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06a8da6cdacef5ddb29462f50d33e007e6790b2e
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Author SHA1 Message Date
Ryan Pachauri
06a8da6cda Correct standard deviation used in CA-C-N angle loss. 
Addresses the following pull requests:
- https://github.com/google-deepmind/alphafold/pull/488
- https://github.com/google-deepmind/alphafold/pull/826

PiperOrigin-RevId: 810526333
Change-Id: Ic78d98cf5261ca9fa75b842a5c54f5efbeff093d
 2025-09-23 11:55:37 -07:00
Ryan Pachauri
e1554305c0 Remove pandas dependency from msa_pairing.py. 
PiperOrigin-RevId: 808194449
Change-Id: Iacda885dd14172e95e0258908384966f338e3c7b
 2025-09-17 09:52:32 -07:00
Ryan Pachauri
2652cafb43 Refactor between_residue_bond_loss to use a shared helper function. 
PiperOrigin-RevId: 808166329
Change-Id: I3d60463cbc8f0ec3cbceab7a445d8f6f2d652ce0
 2025-09-17 08:32:18 -07:00
Ryan Pachauri
cc9042484e Add tests for all_atom.between_residue_bond_loss. 
PiperOrigin-RevId: 807751146
Change-Id: I5e6ac821ae077a798255e437d95fe1c0a528295e
 2025-09-16 10:33:37 -07:00
Ryan Pachauri
c9b9901dda Make run_alphafold.py and shell scripts installable. 
Addresses the following pull request:
*  https://github.com/google-deepmind/alphafold/pull/512

PiperOrigin-RevId: 807688130
Change-Id: Ibd8dcc1357540c6474c0455b3b643298efd652a3
 2025-09-16 07:35:38 -07:00
Ryan Pachauri
2c4a647dc8 Use stable sorting in MSA pairing. 
PiperOrigin-RevId: 807297118
Change-Id: I4360835c5552a3b8b11b444b0553fe7f35869c91
 2025-09-15 10:41:17 -07:00
Ryan Pachauri
dffd48ab62 Deprecate dm-tree in favor of jax.tree. 
PiperOrigin-RevId: 807269228
Change-Id: I64021a2a7119e5c440af4fc98137edd67cb98b0d
 2025-09-15 09:26:23 -07:00
Ryan Pachauri
4db5d8e94c Fix exception causes in data/templates.py 
Addresses:
- https://github.com/google-deepmind/alphafold/pull/652
PiperOrigin-RevId: 807260658
Change-Id: I005dbb6f595cb0785607bb7f135e2a992049d7f6
 2025-09-15 08:59:43 -07:00
Augustin Zidek
c77d8b52d3 Fix unit mismatch issue in Amber relax 
Fixes:
* https://github.com/google-deepmind/alphafold/issues/1091
* https://github.com/google-deepmind/alphafold/issues/923

Thanks Alex! :)

PiperOrigin-RevId: 802200540
Change-Id: Ic6e2aeaf67403ef88cafc07c8532f0cd2e7cb3ce
 2025-09-02 10:33:26 -07:00
Ryan Pachauri
c095a657ad Fix typos. 
Addresses the following pull requests:
* https://github.com/google-deepmind/alphafold/pull/1089
* https://github.com/google-deepmind/alphafold/pull/947
* https://github.com/google-deepmind/alphafold/pull/889

PiperOrigin-RevId: 798028468
Change-Id: I3b6f2874e173f757144533232c661f81b927fd64
 2025-08-21 20:51:32 -07:00
Ryan Pachauri
e57fba02b1 Clarify and fix documentation. 
Addresses the following pull requests:
* https://github.com/google-deepmind/alphafold/pull/1083
* https://github.com/google-deepmind/alphafold/pull/1079
* https://github.com/google-deepmind/alphafold/pull/893

PiperOrigin-RevId: 798021344
Change-Id: I51bbc56998b99d53697b9d95e28cf1d55d562291
 2025-08-21 20:22:24 -07:00
Ryan Pachauri
aba97651a6 Use correct type information in tests. 
PiperOrigin-RevId: 797102858
Change-Id: Ie49cf8102dee57a507d60464c746cf92fa70192f
 2025-08-19 18:38:06 -07:00
Augustin Zidek
29f082183b Remove declaration of support for Python 3.6/3.7 and add 3.11/3.12 
PiperOrigin-RevId: 794552914
Change-Id: Ie3b904a1385801fc900a64e2934092022559dc6e
 2025-08-13 06:35:44 -07:00
Augustin Zidek
79a0210693 Format msa_pairing 
PiperOrigin-RevId: 794545379
Change-Id: I40ca93f7e6864a5906a40168250261c9c56c59ff
 2025-08-13 06:08:01 -07:00
Augustin Zidek
6544d69fc3 Remove unused dependencies 
PiperOrigin-RevId: 794083897
Change-Id: Iecdc0b5d1cd43f1702752eb3655edc1b9894f520
 2025-08-12 06:30:33 -07:00
Augustin Zidek
b1d8619675 Use pytest for testing instead of setup.py test 
PiperOrigin-RevId: 789706772
Change-Id: Id4d58250e03bc41ab7d9a90c3d569266cb2db4ad
 2025-08-01 04:19:07 -07:00
Augustin Zidek
e9b68483fc Fix Docker build due to changes in Conda and don't limit make parallelism 
PiperOrigin-RevId: 783683713
Change-Id: I24599012fabbf9bf5b87597906b1ebb5a70c029c
 2025-07-16 03:10:25 -07:00
Augustin Zidek
b522811d9e Avoid use of deprecated jax.util APIs 
jax.util was deprecated in JAX v0.6.0, and will be removed in JAX v0.7.0.

PiperOrigin-RevId: 759626266
Change-Id: If3dcb9a8151a99ecab1f8ec670bd99bbb31bd5de
 2025-05-16 08:33:10 -07:00
Hana Joo
8050b46921 No public description 
PiperOrigin-RevId: 752767512
Change-Id: I0c29c07cd27b7da3472871e8a8e8c5c257458d80
 2025-04-29 09:32:35 -07:00
DeepMind
020cd6d6cb Add information about PDBe template cutoff date 
PiperOrigin-RevId: 737580394
Change-Id: Id6d3c3f518682d9171c67ac59ce78bf80c6bb27f
 2025-03-17 05:40:18 -07:00
Dariusz Lasecki
2ca41b1991 Deprecate the AlphaFold 2 notebook 
PiperOrigin-RevId: 720951827
Change-Id: Ie30be1252f6e6dc4038be6b307395f45e638d5ad
 2025-01-29 06:32:24 -08:00
DeepMind
24fbdfc3ce Update JSON format docs with new template on/off, cutoff date fields. 
PiperOrigin-RevId: 720186008
Change-Id: I53b84c0b52509f93e85cc8705aeba4888398f5bb
 2025-01-27 08:48:48 -08:00
Augustin Zidek
93e024bd55 Do not use jnp.clip arguments which are not supported in the pinned JAX version. 
PiperOrigin-RevId: 719259712
Change-Id: I7eb76868275c862201cc7eb26fede8c987e5b760
 2025-01-24 05:09:56 -08:00
Augustin Zidek
11a991ea66 Bump Python in Colab to 3.11. 
PiperOrigin-RevId: 718812632
Change-Id: I54b901e7a361a63a2c3f366535dbe2cd3e792b99
 2025-01-23 04:40:44 -08:00
Jake VanderPlas
fa0c5266b3 jax.numpy.clip: update use of deprecated arguments. 
- a is now positional-only
- a_min is now min
- a_max is now max

The old argument names have been deprecated since JAX v0.4.27.

PiperOrigin-RevId: 715343439
Change-Id: I50b086b249360c142f42ed4d8e50d48692c11dfa
 2025-01-14 05:42:09 -08:00
Augustin Zidek
6350ddd63b Update Conda to 24.11.1 to fix Docker build failure and small improvements to the Dockerfile. 
PiperOrigin-RevId: 707479885
Change-Id: Ic3c71229bcf3a935cae86aee64ee7c02220e1085
 2024-12-18 03:26:03 -08:00
Martin Huschenbett
bbd8300d6a Automated Code Change: Suppress pytype errors 
PiperOrigin-RevId: 700257299
Change-Id: If6ce01bd60ab0422eca10578db8d58b1a3137b40
 2024-11-26 01:41:22 -08:00
Augustin Zidek
d95a92aae1 Update the disclaimer to match AlphaFold 3 + run mdformat. 
PiperOrigin-RevId: 696460542
Change-Id: I42defc0a687207ee57801b0aeba78fe1e63b03e6
 2024-11-14 03:34:33 -08:00
Augustin Zidek
85e0be3c7d Make apt output log-friendly by adding the --quiet flag. 
PiperOrigin-RevId: 665259372
Change-Id: I516c7780b8a821065bf19fe3c79dba604f2c917c
 2024-08-20 02:46:14 -07:00
Augustin Zidek
a2217f031e Pin setuptools on a version smaller than 72.0.0. 
PiperOrigin-RevId: 660325717
Change-Id: I11b5cf0b0b7cc8bfa48de170a1653e013d7734a1
 2024-08-07 03:59:31 -07:00
Peter Hawkins
692c01c524 [numpy] Fix users of NumPy APIs that are removed in NumPy 2.0. 
This change migrates users of APIs removed in NumPy 2.0 to their recommended replacements (https://numpy.org/devdocs/numpy_2_0_migration_guide.html).

PiperOrigin-RevId: 655904142
Change-Id: Idcf2384de70cb27cb92e3f421dc8e0a9a6466507
 2024-07-25 04:17:05 -07:00
Augustin Zidek
93a9a042eb Inline SCOPData to be compatible with future Biopython versions. 
PiperOrigin-RevId: 648368396
Change-Id: Icfd8135c5602ca81007dd6074a3258d5ae0187ee
 2024-07-01 07:55:19 -07:00
Jake VanderPlas
5b0e1f2c55 Replace deprecated jax.tree_* functions with jax.tree.* 
The top-level `jax.tree_*` aliases have long been deprecated, and will soon be removed. Alternate APIs are in `jax.tree_util`, with shorter aliases in the `jax.tree` submodule, added in JAX version 0.4.25.

PiperOrigin-RevId: 633878846
Change-Id: I282e177b3c9026b805d6eb5e5d6e6b1287f87e55
 2024-05-15 03:32:25 -07:00
Augustin Zidek
f251de6613 Add documentation for AlphaFold Server JSON file format. 
PiperOrigin-RevId: 631787106
Change-Id: Ib58c166a2945d459c1555dd1920963887b8d7c16
 2024-05-08 07:04:54 -07:00
Hamish Tomlinson
4d4a1aea99 Update openmm in AlphaFold colab. 
PiperOrigin-RevId: 625019041
Change-Id: If6e5b23edeb1f06bd91b4daf1c449d12ed407895
 2024-04-15 11:08:04 -07:00
Hamish Tomlinson
dbe2a438eb Update requirements: 
- Ubuntu to 20.04
- Cuda to 12.2.2
- Tensorflow to 2.16.1
- Jax to 0.4.26
- Openmm to 8.0.0

PiperOrigin-RevId: 624094170
Change-Id: I49391c3f721e93ac8ccd5a4483cdb6f2ec61cd3b
 2024-04-12 01:57:58 -07:00
Hamish Tomlinson
7e7de59cd2 Remove deprecated PRNGKeyArray. 
PiperOrigin-RevId: 623494831
Change-Id: Ie15c1d517fd7b34662d69d05205151d9c7021da4
 2024-04-10 08:01:46 -07:00
Hamish Tomlinson
5208f1b70e Update jax, haiku and chex versions. 
PiperOrigin-RevId: 623469847
Change-Id: I64a812e00e099f6503b9aa1e0cfde1133ea8a774
 2024-04-10 06:04:14 -07:00
Augustin Zidek
6d95d1982e Fix how we extract mmCIF resolution (fix ordering issue). 
Thanks to @ljarosch for reporting and suggesting a fix in https://github.com/google-deepmind/alphafold/issues/915.

PiperOrigin-RevId: 617817805
Change-Id: I46738b248a054d06fe902626cff161fe521e99f1
 2024-03-21 06:03:34 -07:00
Hamish Tomlinson
032e2f2673 Update conda to 24.1.2. 
PiperOrigin-RevId: 611404763
Change-Id: Icc7d637e1de9fa82da76aa8dccd9b9dce8be6246
 2024-02-29 03:01:46 -08:00
Hamish Tomlinson
632ef575c6 Uninstall keras in notebook to avoid the keras initializer fault. 
PiperOrigin-RevId: 603012242
Change-Id: Icf0120e1baf1278862ea62402a86c9eac5932710
 2024-01-31 04:50:56 -08:00
Matthew Johnson
4f447319e4 Loosen overly tight numerical tolerances to allow for one-time random value 
change from https://github.com/google/jax/discussions/18480

PiperOrigin-RevId: 591243740
Change-Id: I86457bfcaae65771ccb4e39d3e4d929335d71652
 2023-12-15 07:13:05 -08:00
Peter Hawkins
1fa9200c7f [JAX] Replace uses of jax.devices("cpu") with jax.local_devices(backend="cpu"). 
An upcoming change to JAX will include non-local (addressable) CPU devices in jax.devices() when JAX is used multicontroller-style, where there are multiple Python processes.

This change preserves the current behavior by replacing uses of jax.devices("cpu"), which previously only returned local devices, with jax.local_devices("cpu"), which will return local devices both now and in the future.

This change is always be safe (i.e., it should always preserve the previous behavior) but it may sometimes be unnecessary if code is never used in a multicontroller setting.

PiperOrigin-RevId: 582680953
Change-Id: I614739de052185c42932ddb91d1d464751442f65
 2023-11-15 08:11:45 -08:00
Augustin Zidek
f715f016d8 Revert a change that is not compatible with JAX 0.3.25. 
PiperOrigin-RevId: 578486539
Change-Id: Id0e535ebf75916b5179791d093ca714e343ccb69
 2023-11-01 05:32:02 -07:00
Augustin Zidek
f78c589304 Update wwPDB paths from ftp.wwpdb.org to files.wwpdb.org. 
See https://www.wwpdb.org/news/news?year=2022#6303be3b707ecd4f63b3d3d9 for the wwPDB announcement.

PiperOrigin-RevId: 575762003
Change-Id: If25ea2777c33b03f03b27d54046c71753cb33038
 2023-10-23 03:14:49 -07:00
DeepMind
bbc133b060 Add assertion to aid type checking. 
PiperOrigin-RevId: 568220760
Change-Id: Ied9e33692bbd7fb8c02b039f64688cc31f005885
 2023-09-25 08:04:59 -07:00
Jake VanderPlas
a8875a9c0d Replace deprecated PRNGKeyArray isinstance checks 
For details, see https://github.com/google/jax/pull/17297

PiperOrigin-RevId: 565705637
Change-Id: I88c4a3003166580e28111c4e410c8412c23ccb9d
 2023-09-15 09:54:49 -07:00
Augustin Zidek
22f6919174 Add a cast to prevent future Pandas typing issues. 
PiperOrigin-RevId: 563001314
Change-Id: I441729e337e5bf782f70beeb92d8cf0c870bc98a
 2023-09-05 23:17:42 -07:00
Augustin Zidek
c9431c4c12 Remove unused imports. 
PiperOrigin-RevId: 562507313
Change-Id: Ic82f113455c0be50c0af1e9df4498991072e554c
 2023-09-04 03:02:00 -07:00
DeepMind
bbe8a844e0 Fix: return correct renaming mask. 
PiperOrigin-RevId: 558140222
Change-Id: I7fb69e8a7c9ce95a26d0816fb8c1c02cba68f660
 2023-08-18 07:26:42 -07:00