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Add chirality checking utility.

Augustin-Zidekpushed 4 commits to main • dc7bb0d…792e61e • 
4 days ago

Update the version in pyproject.toml and version.py to 3.0.1

Augustin-Zidekpushed 2 commits to main • fe088ac…dc7bb0d • 
14 days ago

Add translations of legal terms

Augustin-Zidekpushed 3 commits to main • e7510b1…fe088ac • 
17 days ago

Crop output embeddings to num_tokens, removing padding tokens

Augustin-Zidekpushed 1 commit to main • a3cf058…e7510b1 • 
18 days ago

Check uniqueness and residue numbers when validating bonds

Augustin-Zidekpushed 2 commits to main • 7f6edd0…a3cf058 • 
22 days ago

Fix templates to work with empty a3m

Augustin-Zidekpushed 6 commits to main • 7acc88f…7f6edd0 • 
28 days ago

Make AlphaFold logging more consistent, logical, and brief

Augustin-Zidekpushed 5 commits to main • 231efc9…7acc88f • 
on Jan 27

Antibody-antigen docs: mention that we always used the first bioassembly

Augustin-Zidekpushed 1 commit to main • 20ad0a2…231efc9 • 
on Jan 20

Add antibody-antigen metadata from AlphaFold 3 paper

Augustin-Zidekpushed 1 commit to main • 121716e…20ad0a2 • 
on Jan 20

Provide per-residue pLDDT in the output mmCIF

Augustin-Zidekpushed 1 commit to main • 5c0379c…121716e • 
on Jan 20

Do not test ref_pos which depends on a specific RDKit version

Augustin-Zidekpushed 1 commit to main • 155f844…5c0379c • 
on Jan 16

Fix a typo: featursation -> featurisation

Augustin-Zidekpushed 1 commit to main • f407412…155f844 • 
on Jan 16

Raise when GPU capability is 7 and flash_attention_implementation is …

Augustin-Zidekpushed 1 commit to main • bb9a51b…f407412 • 
on Jan 16

Add num_recycles and num_seeds flags

Augustin-Zidekpushed 1 commit to main • 537a9e1…bb9a51b • 
on Jan 16

Explain the pair_transition_shard_spec format

Augustin-Zidekpushed 1 commit to main • f33a2eb…537a9e1 • 
on Jan 16

jax.numpy.clip: update use of deprecated arguments

Augustin-Zidekpushed 1 commit to main • ea04034…f33a2eb • 
on Jan 16

Use true chain type for paired_msa creation

andycowiepushed 1 commit to main • 3d06f4b…ea04034 • 
on Jan 9

Fix RASA calculation to work with arbitrary chain IDs

Augustin-Zidekpushed 1 commit to main • 17b02c9…3d06f4b • 
on Jan 9

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

Augustin-Zidekpushed 1 commit to main • 765844c…17b02c9 • 
on Jan 9

Test embedding shapes

Augustin-Zidekpushed 1 commit to main • 721348d…765844c • 
on Jan 9

Add documentation for the embeddings output file

Augustin-Zidekpushed 1 commit to main • 1bb31e7…721348d • 
on Jan 9

Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD

Augustin-Zidekpushed 1 commit to main • a647a31…1bb31e7 • 
on Jan 6

Fix incorrect bonds in the input documentation

Augustin-Zidekpushed 1 commit to main • a9c8831…a647a31 • 
on Jan 6

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

Augustin-Zidekpushed 1 commit to main • 4b6b605…a9c8831 • 
on Jan 6

Split Evoformer network into own module, move primary model network t…

Augustin-Zidekpushed 1 commit to main • 9b7d229…4b6b605 • 
on Jan 6

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

Augustin-Zidekpushed 1 commit to main • d691231…9b7d229 • 
on Jan 6

Rename "diffusion" dir to "network" and "model.Diffuser" to "alphafol…

Augustin-Zidekpushed 1 commit to main • b380a7c…d691231 • 
on Jan 6

Fix a typo in the input documentation for the mmcifPath

Augustin-Zidekpushed 1 commit to main • 4158f7a…b380a7c • 
on Dec 20, 2024

Add a comment that HMMER can also be installed using apt instead of b…

Augustin-Zidekpushed 1 commit to main • 06871f3…4158f7a • 
on Dec 20, 2024

Remove abstract model setup, use one concrete model and config

Augustin-Zidekpushed 1 commit to main • e368322…06871f3 • 
on Dec 20, 2024