek

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• Make it possible to set which GPU to use on a multi-GPU system

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  Augustin-Zidek

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• Test embedding shapes

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  Augustin-Zidek

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• Add documentation for the embeddings output file

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  Augustin-Zidek

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Commits on Jan 6, 2025

• Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD

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  Augustin-Zidek

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• Fix incorrect bonds in the input documentation

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  Augustin-Zidek

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• Remove allow_pickle=True which does not exist in Numpy < 2.2.0

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  Augustin-Zidek

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• Split Evoformer network into own module, move primary model network to model/model.py

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  Augustin-Zidek

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• Include the detailed error message directly in the top-level one

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  Augustin-Zidek

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• Rename "diffusion" dir to "network" and "model.Diffuser" to "alphafold3.AlphaFold3"

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  Augustin-Zidek

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Commits on Dec 20, 2024

• Fix a typo in the input documentation for the mmcifPath

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  Augustin-Zidek

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• Add a comment that HMMER can also be installed using apt instead of building it from source

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  Augustin-Zidek

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• Remove abstract model setup, use one concrete model and config

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  Augustin-Zidek

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Commits on Dec 19, 2024

• Add an option to return model embeddings and write them to file

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  Augustin-Zidek

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• Update custom ligand input documentation

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  Augustin-Zidek

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• Add a conformer_max_iterations flag to allow increasing number of RDKit iterations

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  Augustin-Zidek

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Commits on Dec 18, 2024

• Document SMILES string escaping in the input JSON

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  Augustin-Zidek

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• Include MSA and template counts in pipeline logs

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  Augustin-Zidek

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Commits on Dec 17, 2024

• Filter correctly invalid division warning that can be encountered

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  Augustin-Zidek

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• Fix double spaces in two print statements

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  Augustin-Zidek

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• Make all chain constructors keyword-only

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  Augustin-Zidek

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• Fix a typo in the input format documentation

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  Augustin-Zidek

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• Deal properly with non-standard residues in the single-letter sequence

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  Augustin-Zidek

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• Remove unnecessary logging and improve error messages regarding input format

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  Augustin-Zidek

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Commits on Dec 13, 2024

• Small fix for numerical precision when handling PIDs in pallas kernel.

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  jacobjinkelly

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• Add XLA flag workaround for CUDA Capability 7.x GPUs

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  jacobjinkelly

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Commits on Dec 10, 2024

• Expand documentation around running run_alphafold.py

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  jsspencer

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• Create basic Github CI

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  jsspencer

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• Point users towards the many useful command-line flags for run_alphafold.py.

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  jsspencer

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• Use same filename for run_alphafold example input as used in the example command.

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  jsspencer

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• Raise clear errors if cannot create molecule definitions.

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  jsspencer

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• Use OpenEye canonical SMILES when available.

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  jsspencer

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• Remove option to not include intra-ligand bond information.

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  jsspencer

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Commits on Dec 9, 2024

• Simplify logic for reference structure creation

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  Augustin-Zidek

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