8000 Commits · SKKUGE/alphafold · GitHub

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Commits

Commits on Dec 17, 2024

Add .gitignore and VSCode launch configuration
DENGARDEN
committed

Commits on Nov 14, 2024

Update the disclaimer to match AlphaFold 3 + run mdformat.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Aug 20, 2024

Make apt output log-friendly by adding the `--quiet` flag.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Aug 7, 2024

Pin setuptools on a version smaller than 72.0.0.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Jul 25, 2024

[numpy] Fix users of NumPy APIs that are removed in NumPy 2.0.

hawkinsp
authored and
copybara-github
committed

Commits on Jul 1, 2024

Inline SCOPData to be compatible with future Biopython versions.

Augustin-Zidek
authored and
copybara-github
committed

Commits on May 15, 2024

Replace deprecated `jax.tree_*` functions with `jax.tree.*`

Jake VanderPlas
authored and
copybara-github
committed

Commits on May 8, 2024

Add documentation for AlphaFold Server JSON file format.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Apr 15, 2024

Update openmm in AlphaFold colab.

Htomlinson14
authored and
copybara-github
committed

Commits on Apr 12, 2024

Update requirements:

Htomlinson14
authored and
copybara-github
committed

Commits on Apr 10, 2024

Remove deprecated PRNGKeyArray.

Htomlinson14
authored and
copybara-github
committed
Update jax, haiku and chex versions.

Htomlinson14
authored and
copybara-github
committed

Commits on Mar 21, 2024

Fix how we extract mmCIF resolution (fix ordering issue).

Augustin-Zidek
authored and
copybara-github
committed

Commits on Feb 29, 2024

Update conda to 24.1.2.

Htomlinson14
authored and
copybara-github
committed

Commits on Jan 31, 2024

Uninstall keras in notebook to avoid the keras initializer fault.

Htomlinson14
authored and
copybara-github
committed

Commits on Dec 15, 2023

Loosen overly tight numerical tolerances to allow for one-time random value

mattjj
authored and
copybara-github
committed

Commits on Nov 15, 2023

[JAX] Replace uses of jax.devices("cpu") with jax.local_devices(backend="cpu").

hawkinsp
authored and
copybara-github
committed

Commits on Nov 1, 2023

Revert a change that is not compatible with JAX 0.3.25.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Oct 23, 2023

Update wwPDB paths from ftp.wwpdb.org to files.wwpdb.org.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Sep 25, 2023

Add assertion to aid type checking.

DeepMind
authored and
copybara-github
committed

Commits on Sep 15, 2023

Replace deprecated PRNGKeyArray isinstance checks

Jake VanderPlas
authored and
copybara-github
committed

Commits on Sep 6, 2023

Add a cast to prevent future Pandas typing issues.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Sep 4, 2023

Remove unused imports.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Aug 18, 2023

Fix: return correct renaming mask.

DeepMind
authored and
copybara-github
committed

Commits on Aug 16, 2023

Add Conda lib path to `LD_LIBRARY_PATH`.

Augustin-Zidek
authored and
copybara-github
committed

Commits on Aug 10, 2023

Bump jax to 0.4.14 and haiku to 0.0.10.

Htomlinson14
authored and
copybara-github
committed

Commits on Jul 20, 2023

Downgrade to pyopenssl 22.0.0 to fix compatibility issue

Jane333
authored and
copybara-github
committed

Commits on Jul 19, 2023

Update Conda in Colab and fix dependency issues

Jane333
authored and
copybara-github
committed

Commits on Jun 16, 2023

Add saving Protein to mmCIF file and reading Protein from mmCIF file.

dlasecki
authored and
copybara-github
committed

Commits on Jun 1, 2023

Use HTTPS instead of FTP to download all databases and switch to a faster mirror for UniRef90.

Augustin-Zidek
authored and
copybara-github
committed

Commits on May 18, 2023

alphafold: make compatible with JAX custom PRNG

Jake VanderPlas
authored and
copybara-github
committed

Commits on May 10, 2023

Future-proof alphafold prng test for jax custom PRNG

Jake VanderPlas
authored and
copybara-github
committed

Commits on May 3, 2023

Rename get_pae_json function

DeepMind
authored and
copybara-github
committed

Commits on May 2, 2023

Bump SciPy version from 1.7.0 to 1.7.3 for compatibility with Python 3.10.

Augustin-Zidek
authored and
copybara-github
committed
Upgrade OpenMM from 7.5.1 to 7.7.0 and bump Colab Python version to 3.10.

Augustin-Zidek
authored and
copybara-github
committed

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