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Author SHA1 Message Date
Augustin Zidek
1dc1e0ad0b Improve typing and error checks in mask_mean 
PiperOrigin-RevId: 923361640
Change-Id: I708b5b8888e826f24e1ed0f1aa73a48e8174a161
 2026-05-29 05:50:49 -07:00
Augustin Zidek
eb5154f441 Fix two typos in docstrings 
* Reported in https://github.com/google-deepmind/alphafold3/pull/674 by @mooreneural, thanks!

PiperOrigin-RevId: 922659727
Change-Id: I7db6bca087a2bf3c4b2c327e360b804ddf72c9d4
 2026-05-28 03:08:11 -07:00
Augustin Zidek
b712a3d0a1 Fix descriptions being dropped in some places for protein/RNA chains 
* From https://github.com/google-deepmind/alphafold3/pull/677 by @ntnn19. Thank you!

PiperOrigin-RevId: 919589563
Change-Id: I82c6ccf0797b87d9347fda731af00b9c0cc16cea
 2026-05-22 04:03:36 -07:00
Augustin Zidek
7d4a236f71 Fix typing issues revealed by Pyrefly in structure_tables 
PiperOrigin-RevId: 918363044
Change-Id: Ic95af5eaf8fc54fc576816473bda8bbe2a31015b
 2026-05-20 04:22:43 -07:00
Augustin Zidek
5a3d6b6365 Fix typing issues in constants modules revealed by Pyrefly 
PiperOrigin-RevId: 917169884
Change-Id: Ie4410f9dce5edaaadbfbd9126926edcb65132118
 2026-05-18 05:21:52 -07:00
Augustin Zidek
10b18bf702 Fix typing issue in _get_rna_msa revealed by Pyrefly 
PiperOrigin-RevId: 915437887
Change-Id: I1281fa6ba26ee74c90d68061823b19df38787744
 2026-05-14 08:13:11 -07:00
Augustin Zidek
9556a1c9da Fix typing issues found using Pyrefly in folding_input and its test 
PiperOrigin-RevId: 914762494
Change-Id: I5c088e81b7fb7c7c2b136c7c6882175f23ed000c
 2026-05-13 03:29:34 -07:00
Augustin Zidek
9ea7db2d3b Fix KeyError in string_array.remap_multiple for Python 3.14 
PiperOrigin-RevId: 914331813
Change-Id: I66c4693c285489e2ba8ad833ebb6e69b677cdb1d
 2026-05-12 09:47:39 -07:00
Augustin Zidek
8d283f3baf Add basic chem_comp_atoms/chem_comp_bonds data to ChemCompEntry 
Pre-requisite for fixing https://github.com/google-deepmind/alphafold3/issues/189.

PiperOrigin-RevId: 914244255
Change-Id: Id9ca7814ec7fa3786d717f1c28df383df1c7ef72
 2026-05-12 06:13:22 -07:00
Augustin Zidek
881212473a Fix a typing issue (passing ndarray instead of a list) 
PiperOrigin-RevId: 913650173
Change-Id: I279a5fd0f791567d2ed77fe8cf8e796b74e4f193
 2026-05-11 05:36:40 -07:00
Augustin Zidek
8850da42a6 Validate that the output_dir is always set and add a missing argument in overload 
PiperOrigin-RevId: 913567460
Change-Id: I3b393fdc12819265a6916cb2c735964d25b3e375
 2026-05-11 01:48:50 -07:00
Augustin Zidek
eba618977e Fix typing of Nhmmer z values, these are floats 
PiperOrigin-RevId: 911849752
Change-Id: Id19e1a56076a515a227e2839e83919ee2e506d56
 2026-05-07 02:53:05 -07:00
Augustin Zidek
62a93afa5d Fix glycan O1 leaving-atom cleanup for standalone glycans 
Inspired by https://github.com/google-deepmind/alphafold3/issues/650 and
https://github.com/google-deepmind/alphafold3/pull/633.

PiperOrigin-RevId: 911350518
Change-Id: Ia68e36e3580fb6092fdaeb62352df7e06991b58c
 2026-05-06 08:24:14 -07:00
Augustin Zidek
97639fff6f Pass correctly all options to Jackhmmer/Nhmmer 
* Missed in 805adc3863
* Addresses https://github.com/google-deepmind/alphafold3/issues/663

PiperOrigin-RevId: 911311422
Change-Id: Ia9ba0b17d0adcb2ebceacd2c851f04d5c6dc68f1
 2026-05-06 06:54:41 -07:00
Augustin Zidek
481beec819 Add fallback version for Docker 
* Fixes a bug introduced in 3dfc5a91be.
* Addresses https://github.com/google-deepmind/alphafold3/issues/665.

PiperOrigin-RevId: 911264939
Change-Id: I3fe04842e4ebd46fcac4cc6b851026d401720538
 2026-05-06 04:59:43 -07:00
Augustin Zidek
011b6cf42b Refactor to_mmcif_dict to not use getattr 
PiperOrigin-RevId: 904939640
Change-Id: I18c6d3c3493d2445bc4ffb68099cfb684b21289d
 2026-04-24 04:06:17 -07:00
Augustin Zidek
3dfc5a91be Support dynamic version for dev and releases 
Suggested in https://github.com/google-deepmind/alphafold3/pull/617.

PiperOrigin-RevId: 904448492
Change-Id: Ibe74967fbf768336ba2ce71ffa2841f40dca859c
 2026-04-23 07:33:40 -07:00
Augustin Zidek
de4e7a4f2d Remove unused cleaned_struc from ConvertModelOutput 
PiperOrigin-RevId: 903796755
Change-Id: I8d32cdd03d5d3240fb8f715973264b530a1eb55b
 2026-04-22 05:56:01 -07:00
Augustin Zidek
6f882ad224 Use pathlib.Path.home() instead of os.environ.get('HOME') 
PiperOrigin-RevId: 903780979
Change-Id: I18b2580c65fc7c7411b5db3f8bd48d1b0535faa0
 2026-04-22 05:14:40 -07:00
Augustin Zidek
e9adcd4dbf Clean up structure cleaning - remove unused code paths 
PiperOrigin-RevId: 903711715
Change-Id: I953f1b27c6a0b30cc79a6cbd3ee3503d1f24a7ec
 2026-04-22 02:33:06 -07:00
Augustin Zidek
cfeeedd24d Optimize CIF loop parsing by ~4% - remove modulo in the hot path 
PiperOrigin-RevId: 903070425
Change-Id: Ibc7fc6735231504a4a9c5f11793854ce332d8c46
 2026-04-21 01:37:04 -07:00
Augustin Zidek
f6a5aecf6e Bump the version to v3.0.2 
PiperOrigin-RevId: 902499234
Change-Id: If20dc9fccf13c0718fb37701b251e25aa2a4dc87
v3.0.2 		2026-04-20 01:54:13 -07:00
DeepMind
24cded8e86 Expose an API to run the model pipeline with a Structure 
PiperOrigin-RevId: 897648577
Change-Id: I6342d35ea75b5c6bf15b6dcad2aa6bfc11764c19
 2026-04-10 05:54:27 -07:00
Amer Elsheikh
177df6a5c1 Remove obsolete : ... from all python functions parameters annotations. 
PiperOrigin-RevId: 897312424
Change-Id: I43029f4c467178b53bab07a7b6798cf688c86006
 2026-04-09 14:48:18 -07:00
Augustin Zidek
87bd9e678d Add a missing newline for consistency 
PiperOrigin-RevId: 892857617
Change-Id: I780db2503f65cc35d28971dc9479256d98275e9e
 2026-04-01 04:39:52 -07:00
Augustin Zidek
f236bc4e8c Use && instead of ; when building HMMER to stop if there are errors 
Suggested in https://github.com/google-deepmind/alphafold3/pull/639/files

PiperOrigin-RevId: 892848172
Change-Id: I483403805e4252d150b19b482917736bddca47fa
 2026-04-01 04:13:59 -07:00
Augustin Zidek
4d20ed540b Import from collections.abc instead of typing 
PiperOrigin-RevId: 892386825
Change-Id: Ic04bb7a133d90ab9ac900061e3684e1f086d6ac7
 2026-03-31 09:31:43 -07:00
Augustin Zidek
58d22e2db5 Fix some Structure type issues uncovered by Pyrefly 
PiperOrigin-RevId: 891687351
Change-Id: I9c69179100e9328113a578d45e5f997b07d300a2
 2026-03-30 06:34:28 -07:00
Akvile Zemgulyte
0f82e0c94c wrap reader into io.BufferedReader. 
PiperOrigin-RevId: 889374560
Change-Id: Ie829d2eb1f06dc024b1848747540b50c11e8d9d6
 2026-03-25 12:25:38 -07:00
Augustin Zidek
02650a5ded Use --run_*=false instead of --norun_* in docs. 
PiperOrigin-RevId: 886655698
Change-Id: If37e31d659c5b31856ce9bb6cb215b49bb7a96f8
 2026-03-20 02:19:27 -07:00
Augustin Zidek
608edb684d Update to Tokamax 0.0.11 and JAX 0.9.1 
PiperOrigin-RevId: 881449511
Change-Id: I581853a7c2609a2541f46d22901cc463d5b6b08a
 2026-03-10 08:36:19 -07:00
Augustin Zidek
5f7eb57e22 Improve the error when components.cif is not found 
PiperOrigin-RevId: 879668429
Change-Id: I7a6ea91c9ddc7696577e156787cb364d1ff79016
 2026-03-06 09:15:59 -08:00
Augustin Zidek
e58932a036 Use the same license format in .h files as in .cc files 
PiperOrigin-RevId: 878462983
Change-Id: I9480568ba1601306bcb1411e4403f5d6d30de579
 2026-03-04 06:38:48 -08:00
Augustin Zidek
6daafb546f Remove unused utility functions 
PiperOrigin-RevId: 875760003
Change-Id: I23d7759ddf0835394dbd6b6ab3c304fa52c6a9b1
 2026-02-26 09:32:05 -08:00
James Spencer
1e9ece2cfb Respect LIBCIFPP_DATA_PATH if set, rather than attempt to find it. 
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
 2026-02-25 05:01:49 -08:00
Augustin Zidek
9e10da6725 Add CifDict.to_dict() method for faster serialisation 
* Speeds up ccd_pickle_gen from 22.9 s to 19.9 s.

PiperOrigin-RevId: 874118133
Change-Id: I2692c09f8aa8b58a81d0bf3bdf83684934961a66
 2026-02-23 09:41:10 -08:00
Augustin Zidek
203e93dfc6 Use const for iter/keys/values/items and release GIL for contains in KeyView 
PiperOrigin-RevId: 874098884
Change-Id: I3d55627a3752809600e0c2babd067ead5d5a436b
 2026-02-23 08:58:51 -08:00
Augustin Zidek
4ca8a65692 Document the discrepancy between AlphaFold 3 and AlphaFold Server in Known Issues 
Big thanks to @stianale for reporting this in https://github.com/google-deepmind/alphafold3/issues/492.

PiperOrigin-RevId: 872892863
Change-Id: Ia24bb492daea44534be4ac743fb304bc72fe9741
 2026-02-20 07:34:06 -08:00
Augustin Zidek
ea1667690e Update Docker build instructions for AlmaLinux/Rocky/RHEL users 
Addresses https://github.com/google-deepmind/alphafold3/issues/612.

PiperOrigin-RevId: 872822931
Change-Id: Ibb4db9640805e4b59b68d93b13595224636a1af6
 2026-02-20 03:41:05 -08:00
Augustin Zidek
c20f070859 Exit if any of the required programs is not installed 
Thanks for the suggestion, @Ashutosh0x.

PiperOrigin-RevId: 872800291
Change-Id: If1266222844de98850b7ae4141e2f50001cc4d63
 2026-02-20 02:25:13 -08:00
Augustin Zidek
703d5c8375 Make sharded Jackhmmer result merging more robust in case of e-value 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
 2026-02-16 08:30:20 -08:00
Augustin Zidek
2761bf1cfc Use the logging name instead of the one from fold_input 
PiperOrigin-RevId: 870860151
Change-Id: I1d4485e1e08c3ca790899c33190b989d103eaf56
 2026-02-16 06:13:52 -08:00
Augustin Zidek
e2b8ffd6a7 Implement relevant improvements from #615 
PiperOrigin-RevId: 868589660
Change-Id: Iac82ddf73f9f82118b935550afbe0ea13f6cd2eb
 2026-02-11 03:27:47 -08:00
Augustin Zidek
ceb32296c7 Move CONTRIBUTING.md to the root directory 
PiperOrigin-RevId: 867451876
Change-Id: Ibdaaee8902a1c1150e99225632300778c016f5f6
 2026-02-09 00:41:32 -08:00
Augustin Zidek
ebfe70a27a Update Tokamax to 0.0.10 
* 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
 2026-02-04 09:41:35 -08:00
Augustin Zidek
c13d928a34 Update RDKit to 2025.9.4 
PiperOrigin-RevId: 865437867
Change-Id: Iaa116d661bb5743e285efcfe7115f8242f7c0db9
 2026-02-04 09:15:20 -08:00
Augustin Zidek
cf4bb5bd9e Use UV_LINK_MODE=copy to prevent Docker build issues on some platforms 
Relevant issues:
* https://github.com/google-deepmind/alphafold3/issues/603
* https://github.com/google-deepmind/alphafold3/issues/612

PiperOrigin-RevId: 865416421
Change-Id: Idaf8e531a62638bce5e0748f64a7ddc00b554677
 2026-02-04 08:18:53 -08:00
Augustin Zidek
6b50e384d3 Add the glycan modeling paper in the list of community tools 
Adapted from https://github.com/google-deepmind/alphafold3/pull/608/changes, thanks @chinchc.

PiperOrigin-RevId: 862720014
Change-Id: I021eef0b46158e8ce28e97d9172ba6e79ef3f30c
 2026-01-29 07:03:17 -08:00
Augustin Zidek
22b9ab80d3 Make AlphaFold 3 uv setup compatible with aarch64 
Addresses https://github.com/google-deepmind/alphafold3/issues/593.

PiperOrigin-RevId: 858480255
Change-Id: I7862b204300d137e367bbaaf31213f7164fdd8d1
 2026-01-20 01:56:05 -08:00
Augustin Zidek
c7a1ad5c51 Add a documentation on model parameters 
Addresses https://github.com/google-deepmind/alphafold3/issues/594.

PiperOrigin-RevId: 857083798
Change-Id: I1d8e42ab6e53075a2c05d70d10a14a8e686fa566
 2026-01-16 04:04:09 -08:00