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• c77e5d2a89 Update AFS custom template JSON input description main DeepMind 2026-04-22 10:03:21 -07:00
• 7e1e321dfd Remove dead TF data transform functions Augustin Zidek 2026-04-14 01:35:17 -07:00
• 425615ec1a Remove unused transform Augustin Zidek 2026-04-13 04:35:00 -07:00
• 27fb0c0b89 Update the AFDB readme to use gcloud storage instead of gsutil Augustin Zidek 2026-04-07 01:08:21 -07:00
• 4593e8c411 Remove support for Python versions that are no longer supported Augustin Zidek 2026-04-02 08:38:04 -07:00
• c015a39b99 Update AFS custom template JSON input description DeepMind 2026-03-31 02:17:45 -07:00
• 42719e135a Update technical note for v2.3.0 to mention the change in distillation set. Josh Abramson 2026-03-12 09:35:11 -07:00
• a4315dd7b8 Stop using Conda to install OpenMM and PDBfixer - both now on PyPI Augustin Zidek 2026-03-10 08:34:51 -07:00
• 636a18bae7 Inline softmax implementation so that we don't break with old JAX Augustin Zidek 2026-03-03 08:39:51 -08:00
• dc61fb4a31 Fix Numpy 2.4 compatibility Augustin Zidek 2026-02-03 01:26:16 -08:00
• 59cbb686da Add pyink configuration to pyproject.toml Augustin Zidek 2026-01-09 01:02:18 -08:00
• 40be3ec6c7 [Remove scipy dependency] Remove last traces of scipy. Harsh Tiku 2025-10-31 02:44:24 -07:00
• d172b1a6c7 [Remove scipy dependency] Use custom ks_normal_test to test normality of distribution. This approximates the p value of the distribution. Harsh Tiku 2025-10-30 07:46:31 -07:00
• 78a01da677 Migrate softmax calls from scipy to jax.scipy. Harsh Tiku 2025-10-27 04:11:38 -07:00
• a138beeaf1 Replace custom block_diagonal with jax.scipy.linalg.block_diag. Harsh Tiku 2025-10-27 02:28:38 -07:00
• cd0357af72 Migrate from setup.py to pyproject.toml Augustin Zidek 2025-10-24 08:07:38 -07:00
• a2581aef15 Replace scipy.linalg.block_diag with a NumPy implementation. Harsh Tiku 2025-10-24 04:07:31 -07:00
• 09ed0c5d5a Make layer_norm epsilon a constant. Ryan Pachauri 2025-10-16 11:39:08 -07:00
• 1b10a6058c Revert: Bring model config creation in one place by simplifying num_ensemble setting Augustin Zidek 2025-10-15 07:22:25 -07:00
• 075671a612 Add crop_size to EvalConfig. Harsh Tiku 2025-10-13 03:00:19 -07:00
• 87b9b24941 Remove redundant TF import that was left over Augustin Zidek 2025-10-07 03:33:50 -07:00
• 6979980500 Remove the unused tf.Example codepath Augustin Zidek 2025-10-07 01:04:52 -07:00
• 9b2ed02ff6 Remove unused utility function Augustin Zidek 2025-10-02 08:11:23 -07:00
• 2b2aaafa77 Remove redundant dependencies in a test Augustin Zidek 2025-10-02 06:06:52 -07:00
• 12f16df5e3 Use /usr/bin/env for bash shebang. Ryan Pachauri 2025-10-01 11:41:44 -07:00
• c7625926bc Add rsync notice for for DB download. Ryan Pachauri 2025-09-30 12:12:02 -07:00
• 8815b4657f Remove redundant module docstrings from test files. Akvile Zemgulyte 2025-09-29 08:36:27 -07:00
• 25102bf040 Add a context managed unfreeze() method in base_config Harsh Tiku 2025-09-29 07:20:40 -07:00
• dbaafbcdea Run Pyformat on the entire AlphaFold 2 codebase. Augustin Zidek 2025-09-29 06:27:41 -07:00
• ecdc85103f Bring model config creation in one place by simplifying num_ensemble setting Harsh Tiku 2025-09-25 07:42:28 -07:00
• 1ff6388c67 Rename variables for clarity Harsh Tiku 2025-09-25 02:18:38 -07:00
• 4b81ad9cfe Add CPU/thread control to MSA tools and update dependencies. Ryan Pachauri 2025-09-24 08:29:46 -07:00
• 77816c74dc # Refactor AlphaFold model configuration to use dataclasses Harsh Tiku 2025-09-24 07:20:09 -07:00
• 06a8da6cda Correct standard deviation used in CA-C-N angle loss. Ryan Pachauri 2025-09-23 11:54:57 -07:00
• e1554305c0 Remove pandas dependency from msa_pairing.py. Ryan Pachauri 2025-09-17 09:51:59 -07:00
• 2652cafb43 Refactor between_residue_bond_loss to use a shared helper function. Ryan Pachauri 2025-09-17 08:31:42 -07:00
• cc9042484e Add tests for all_atom.between_residue_bond_loss. Ryan Pachauri 2025-09-16 10:33:07 -07:00
• c9b9901dda Make run_alphafold.py and shell scripts installable. Ryan Pachauri 2025-09-16 07:35:05 -07:00
• 2c4a647dc8 Use stable sorting in MSA pairing. Ryan Pachauri 2025-09-15 10:40:42 -07:00
• dffd48ab62 Deprecate dm-tree in favor of jax.tree. Ryan Pachauri 2025-09-15 09:25:48 -07:00
• 4db5d8e94c Fix exception causes in data/templates.py Ryan Pachauri 2025-09-15 08:59:04 -07:00
• c77d8b52d3 Fix unit mismatch issue in Amber relax Augustin Zidek 2025-09-02 10:32:55 -07:00
• c095a657ad Fix typos. Ryan Pachauri 2025-08-21 20:51:02 -07:00
• e57fba02b1 Clarify and fix documentation. Ryan Pachauri 2025-08-21 20:21:56 -07:00
• aba97651a6 Use correct type information in tests. Ryan Pachauri 2025-08-19 18:37:25 -07:00
• 29f082183b Remove declaration of support for Python 3.6/3.7 and add 3.11/3.12 Augustin Zidek 2025-08-13 06:35:11 -07:00
• 79a0210693 Format msa_pairing Augustin Zidek 2025-08-13 06:06:55 -07:00
• 6544d69fc3 Remove unused dependencies Augustin Zidek 2025-08-12 06:29:56 -07:00
• b1d8619675 Use pytest for testing instead of setup.py test Augustin Zidek 2025-08-01 04:18:25 -07:00
• e9b68483fc Fix Docker build due to changes in Conda and don't limit make parallelism Augustin Zidek 2025-07-16 03:09:33 -07:00
• b522811d9e Avoid use of deprecated jax.util APIs Augustin Zidek 2025-05-16 08:32:39 -07:00
• 8050b46921 No public description Hana Joo 2025-04-29 09:30:32 -07:00
• 020cd6d6cb Add information about PDBe template cutoff date DeepMind 2025-03-17 05:39:43 -07:00
• 2ca41b1991 Deprecate the AlphaFold 2 notebook Dariusz Lasecki 2025-01-29 06:31:58 -08:00
• 24fbdfc3ce Update JSON format docs with new template on/off, cutoff date fields. DeepMind 2025-01-27 08:48:23 -08:00
• 93e024bd55 Do not use jnp.clip arguments which are not supported in the pinned JAX version. Augustin Zidek 2025-01-24 05:09:31 -08:00
• 11a991ea66 Bump Python in Colab to 3.11. Augustin Zidek 2025-01-23 04:40:13 -08:00
• fa0c5266b3 jax.numpy.clip: update use of deprecated arguments. Jake VanderPlas 2025-01-14 05:41:35 -08:00
• 6350ddd63b Update Conda to 24.11.1 to fix Docker build failure and small improvements to the Dockerfile. Augustin Zidek 2024-12-18 03:25:29 -08:00
• bbd8300d6a Automated Code Change: Suppress pytype errors Martin Huschenbett 2024-11-26 01:40:44 -08:00
• d95a92aae1 Update the disclaimer to match AlphaFold 3 + run mdformat. Augustin Zidek 2024-11-14 03:33:52 -08:00
• 85e0be3c7d Make apt output log-friendly by adding the --quiet flag. Augustin Zidek 2024-08-20 02:45:38 -07:00
• a2217f031e Pin setuptools on a version smaller than 72.0.0. Augustin Zidek 2024-08-07 03:58:52 -07:00
• 692c01c524 [numpy] Fix users of NumPy APIs that are removed in NumPy 2.0. Peter Hawkins 2024-07-25 04:16:31 -07:00
• 93a9a042eb Inline SCOPData to be compatible with future Biopython versions. Augustin Zidek 2024-07-01 07:54:28 -07:00
• 5b0e1f2c55 Replace deprecated jax.tree_* functions with jax.tree.* Jake VanderPlas 2024-05-15 03:30:40 -07:00
• f251de6613 Add documentation for AlphaFold Server JSON file format. Augustin Zidek 2024-05-08 07:03:06 -07:00
• 4d4a1aea99 Update openmm in AlphaFold colab. Hamish Tomlinson 2024-04-15 11:07:20 -07:00
• 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 Hamish Tomlinson 2024-04-12 01:57:12 -07:00
• 7e7de59cd2 Remove deprecated PRNGKeyArray. Hamish Tomlinson 2024-04-10 08:01:12 -07:00
• 5208f1b70e Update jax, haiku and chex versions. Hamish Tomlinson 2024-04-10 06:03:27 -07:00
• 6d95d1982e Fix how we extract mmCIF resolution (fix ordering issue). Augustin Zidek 2024-03-21 06:02:51 -07:00
• 032e2f2673 Update conda to 24.1.2. Hamish Tomlinson 2024-02-29 03:01:05 -08:00
• 632ef575c6 Uninstall keras in notebook to avoid the keras initializer fault. Hamish Tomlinson 2024-01-31 04:50:09 -08:00
• 4f447319e4 Loosen overly tight numerical tolerances to allow for one-time random value change from https://github.com/google/jax/discussions/18480 Matthew Johnson 2023-12-15 07:12:30 -08:00
• 1fa9200c7f [JAX] Replace uses of jax.devices("cpu") with jax.local_devices(backend="cpu"). Peter Hawkins 2023-11-15 08:11:03 -08:00
• f715f016d8 Revert a change that is not compatible with JAX 0.3.25. Augustin Zidek 2023-11-01 05:31:26 -07:00
• f78c589304 Update wwPDB paths from ftp.wwpdb.org to files.wwpdb.org. Augustin Zidek 2023-10-23 03:14:06 -07:00
• bbc133b060 Add assertion to aid type checking. DeepMind 2023-09-25 08:04:16 -07:00
• a8875a9c0d Replace deprecated PRNGKeyArray isinstance checks Jake VanderPlas 2023-09-15 09:54:13 -07:00
• 22f6919174 Add a cast to prevent future Pandas typing issues. Augustin Zidek 2023-09-05 23:17:11 -07:00
• c9431c4c12 Remove unused imports. Augustin Zidek 2023-09-04 03:01:22 -07:00
• bbe8a844e0 Fix: return correct renaming mask. DeepMind 2023-08-18 07:26:14 -07:00
• 82ef354ca3 Add Conda lib path to LD_LIBRARY_PATH. Augustin Zidek 2023-08-16 08:02:52 -07:00
• 7c9114c842 Bump jax to 0.4.14 and haiku to 0.0.10. Hamish Tomlinson 2023-08-10 06:27:29 -07:00
• 69afc4df91 Downgrade to pyopenssl 22.0.0 to fix compatibility issue Jana Cavojska 2023-07-20 10:26:45 -07:00
• 6cb85e9684 Update Conda in Colab and fix dependency issues Jana Cavojska 2023-07-19 02:48:20 -07:00
• 6c4d833fbd Add saving Protein to mmCIF file and reading Protein from mmCIF file. Dariusz Lasecki 2023-06-16 07:35:02 -07:00
• 4bd3ff76cc Use HTTPS instead of FTP to download all databases and switch to a faster mirror for UniRef90. Augustin Zidek 2023-06-01 03:33:29 -07:00
• 9bbfdc7c81 alphafold: make compatible with JAX custom PRNG Jake VanderPlas 2023-05-18 03:05:16 -07:00
• d885c55750 Future-proof alphafold prng test for jax custom PRNG Jake VanderPlas 2023-05-10 09:31:42 -07:00
• 6a3af1adb3 Rename get_pae_json function DeepMind 2023-05-03 05:03:21 -07:00
• c1e92dc524 Bump SciPy version from 1.7.0 to 1.7.3 for compatibility with Python 3.10. Augustin Zidek 2023-05-02 11:57:37 -07:00
• 955737f12c Upgrade OpenMM from 7.5.1 to 7.7.0 and bump Colab Python version to 3.10. Augustin Zidek 2023-05-02 04:32:59 -07:00
• 2819de4ddd Add pLDDT and PAE files saving to AF runner, update Colab. DeepMind 2023-04-20 02:21:56 -07:00
• 4d83e3fc08 Bump version to 2.3.2 in setup.py and colab. Hamish Tomlinson 2023-04-11 02:22:30 -07:00
• 3f31725591 Upgrade pyopenssl in colab. v2.3.2 Hamish Tomlinson 2023-03-27 04:50:17 -07:00
• e51692c9ae Change softmax to use where and float32. Hamish Tomlinson 2023-03-27 03:43:55 -07:00
• e1d2d53af8 Re-enable form cellview. Hamish Tomlinson 2023-03-20 09:15:50 -07:00
• 2e6a78f08b Bump Python in Colab to 3.9. Augustin Zidek 2023-03-10 08:10:38 -08:00