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Commits on May 8, 2024

• Add documentation for AlphaFold Server JSON file format.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedMay 8, 2024
  f251de6

Commits on Apr 15, 2024

• Update openmm in AlphaFold colab.

  

  Htomlinson14

  authored and

  copybara-github

  committedApr 15, 2024
  4d4a1ae

Commits on Apr 12, 2024

• Update requirements:

  

  Htomlinson14

  authored and

  copybara-github

  committedApr 12, 2024
  dbe2a43

Commits on Apr 10, 2024

• Remove deprecated PRNGKeyArray.

  

  Htomlinson14

  authored and

  copybara-github

  committedApr 10, 2024
  7e7de59

• Update jax, haiku and chex versions.

  

  Htomlinson14

  authored and

  copybara-github

  committedApr 10, 2024
  5208f1b

Commits on Mar 21, 2024

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

  

  Augustin-Zidek

  authored and

  copybara-github

  committedMar 21, 2024
  6d95d19

Commits on Feb 29, 2024

• Update conda to 24.1.2.

  

  Htomlinson14

  authored and

  copybara-github

  committedFeb 29, 2024
  032e2f2

Commits on Jan 31, 2024

• Uninstall keras in notebook to avoid the keras initializer fault.

  

  Htomlinson14

  authored and

  copybara-github

  committedJan 31, 2024
  632ef57

Commits on Dec 15, 2023

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

  

  mattjj

  authored and

  copybara-github

  committedDec 15, 2023
  4f44731

Commits on Nov 15, 2023

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

  

  hawkinsp

  authored and

  copybara-github

  committedNov 15, 2023
  1fa9200

Commits on Nov 1, 2023

• Revert a change that is not compatible with JAX 0.3.25.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedNov 1, 2023
  f715f01

Commits on Oct 23, 2023

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

  

  Augustin-Zidek

  authored and

  copybara-github

  committedOct 23, 2023
  f78c589

Commits on Sep 25, 2023

• Add assertion to aid type checking.

  

  DeepMind

  authored and

  copybara-github

  committedSep 25, 2023
  bbc133b

Commits on Sep 15, 2023

• Replace deprecated PRNGKeyArray isinstance checks

  

  Jake VanderPlas

  authored and

  copybara-github

  committedSep 15, 2023
  a8875a9

Commits on Sep 6, 2023

• Add a cast to prevent future Pandas typing issues.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedSep 6, 2023
  22f6919

Commits on Sep 4, 2023

• Remove unused imports.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedSep 4, 2023
  c9431c4

Commits on Aug 18, 2023

• Fix: return correct renaming mask.

  

  DeepMind

  authored and

  copybara-github

  committedAug 18, 2023
  bbe8a84

Commits on Aug 16, 2023

• Add Conda lib path to LD_LIBRARY_PATH.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedAug 16, 2023
  82ef354

Commits on Aug 10, 2023

• Bump jax to 0.4.14 and haiku to 0.0.10.

  

  Htomlinson14

  authored and

  copybara-github

  committedAug 10, 2023
  7c9114c

Commits on Jul 20, 2023

• Downgrade to pyopenssl 22.0.0 to fix compatibility issue

  

  Jane333

  authored and

  copybara-github

  committedJul 20, 2023
  69afc4d

Commits on Jul 19, 2023

• Update Conda in Colab and fix dependency issues

  

  Jane333

  authored and

  copybara-github

  committedJul 19, 2023
  6cb85e9

Commits on Jun 16, 2023

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

  

  dlasecki

  authored and

  copybara-github

  committedJun 16, 2023
  6c4d833

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

  committedJun 1, 2023
  4bd3ff7

Commits on May 18, 2023

• alphafold: make compatible with JAX custom PRNG

  

  Jake VanderPlas

  authored and

  copybara-github

  committedMay 18, 2023
  9bbfdc7

Commits on May 10, 2023

• Future-proof alphafold prng test for jax custom PRNG

  

  Jake VanderPlas

  authored and

  copybara-github

  committedMay 10, 2023
  d885c55

Commits on May 3, 2023

• Rename get_pae_json function

  

  DeepMind

  authored and

  copybara-github

  committedMay 3, 2023
  6a3af1a

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

  committedMay 2, 2023
  c1e92dc

• Upgrade OpenMM from 7.5.1 to 7.7.0 and bump Colab Python version to 3.10.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedMay 2, 2023
  955737f

Commits on Apr 20, 2023

• Add pLDDT and PAE files saving to AF runner, update Colab.

  

  DeepMind

  authored and

  copybara-github

  committedApr 20, 2023
  2819de4

Commits on Apr 11, 2023

• Bump version to 2.3.2 in setup.py and colab.

  

  Htomlinson14

  authored and

  copybara-github

  committedApr 11, 2023
  4d83e3f

Commits on Mar 27, 2023

• Upgrade pyopenssl in colab.

  

  Htomlinson14

  authored and

  copybara-github

  committedMar 27, 2023
  3f31725

• Change softmax to use where and float32.

  

  Htomlinson14

  authored and

  copybara-github

  committedMar 27, 2023
  e51692c

Commits on Mar 20, 2023

• Re-enable form cellview.

  

  Htomlinson14

  authored and

  copybara-github

  committedMar 20, 2023
  e1d2d53

Commits on Mar 10, 2023

• Bump Python in Colab to 3.9.

  

  Augustin-Zidek

  authored and

  copybara-github

  committedMar 10, 2023
  2e6a78f

Commits on Mar 6, 2023

• Turn off bfloat16 in colab.

  

  Htomlinson14

  authored and

  copybara-github

  committedMar 6, 2023
  651fe8c

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