Activity
Add chirality checking utility.
Add chirality checking utility.
Update the version in pyproject.toml and version.py to 3.0.1
Update the version in pyproject.toml and version.py to 3.0.1
Add translations of legal terms
Add translations of legal terms
Crop output embeddings to num_tokens, removing padding tokens
Crop output embeddings to num_tokens, removing padding tokens
Check uniqueness and residue numbers when validating bonds
Check uniqueness and residue numbers when validating bonds
Fix templates to work with empty a3m
Fix templates to work with empty a3m
Make AlphaFold logging more consistent, logical, and brief
Make AlphaFold logging more consistent, logical, and brief
Antibody-antigen docs: mention that we always used the first bioassembly
Antibody-antigen docs: mention that we always used the first bioassembly
Add antibody-antigen metadata from AlphaFold 3 paper
Add antibody-antigen metadata from AlphaFold 3 paper
Provide per-residue pLDDT in the output mmCIF
Provide per-residue pLDDT in the output mmCIF
Do not test ref_pos which depends on a specific RDKit version
Do not test ref_pos which depends on a specific RDKit version
Fix a typo: featursation -> featurisation
Fix a typo: featursation -> featurisation
Raise when GPU capability is 7 and flash_attention_implementation is …
Raise when GPU capability is 7 and flash_attention_implementation is …
Add num_recycles and num_seeds flags
Add num_recycles and num_seeds flags
Explain the pair_transition_shard_spec format
Explain the pair_transition_shard_spec format
jax.numpy.clip: update use of deprecated arguments
jax.numpy.clip: update use of deprecated arguments
Use true chain type for paired_msa creation
Use true chain type for paired_msa creation
Fix RASA calculation to work with arbitrary chain IDs
Fix RASA calculation to work with arbitrary chain IDs
Make it possible to set which GPU to use on a multi-GPU system
Make it possible to set which GPU to use on a multi-GPU system
Add documentation for the embeddings output file
Add documentation for the embeddings output file
Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD
Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD
Fix incorrect bonds in the input documentation
Fix incorrect bonds in the input documentation
Remove allow_pickle=True which does not exist in Numpy < 2.2.0
Remove allow_pickle=True which does not exist in Numpy < 2.2.0
Split Evoformer network into own module, move primary model network t…
Split Evoformer network into own module, move primary model network t…
Include the detailed error message directly in the top-level one
Include the detailed error message directly in the top-level one
Rename "diffusion" dir to "network" and "model.Diffuser" to "alphafol…
Rename "diffusion" dir to "network" and "model.Diffuser" to "alphafol…
Fix a typo in the input documentation for the mmcifPath
Fix a typo in the input documentation for the mmcifPath
Add a comment that HMMER can also be installed using apt instead of b…
Add a comment that HMMER can also be installed using apt instead of b…
Remove abstract model setup, use one concrete model and config
Remove abstract model setup, use one concrete model and config