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Update fork to AlphaFold 3 v3.0.3#1

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DimaMolod merged 67 commits into
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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

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@DimaMolod

@DimaMolod DimaMolod commented Jun 15, 2026

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Summary

  • Update the KosinskiLab AlphaFold 3 fork to official google-deepmind/alphafold3 v3.0.3 (7b197fe859790fc3e04d03ea70dd0b9ba48881c9).
  • Reapply the AlphaPulldown-specific gapped/discontinuous residue ID support commits on top.
  • Keep the Tokamax/JAX 0.9 RTX/Blackwell-compatible ancestry introduced before v3.0.2.

Validation

  • git merge-base --is-ancestor v3.0.3 HEAD -> yes.
  • git merge-base --is-ancestor 389078218c0604cf85caf4e2e9a830e456ff31d1 HEAD -> yes.
  • git merge-base --is-ancestor 608edb684db9f6fd0e677fea01c4cefc60f8a8aa HEAD -> yes.
  • python -m compileall src/alphafold3/common/folding_input.py src/alphafold3/structure/parsing.py src/alphafold3/structure/structure_tables.py -> passed via AlphaPulldown checkout.
  • AlphaPulldown AF3 backend helper tests with this submodule -> 30 passed.

Follow-up AlphaPulldown submodule PR: KosinskiLab/AlphaPulldown#625

rpachauri and others added 30 commits November 29, 2025 19:03
@rpachauri @copybara-github
Migrate AF3 to tokamax.gated_linear_unit and `tokamax.dot_product_a…
3890782 
…ttention`.

PiperOrigin-RevId: 838262306
Change-Id: I321a78b2a7d0d5cdeabe797c59b1e9c03e33780d
@joshabramson @copybara-github
remove unused msa and template store code.
3a09f04 
PiperOrigin-RevId: 839187236
Change-Id: I5144812d68e0525f3ea84f32a94d0f4ab89b43ec
@Augustin-Zidek @copybara-github
Add CONTRIBUTING.md
8eaae04 
PiperOrigin-RevId: 854113365
Change-Id: I1a45e75f3138d848943e1442e1d0b1787f1f699f
@Augustin-Zidek @copybara-github
Upgrade GitHub Actions to the latest version (v6)
a701815 
Thanks to salmanmkc@ who suggested this in google-deepmind/alphafold3#571.

PiperOrigin-RevId: 854113440
Change-Id: Ib71810028c7492604978eb1c2f9e46d5f57486b5
@Augustin-Zidek @copybara-github
Update tokamax dependency to version 0.0.8
b78e215 
* This fixes an issue with immutabledict dependency missing in previous versions of Tokamax.
* JAX and Haiku have to be updated as well.

PiperOrigin-RevId: 854207701
Change-Id: I8c30856504f44e43e3a058e89b0866922ca56a5b
@Augustin-Zidek @copybara-github
Update CONTRIBUTING.md with a policy for AI-generated code
d7ab550 
PiperOrigin-RevId: 855264083
Change-Id: I0c6b826c2edf3a0939d03407cf6e9ddaf8d383f6
@Augustin-Zidek @copybara-github
Force the legacy git backend to prevent build errors with new git ver…
2f40800 
…sions

PiperOrigin-RevId: 856186746
Change-Id: I447a4a3ab65674da75a908816208a6fe377232ed
@Augustin-Zidek @copybara-github
Modernize setup, switch to Python 3.12, and migrate to uv
8d37fc1 
PiperOrigin-RevId: 856564478
Change-Id: I31af1c170846fb787235dfc03b3a6da0464f51be
@Augustin-Zidek @copybara-github
Add JAAG to community tools documentation
3e2bc0c 
Addresses:
* google-deepmind/alphafold3#583
* google-deepmind/alphafold3#537
PiperOrigin-RevId: 856584357
Change-Id: Ifdd92878a01f30512381302cc0945cb454e9db1d
@Augustin-Zidek @copybara-github
Make everything past model_runner mandatory kwarg in process_fold_input
8d0a8db 
PiperOrigin-RevId: 856615431
Change-Id: I1e2a126e96e16dd2660f6e9fec9d9ffa02eeb7b2
@Augustin-Zidek @copybara-github
Add a flag to compress large output files using zstandard
f6032f0 
Inspired by google-deepmind/alphafold3#544 (thank you @ntnn19), but with some differences:
1. Uses zstandard instead of gzip for faster compression times and better compression ratios.
2. Compresses only large files.
3. Doesn't compress already compressed files (distogram and embeddings).
4. Doesn't write large temporary files, compresses directly.

PiperOrigin-RevId: 856630504
Change-Id: I4413e26c9d2e8e4592c372dc675dcfa6044fc257
@Augustin-Zidek @copybara-github
Add a documentation on model parameters
c7a1ad5 
Addresses google-deepmind/alphafold3#594.

PiperOrigin-RevId: 857083798
Change-Id: I1d8e42ab6e53075a2c05d70d10a14a8e686fa566
@Augustin-Zidek @copybara-github
Make AlphaFold 3 uv setup compatible with aarch64
22b9ab8 
Addresses google-deepmind/alphafold3#593.

PiperOrigin-RevId: 858480255
Change-Id: I7862b204300d137e367bbaaf31213f7164fdd8d1
@Augustin-Zidek @copybara-github
Add the glycan modeling paper in the list of community tools
6b50e38 
Adapted from https://github.com/google-deepmind/alphafold3/pull/608/changes, thanks @chinchc.

PiperOrigin-RevId: 862720014
Change-Id: I021eef0b46158e8ce28e97d9172ba6e79ef3f30c
@Augustin-Zidek @copybara-github
Use UV_LINK_MODE=copy to prevent Docker build issues on some platforms
cf4bb5b 
Relevant issues:
* google-deepmind/alphafold3#603
* google-deepmind/alphafold3#612

PiperOrigin-RevId: 865416421
Change-Id: Idaf8e531a62638bce5e0748f64a7ddc00b554677
@Augustin-Zidek @copybara-github
Update RDKit to 2025.9.4
c13d928 
PiperOrigin-RevId: 865437867
Change-Id: Iaa116d661bb5743e285efcfe7115f8242f7c0db9
@Augustin-Zidek @copybara-github
Update Tokamax to 0.0.10
ebfe70a 
* Removes transitive TensorFlow dependency and others.
* Remove setuptools dependency which is no longer needed.
* Bump JAX to 0.8.2 (required by Tokamax).

PiperOrigin-RevId: 865449256
Change-Id: Iab74fa7ccf36db5c38e7c3d3d37e818a1d9d3952
@Augustin-Zidek @copybara-github
Move CONTRIBUTING.md to the root directory
ceb3229 
PiperOrigin-RevId: 867451876
Change-Id: Ibdaaee8902a1c1150e99225632300778c016f5f6
@Augustin-Zidek @copybara-github
Implement relevant improvements from #615
e2b8ffd 
PiperOrigin-RevId: 868589660
Change-Id: Iac82ddf73f9f82118b935550afbe0ea13f6cd2eb
@Augustin-Zidek @copybara-github
Use the logging name instead of the one from fold_input
2761bf1 
PiperOrigin-RevId: 870860151
Change-Id: I1d4485e1e08c3ca790899c33190b989d103eaf56
@Augustin-Zidek @copybara-github
Make sharded Jackhmmer result merging more robust in case of e-value …
703d5c8 
…ties

E-values could be equal, but bit score might have higher resolution. Use that for tie brakes before resorting to the name.

PiperOrigin-RevId: 870903887
Change-Id: I5c8648456c85ef4d1ff4dfeb15b459ba204184e3
@Augustin-Zidek @copybara-github
Exit if any of the required programs is not installed
c20f070 
Thanks for the suggestion, @Ashutosh0x.

PiperOrigin-RevId: 872800291
Change-Id: If1266222844de98850b7ae4141e2f50001cc4d63
@Augustin-Zidek @copybara-github
Update Docker build instructions for AlmaLinux/Rocky/RHEL users
ea16676 
Addresses google-deepmind/alphafold3#612.

PiperOrigin-RevId: 872822931
Change-Id: Ibb4db9640805e4b59b68d93b13595224636a1af6
@Augustin-Zidek @copybara-github
Document the discrepancy between AlphaFold 3 and AlphaFold Server in …
4ca8a65 
…Known Issues

Big thanks to @stianale for reporting this in google-deepmind/alphafold3#492.

PiperOrigin-RevId: 872892863
Change-Id: Ia24bb492daea44534be4ac743fb304bc72fe9741
@Augustin-Zidek @copybara-github
Use const for iter/keys/values/items and release GIL for contains in …
203e93d 
…KeyView

PiperOrigin-RevId: 874098884
Change-Id: I3d55627a3752809600e0c2babd067ead5d5a436b
@Augustin-Zidek @copybara-github
Add CifDict.to_dict() method for faster serialisation
9e10da6 
* Speeds up ccd_pickle_gen from 22.9 s to 19.9 s.

PiperOrigin-RevId: 874118133
Change-Id: I2692c09f8aa8b58a81d0bf3bdf83684934961a66
@jsspencer @copybara-github
Respect LIBCIFPP_DATA_PATH if set, rather than attempt to find it.
1e9ece2 
This enables non-standard installs to find component.cif from libcifpp rather
than require increasingly elaborate heuristics to locate it.

PiperOrigin-RevId: 875098340
Change-Id: I7b186a9958e04628c65644aabfa88d977a86db13
@Augustin-Zidek @copybara-github
Remove unused utility functions
6daafb5 
PiperOrigin-RevId: 875760003
Change-Id: I23d7759ddf0835394dbd6b6ab3c304fa52c6a9b1
@Augustin-Zidek @copybara-github
Use the same license format in .h files as in .cc files
e58932a 
PiperOrigin-RevId: 878462983
Change-Id: I9480568ba1601306bcb1411e4403f5d6d30de579
@Augustin-Zidek @copybara-github
Improve the error when components.cif is not found
5f7eb57 
PiperOrigin-RevId: 879668429
Change-Id: I7a6ea91c9ddc7696577e156787cb364d1ff79016
Augustin-Zidek and others added 28 commits April 20, 2026 01:54
@Augustin-Zidek @copybara-github
Bump the version to v3.0.2
f6a5aec 
PiperOrigin-RevId: 902499234
Change-Id: If20dc9fccf13c0718fb37701b251e25aa2a4dc87
@Augustin-Zidek @copybara-github
Optimize CIF loop parsing by ~4% - remove modulo in the hot path
cfeeedd 
PiperOrigin-RevId: 903070425
Change-Id: Ibc7fc6735231504a4a9c5f11793854ce332d8c46
@Augustin-Zidek @copybara-github
Clean up structure cleaning - remove unused code paths
e9adcd4 
PiperOrigin-RevId: 903711715
Change-Id: I953f1b27c6a0b30cc79a6cbd3ee3503d1f24a7ec
@Augustin-Zidek @copybara-github
Use pathlib.Path.home() instead of os.environ.get('HOME')
6f882ad 
PiperOrigin-RevId: 903780979
Change-Id: I18b2580c65fc7c7411b5db3f8bd48d1b0535faa0
@Augustin-Zidek @copybara-github
Remove unused cleaned_struc from ConvertModelOutput
de4e7a4 
PiperOrigin-RevId: 903796755
Change-Id: I8d32cdd03d5d3240fb8f715973264b530a1eb55b
@Augustin-Zidek @copybara-github
Support dynamic version for dev and releases
3dfc5a9 
Suggested in google-deepmind/alphafold3#617.

PiperOrigin-RevId: 904448492
Change-Id: Ibe74967fbf768336ba2ce71ffa2841f40dca859c
@Augustin-Zidek @copybara-github
Refactor to_mmcif_dict to not use getattr
011b6cf 
PiperOrigin-RevId: 904939640
Change-Id: I18c6d3c3493d2445bc4ffb68099cfb684b21289d
@Augustin-Zidek @copybara-github
Add fallback version for Docker
481beec 
* Fixes a bug introduced in google-deepmind/alphafold3@3dfc5a9.
* Addresses google-deepmind/alphafold3#665.

PiperOrigin-RevId: 911264939
Change-Id: I3fe04842e4ebd46fcac4cc6b851026d401720538
@Augustin-Zidek @copybara-github
Pass correctly all options to Jackhmmer/Nhmmer
97639ff 
* Missed in google-deepmind/alphafold3@805adc3
* Addresses google-deepmind/alphafold3#663

PiperOrigin-RevId: 911311422
Change-Id: Ia9ba0b17d0adcb2ebceacd2c851f04d5c6dc68f1
@Augustin-Zidek @copybara-github
Fix glycan O1 leaving-atom cleanup for standalone glycans
62a93af 
Inspired by google-deepmind/alphafold3#650 and
google-deepmind/alphafold3#633.

PiperOrigin-RevId: 911350518
Change-Id: Ia68e36e3580fb6092fdaeb62352df7e06991b58c
@Augustin-Zidek @copybara-github
Fix typing of Nhmmer z values, these are floats
eba6189 
PiperOrigin-RevId: 911849752
Change-Id: Id19e1a56076a515a227e2839e83919ee2e506d56
@Augustin-Zidek @copybara-github
Validate that the output_dir is always set and add a missing argument…
8850da4 
… in overload

PiperOrigin-RevId: 913567460
Change-Id: I3b393fdc12819265a6916cb2c735964d25b3e375
@Augustin-Zidek @copybara-github
Fix a typing issue (passing ndarray instead of a list)
8812124 
PiperOrigin-RevId: 913650173
Change-Id: I279a5fd0f791567d2ed77fe8cf8e796b74e4f193
@Augustin-Zidek @copybara-github
Add basic chem_comp_atoms/chem_comp_bonds data to ChemCompEntry
8d283f3 
Pre-requisite for fixing google-deepmind/alphafold3#189.

PiperOrigin-RevId: 914244255
Change-Id: Id9ca7814ec7fa3786d717f1c28df383df1c7ef72
@Augustin-Zidek @copybara-github
Fix KeyError in string_array.remap_multiple for Python 3.14
9ea7db2 
PiperOrigin-RevId: 914331813
Change-Id: I66c4693c285489e2ba8ad833ebb6e69b677cdb1d
@Augustin-Zidek @copybara-github
Fix typing issues found using Pyrefly in folding_input and its test
9556a1c 
PiperOrigin-RevId: 914762494
Change-Id: I5c088e81b7fb7c7c2b136c7c6882175f23ed000c
@Augustin-Zidek @copybara-github
Fix typing issue in _get_rna_msa revealed by Pyrefly
10b18bf 
PiperOrigin-RevId: 915437887
Change-Id: I1281fa6ba26ee74c90d68061823b19df38787744
@Augustin-Zidek @copybara-github
Fix typing issues in constants modules revealed by Pyrefly
5a3d6b6 
PiperOrigin-RevId: 917169884
Change-Id: Ie4410f9dce5edaaadbfbd9126926edcb65132118
@Augustin-Zidek @copybara-github
Fix typing issues revealed by Pyrefly in structure_tables
7d4a236 
PiperOrigin-RevId: 918363044
Change-Id: Ic95af5eaf8fc54fc576816473bda8bbe2a31015b
@Augustin-Zidek @copybara-github
Fix descriptions being dropped in some places for protein/RNA chains
b712a3d 
* From google-deepmind/alphafold3#677 by @ntnn19. Thank you!

PiperOrigin-RevId: 919589563
Change-Id: I82c6ccf0797b87d9347fda731af00b9c0cc16cea
@Augustin-Zidek @copybara-github
Fix two typos in docstrings
eb5154f 
* Reported in google-deepmind/alphafold3#674 by @mooreneural, thanks!

PiperOrigin-RevId: 922659727
Change-Id: I7db6bca087a2bf3c4b2c327e360b804ddf72c9d4
@Augustin-Zidek @copybara-github
Improve typing and error checks in mask_mean
1dc1e0a 
PiperOrigin-RevId: 923361640
Change-Id: I708b5b8888e826f24e1ed0f1aa73a48e8174a161
@Augustin-Zidek @copybara-github
Speed up serialization of the confidences JSON ~30x
3aea02b 
Time for a 5000-residue protein went from 43 s to 1.3 s.

PiperOrigin-RevId: 926000806
Change-Id: I795c339fdf42b0b68ace54143282b680564531a5
@Augustin-Zidek @copybara-github
Fix typing issue (Numpy 1D array instead of a float)
f971361 
PiperOrigin-RevId: 928373603
Change-Id: I2766d061480106dce043fbb31d2953ac9e7548b8
@Augustin-Zidek @copybara-github
Change the code license from CC BY-NC-SA 4.0 to Apache 2.0
7b197fe 
Only the code is re-licensed, the weights license and terms of use stay the same.

PiperOrigin-RevId: 929131215
Change-Id: I3e5188067facefab807ec1cd71234b4eb74b32a1
@DimaMolod
Support gapped residue ids for discontinuous chains
dee2262
@DimaMolod
Preserve duplicate residue IDs in structure tables
c494eb8
@DimaMolod
Mark fork main as merged into v3.0.3 update
9e35ea9
@DimaMolod DimaMolod merged commit 86b9ea3 into main Jun 15, 2026
1 check passed
@DimaMolod DimaMolod deleted the ap-gapped-discontinuous-chains-v3.0.3 branch June 15, 2026 09:41
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7 participants

@DimaMolod @rpachauri @joshabramson @Augustin-Zidek @jsspencer @akviz @QEDady