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Update fork to AlphaFold 3 v3.0.3 - #1

Merged

DimaMolod merged 67 commits into

mainfrom

ap-gapped-discontinuous-chains-v3.0.3

Jun 15, 2026

Merged

Update fork to AlphaFold 3 v3.0.3#1
DimaMolod merged 67 commits into
mainfrom
ap-gapped-discontinuous-chains-v3.0.3

Commits on Nov 30, 2025
- Migrate AF3 to `tokamax.gated_linear_unit` and `tokamax.dot_product_attention`.
  
  rpachauri
  authored and
  copybara-github
  committed
  3890782
Commits on Dec 2, 2025
- remove unused msa and template store code.
  
  joshabramson
  authored and
  copybara-github
  committed
  3a09f04
Commits on Jan 9, 2026
- Add CONTRIBUTING.md
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8eaae04
- Upgrade GitHub Actions to the latest version (v6)
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  a701815
- Update tokamax dependency to version 0.0.8
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  b78e215
Commits on Jan 12, 2026
- Update CONTRIBUTING.md with a policy for AI-generated code
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  d7ab550
Commits on Jan 14, 2026
- Force the legacy git backend to prevent build errors with new git versions
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  2f40800
Commits on Jan 15, 2026
- Modernize setup, switch to Python 3.12, and migrate to uv
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8d37fc1
- Add JAAG to community tools documentation
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  3e2bc0c
- Make everything past model_runner mandatory kwarg in process_fold_input
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8d0a8db
- Add a flag to compress large output files using zstandard
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  f6032f0
Commits on Jan 16, 2026
- Add a documentation on model parameters
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  c7a1ad5
Commits on Jan 20, 2026
- Make AlphaFold 3 uv setup compatible with aarch64
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  22b9ab8
Commits on Jan 29, 2026
- Add the glycan modeling paper in the list of community tools
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  6b50e38
Commits on Feb 4, 2026
- Use UV_LINK_MODE=copy to prevent Docker build issues on some platforms
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  cf4bb5b
- Update RDKit to 2025.9.4
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  c13d928
- Update Tokamax to 0.0.10
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  ebfe70a
Commits on Feb 9, 2026
- Move CONTRIBUTING.md to the root directory
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  ceb3229
Commits on Feb 11, 2026
- Implement relevant improvements from #615
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  e2b8ffd
Commits on Feb 16, 2026
- Use the logging name instead of the one from fold_input
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  2761bf1
- Make sharded Jackhmmer result merging more robust in case of e-value ties
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  703d5c8
Commits on Feb 20, 2026
- Exit if any of the required programs is not installed
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  c20f070
- Update Docker build instructions for AlmaLinux/Rocky/RHEL users
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  ea16676
- Document the discrepancy between AlphaFold 3 and AlphaFold Server in Known Issues
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  4ca8a65
Commits on Feb 23, 2026
- Use const for iter/keys/values/items and release GIL for contains in KeyView
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  203e93d
- Add CifDict.to_dict() method for faster serialisation
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  9e10da6
Commits on Feb 25, 2026
- Respect LIBCIFPP_DATA_PATH if set, rather than attempt to find it.
  
  jsspencer
  authored and
  copybara-github
  committed
  1e9ece2
Commits on Feb 26, 2026
- Remove unused utility functions
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  6daafb5
Commits on Mar 4, 2026
- Use the same license format in .h files as in .cc files
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  e58932a
Commits on Mar 6, 2026
- Improve the error when components.cif is not found
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  5f7eb57
Commits on Mar 10, 2026
- Update to Tokamax 0.0.11 and JAX 0.9.1
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  608edb6
Commits on Mar 20, 2026
- Use `--run_*=false` instead of `--norun_*` in docs.
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  02650a5
Commits on Mar 25, 2026
- wrap reader into io.BufferedReader.
  
  akviz
  authored and
  copybara-github
  committed
  0f82e0c
Commits on Mar 30, 2026
- Fix some Structure type issues uncovered by Pyrefly
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  58d22e2
Commits on Mar 31, 2026
- Import from collections.abc instead of typing
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  4d20ed5
Commits on Apr 1, 2026
- Use && instead of ; when building HMMER to stop if there are errors
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  f236bc4
- Add a missing newline for consistency
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  87bd9e6
Commits on Apr 9, 2026
- Remove obsolete `: ...` from all python functions parameters annotations.
  
  QEDady
  authored and
  copybara-github
  committed
  177df6a
Commits on Apr 10, 2026
- Expose an API to run the model pipeline with a Structure
  
  DeepMind
  authored and
  copybara-github
  committed
  24cded8
Commits on Apr 20, 2026
- Bump the version to v3.0.2
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  f6a5aec
Commits on Apr 21, 2026
- Optimize CIF loop parsing by ~4% - remove modulo in the hot path
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  cfeeedd
Commits on Apr 22, 2026
- Clean up structure cleaning - remove unused code paths
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  e9adcd4
- Use pathlib.Path.home() instead of os.environ.get('HOME')
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  6f882ad
- Remove unused cleaned_struc from ConvertModelOutput
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  de4e7a4
Commits on Apr 23, 2026
- Support dynamic version for dev and releases
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  3dfc5a9
Commits on Apr 24, 2026
- Refactor to_mmcif_dict to not use getattr
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  011b6cf
Commits on May 6, 2026
- Add fallback version for Docker
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  481beec
- Pass correctly all options to Jackhmmer/Nhmmer
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  97639ff
- Fix glycan O1 leaving-atom cleanup for standalone glycans
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  62a93af
Commits on May 7, 2026
- Fix typing of Nhmmer z values, these are floats
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  eba6189
Commits on May 11, 2026
- Validate that the output_dir is always set and add a missing argument in overload
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8850da4
- Fix a typing issue (passing ndarray instead of a list)
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8812124
Commits on May 12, 2026
- Add basic chem_comp_atoms/chem_comp_bonds data to ChemCompEntry
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  8d283f3
- Fix KeyError in string_array.remap_multiple for Python 3.14
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  9ea7db2
Commits on May 13, 2026
- Fix typing issues found using Pyrefly in folding_input and its test
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  9556a1c
Commits on May 14, 2026
- Fix typing issue in _get_rna_msa revealed by Pyrefly
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  10b18bf
Commits on May 18, 2026
- Fix typing issues in constants modules revealed by Pyrefly
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  5a3d6b6
Commits on May 20, 2026
- Fix typing issues revealed by Pyrefly in structure_tables
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  7d4a236
Commits on May 22, 2026
- Fix descriptions being dropped in some places for protein/RNA chains
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  b712a3d
Commits on May 28, 2026
- Fix two typos in docstrings
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  eb5154f
Commits on May 29, 2026
- Improve typing and error checks in mask_mean
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  1dc1e0a
Commits on Jun 3, 2026
- Speed up serialization of the confidences JSON ~30x
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  3aea02b
Commits on Jun 8, 2026
- Fix typing issue (Numpy 1D array instead of a float)
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  f971361
Commits on Jun 9, 2026
- Change the code license from CC BY-NC-SA 4.0 to Apache 2.0
  
  Augustin-Zidek
  authored and
  copybara-github
  committed
  7b197fe
Commits on Jun 15, 2026
- Support gapped residue ids for discontinuous chains
  DimaMolod
  committed
  dee2262
- Preserve duplicate residue IDs in structure tables
  DimaMolod
  committed
  c494eb8
- Mark fork main as merged into v3.0.3 update
  DimaMolod
  committed
  9e35ea9

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