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40be3ec6c764fd7e8f4478ac6280f438058e271a
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Author SHA1 Message Date
Harsh Tiku
40be3ec6c7 [Remove scipy dependency] Remove last traces of scipy. 
PiperOrigin-RevId: 826401490
Change-Id: I8754e8ed8af7997c90d9f48cefee69e4e7e8243f
 2025-10-31 02:45:18 -07:00
Harsh Tiku
d172b1a6c7 [Remove scipy dependency] Use custom ks_normal_test to test normality of distribution. This approximates the p value of the distribution. 
PiperOrigin-RevId: 826028289
Change-Id: Ibb8583ba9143a4ce9f8926b3948a58ee0a8d4abd
 2025-10-30 07:47:05 -07:00
Harsh Tiku
78a01da677 Migrate softmax calls from scipy to jax.scipy. 
PiperOrigin-RevId: 824452619
Change-Id: Ife5ad712ed56e3b3af92a7ad74b40167f8ed59ad
 2025-10-27 04:12:23 -07:00
Harsh Tiku
a138beeaf1 Replace custom block_diagonal with jax.scipy.linalg.block_diag. 
PiperOrigin-RevId: 824421836
Change-Id: I036ee6f72d0364c56fe62a24296d7fba4ae521fd
 2025-10-27 02:29:07 -07:00
Augustin Zidek
cd0357af72 Migrate from setup.py to pyproject.toml 
PiperOrigin-RevId: 823533906
Change-Id: I8c9193164025c96946fa5462259e0adb03c4239e
 2025-10-24 08:08:18 -07:00
Harsh Tiku
a2581aef15 Replace scipy.linalg.block_diag with a NumPy implementation. 
PiperOrigin-RevId: 823466399
Change-Id: Iae1e460355dea38706524f40de17ba07df86e529
 2025-10-24 04:08:01 -07:00
Ryan Pachauri
09ed0c5d5a Make layer_norm epsilon a constant. 
PiperOrigin-RevId: 820327627
Change-Id: Ib7e8ec29db052ac2c4fd79658203bdea2a2845d9
 2025-10-16 11:39:48 -07:00
Augustin Zidek
1b10a6058c Revert: Bring model config creation in one place by simplifying num_ensemble setting 
PiperOrigin-RevId: 819744016
Change-Id: I15a626c646b45c8c23d6dbd5c8d75314920cbf12
 2025-10-15 07:23:02 -07:00
Harsh Tiku
075671a612 Add crop_size to EvalConfig. 
PiperOrigin-RevId: 818570622
Change-Id: I7d8ff6402c67bcb6c047395a7abc7dcbc4b22800
 2025-10-13 03:00:50 -07:00
Augustin Zidek
87b9b24941 Remove redundant TF import that was left over 
PiperOrigin-RevId: 816130447
Change-Id: I63ca4f0a43c4490fedab6e5a225f5289144e464e
 2025-10-07 03:34:27 -07:00
Augustin Zidek
6979980500 Remove the unused tf.Example codepath 
PiperOrigin-RevId: 816086502
Change-Id: I30730ca7bb645f6dd3418a2450c68d27024d96ed
 2025-10-07 01:05:29 -07:00
Augustin Zidek
9b2ed02ff6 Remove unused utility function 
PiperOrigin-RevId: 814239959
Change-Id: I663c91b969fd942c8c560ecb504ea21ab8d1be5d
 2025-10-02 08:11:56 -07:00
Augustin Zidek
2b2aaafa77 Remove redundant dependencies in a test 
PiperOrigin-RevId: 814201120
Change-Id: I77bee8b119e2d26ef5b4d2deb0a7615c6e5d0cfc
 2025-10-02 06:08:28 -07:00
Ryan Pachauri
12f16df5e3 Use /usr/bin/env for bash shebang. 
Using env honors user preference if they override bash in $PATH or use a linux distribution that does not store bash at /bin/bash.

Addresses the following pull request:
- https://github.com/google-deepmind/alphafold/pull/913

PiperOrigin-RevId: 813843957
Change-Id: I2fa35a7ecec8a17472ad84d27e09b266952fd14d
 2025-10-01 11:42:30 -07:00
Ryan Pachauri
c7625926bc Add rsync notice for for DB download. 
Addresses the following pull request:
- https://github.com/google-deepmind/alphafold/pull/1033

PiperOrigin-RevId: 813372673
Change-Id: I27ef523d86e3a0aeba432e12ceab7cd5f67b3478
 2025-09-30 12:12:37 -07:00
Akvile Zemgulyte
8815b4657f Remove redundant module docstrings from test files. 
PiperOrigin-RevId: 812801763
Change-Id: I07864c53194bfbe9f12f8743b8c8776f70fb1119
 2025-09-29 08:36:57 -07:00
Harsh Tiku
25102bf040 Add a context managed unfreeze() method in base_config 
PiperOrigin-RevId: 812777327
Change-Id: I19480f4c103f65280ddf8f396c63351e80144978
 2025-09-29 07:21:11 -07:00
Augustin Zidek
dbaafbcdea Run Pyformat on the entire AlphaFold 2 codebase. 
PiperOrigin-RevId: 812761281
Change-Id: Iee46a5b923fa6ea512d5ca25fd06f75578e88276
 2025-09-29 06:28:09 -07:00
Harsh Tiku
ecdc85103f Bring model config creation in one place by simplifying num_ensemble setting 
PiperOrigin-RevId: 811346971
Change-Id: Idbd6e84ab372dad81d8f3eb6e1a1af12daf4baeb
 2025-09-25 07:42:58 -07:00
Harsh Tiku
1ff6388c67 Rename variables for clarity 
PiperOrigin-RevId: 811255472
Change-Id: Ie7626469542c3126a5960aca0cd65ecad723ed58
 2025-09-25 02:19:09 -07:00
Ryan Pachauri
4b81ad9cfe Add CPU/thread control to MSA tools and update dependencies. 
Addresses the following pull request:
*  https://github.com/google-deepmind/alphafold/pull/358

PiperOrigin-RevId: 810894445
Change-Id: Ib424b3f331c5168f4505edd154b860420e89237e
 2025-09-24 08:30:25 -07:00
Harsh Tiku
77816c74dc # Refactor AlphaFold model configuration to use dataclasses 
This changelist begins the migration of the AlphaFold model configuration from
`ml_collections.ConfigDict` to a more robust and type-safe system based on Python's `dataclasses`.

This is the **first step** in a larger effort. Future changes will update all call sites to use the new `get_model_config()` function.

---

## Key Changes

### `base_config.py`
- Introduced a new **`BaseConfig`** class, serving as a base for all configuration dataclasses.
- Features:
  - **Automatic coercion** of nested dictionaries into the appropriate dataclass instances during initialization.
  - **`as_dict()`** method for converting the configuration object back into a dictionary.
  - **`freeze()`** method to make the configuration and all its sub-configs immutable.

### `config.py`
- Entire configuration schema redefined using a hierarchy of `BaseConfig` subclasses
  (e.g., `AlphaFoldConfig`, `Model`, `Heads`) — making the structure explicit and statically verifiable.
- Introduced **`get_model_config(model_name)`** as the primary entrypoint to access model configurations.
  - Returns a fully initialized, type-safe `AlphaFoldConfig` object.
- **Model-specific variations**:
  - Previously handled by updating a dictionary (`CONFIG_DIFFS`).
  - Now handled via a **mapping of functions (`CONFIG_DIFF_OPS`)**, improving clarity and safety.

### Testing
- Added **`base_config_test.py`** to validate the functionality of the new `BaseConfig` class.
- Added **`config_test.py`** to verify that:
  - `get_model_config` produces equivalent configurations to the legacy `model_config`.
  - Refactoring does not alter behavior.
---

PiperOrigin-RevId: 810873050
Change-Id: I7c96c23c1d168d722af41efcf98d44cc11ca7707
 2025-09-24 07:20:51 -07:00
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