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Update fork to AlphaFold 3 v3.0.4 - #3

Merged

DimaMolod merged 26 commits into

mainfrom

exp/af3-v3.0.4

Oct 7, 2026

Merged

Update fork to AlphaFold 3 v3.0.4#3
DimaMolod merged 26 commits into
mainfrom
exp/af3-v3.0.4

Commits on Jun 23, 2026
- Add early validation that RNG seeds are uint32s
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  a84d263
Commits on Jun 25, 2026
- Add missing type annotations
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  b2f3d45
- Enable Google Cloud Storage (`gs://`) path support in AlphaFold3 using `etils.epath`.
  
  DeepMind
  authored and
  copybara-github
  committed
  37bff5f
Commits on Jul 1, 2026
- Use less memory in the OuterProductMean
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  7b4c2a5
- Fix model loading for etils file providers that do not support `readinto`.
  
  DeepMind
  authored and
  copybara-github
  committed
  b1f7802
Commits on Jul 3, 2026
- No public description
  
  h-joo
  authored and
  copybara-github
  committed
  4958a9b
Commits on Jul 7, 2026
- Add a flag to control whether Terms of Use are saved in the output directory
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  7c1f195
Commits on Jul 8, 2026
- Fix np.savez_compressed failure writing to unseekable epath backends
  
  DeepMind
  authored and
  copybara-github
  committed
  ded9d57
Commits on Jul 9, 2026
- Do not serialize empty templateIndices as None
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  62136ec
- Add chain IDs in the summary confidence JSON for easier use
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  e68269f
- Add a note that user-provided CCD can be used for custom modified polymer residues
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  cbdd420
Commits on Jul 10, 2026
- Add a directory with example input JSON files
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  4d610bc
Commits on Jul 13, 2026
- Delete the ref_pos entry only after the pickle is written
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  0d3facb
Commits on Jul 15, 2026
- Fix numerical instability that prevents AF3 from running without a GPU
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  fd39d2c
Commits on Jul 16, 2026
- Make the num_cpus function compatible with platforms without os.sched_getaffinity (e.g. MacOS)
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  27f4d6d
- Add a flag to run on CPU only
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  7ecd64f
Commits on Jul 17, 2026
- Make run_alphafold runnable without a GPU and on Mac OS
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  f43a5c4
Commits on Jul 21, 2026
- Bump JAX and Tokamax to newer versions to fix unified memory on Blackwell
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  a3b8355
Commits on Jul 23, 2026
- Update the instructions on how to obtain AlphaFold 3 weights
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  dd1a7ba
- Fix broken formatting in the README
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  4e62292
- Replace --use_cpu_only with --jax_backend for future expandability
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  98a15dc
Commits on Jul 26, 2026
- Suppressions for pyrefly
  
  h-joo
  authored and
  copybara-github
  committed
  01bd8d1
Commits on Jul 27, 2026
- Add a missing backslash and remove a trailing one in a multiline command
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8a84535
Commits on Jul 28, 2026
- Add support for using Apple Silicon GPU
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  85c4d20
Commits on Oct 6, 2026
- Update fork to AlphaFold 3 v3.0.4
  
  DimaMolod
  and
  claude
  committed
  de1577e
- Make the data test robust to RDKit/CCD updates
  
  Augustin-Zidek
  authored and
  DimaMolod
  committed
  ba044f4

Commits

Commits on Jun 23, 2026

Commits on Jun 25, 2026

Commits on Jul 1, 2026

Commits on Jul 3, 2026

Commits on Jul 7, 2026

Commits on Jul 8, 2026

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Commits on Jul 13, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 17, 2026

Commits on Jul 21, 2026

Commits on Jul 23, 2026

Commits on Jul 26, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Commits on Oct 6, 2026