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Commits on Feb 8, 2022

• Remove unused code.

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Commits on Feb 14, 2022

• Add split_rng=False (current default) to sharded_map.

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Commits on Feb 16, 2022

• Improve support for num_recycle=0.

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Commits on Feb 17, 2022

• Enable multiple seeds per model for AlphaFold-Multimer.

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Commits on Feb 18, 2022

• Fix random_seed overflow when seeds per model > 1.

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• Remove prokaryotic pairing from AFOS.

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Commits on Feb 21, 2022

• Remove unused bias arg in GlobalAttention.

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Commits on Feb 23, 2022

• Simplify mounting of files.

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Commits on Mar 2, 2022

• No longer use runtime=nvidia to expose GPUs to the container.

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• Remove unused function casp_model_names.

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Commits on Mar 3, 2022

• Update multimer models to v2.

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Commits on Mar 7, 2022

• Update change-log to briefly describe the change in AlphaFold-Multimer models.

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• Update open source between_residue_clash_loss to take into account multiple chains.

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Commits on Mar 8, 2022

• Add instructions for using multimer v1 model weights.

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Commits on Mar 16, 2022

• Add info for getting in touch via email to colab and readme.

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• Fix readme wording.

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Commits on Mar 17, 2022

• Do not reuse the temporary output directory in run_alphafold_test.

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Commits on Mar 21, 2022

• Silence some pytype errors.

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Commits on May 19, 2022

• Mention the workaround for the Nvidia public key issue in the README.

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Commits on May 25, 2022

• Fix AlphaFold version in setup.py.

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Commits on May 31, 2022

• Fix jax.tree_multimap deprecation warning.

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• Add support for CUDA patch versions.

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Commits on Jun 7, 2022

• Clarify that AlphaFold works only under Linux.

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Commits on Jun 13, 2022

• Pin protobuf version to 3.20.1.

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• Bump AlphaFold version to 2.2.1.

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• Replace period with hyphens in place, instead of declaring environment variable.

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• Bump AlphaFold version to v2.2.2.

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Commits on Jun 14, 2022

• Remove unused type hint from run_alphafold script.

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• Move disable_v2_behaviour() to setUp to enable running tests in test suites.

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• Add matplotlib test dependency so we can run notebook_utils_test.

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• Remove unneeded __init__.py

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• Migrate from collections.Iterable to collections.abc.Iterable.

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Commits on Jun 20, 2022

• Fix Dockerfile breakage due to jax-ml/jax#11142.

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Commits on Jul 28, 2022

• Add a readme file for the AlphaFold Protein Structure Database.

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• Internal change

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Commits on Aug 12, 2022

• Changed PAE json output to new format that matches the format used in AFDB.

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Commits on Aug 25, 2022

• Pin Conda version to 4.13.0.

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• Bump the version to 2.2.3.

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Commits on Aug 31, 2022

• Make using GPU in relaxation optional, with default not to use.

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Commits on Sep 16, 2022

• Update Jax and Haiku versions

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• Reduce size of docker image by cleaning apt, conda and pip caches

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• Fix incorrect length_scale argument

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Commits on Sep 21, 2022

• Bump version to 2.2.4

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Commits on Sep 22, 2022

• Fix missing comma in AlphaFold-Multimer BibTeX entry.

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Commits on Oct 12, 2022

• Update version in colab

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Commits on Oct 13, 2022

• [JAX] Import scipy submodules directly in code that uses them.

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Commits on Nov 1, 2022

• Update the readme file for the AlphaFold Protein Structure Database (version 4).

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Commits on Nov 26, 2022

• Updated Jax to 0.3.25 and Haiku to 0.0.9

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Commits on Dec 1, 2022

• Bump python in colab to 3.8

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Commits on Dec 11, 2022

• Release code for v2.3.0

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• Update readme.

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Commits on Dec 13, 2022

• Set environment variables before any other code is executed.

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Commits on Dec 15, 2022

• [NumPy] Remove references to deprecated NumPy type aliases.

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• Add query_multiple to Jackhmmer.

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• Restore the max sequence limit to 4000 now that unified memory is fixed.

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Commits on Dec 19, 2022

• [NumPy] Remove references to deprecated NumPy type aliases.

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Commits on Dec 20, 2022

• Speed up Colab multimer MSA search: fetch each db chunk only once and run all queries against it.

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Commits on Dec 21, 2022

• Add eval_dropout option for using dropout in trunk at eval time.

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• Adding prediction timings to README.

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Commits on Dec 23, 2022

• Adding recycle information for timings.

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Commits on Jan 10, 2023

• Fix GPU relax for longer chains by pinning large memory ops to cpu.

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Commits on Jan 11, 2023

• Update of README.md

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• Bump version to 2.3.1

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Commits on Jan 12, 2023

• Fix typo in a comment in residue constants.

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• Use shutil to zip and download colab outputs

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Commits on Jan 13, 2023

• Add ability to only run relax for the best unrelaxed model.

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Commits on Jan 17, 2023

• Remove jax dependency from results pkl

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Commits on Jan 23, 2023

• Update tensorflow

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Commits on Jan 27, 2023

• Improve documentation on how to install aria2c.

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• Update readme for relaxation flag.

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Commits on Feb 1, 2023

• Make _chem_comp.type logic case-insensitive.

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Commits on Feb 9, 2023

• Add cell execution order error checking.

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Commits on Feb 21, 2023

• Improve readme explanation of ranked_*.pdb.

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Commits on Feb 24, 2023

• Fix incorrect type annotations.

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Commits on Mar 6, 2023

• Turn off bfloat16 in colab.

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Commits on Mar 10, 2023

• Bump Python in Colab to 3.9.

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Commits on Mar 20, 2023

• Re-enable form cellview.

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Commits on Mar 27, 2023

• Change softmax to use where and float32.

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• Upgrade pyopenssl in colab.

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

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Commits on Apr 20, 2023

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

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

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

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Commits on May 3, 2023

• Rename get_pae_json function

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Commits on May 10, 2023

• Future-proof alphafold prng test for jax custom PRNG

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Commits on May 18, 2023

• alphafold: make compatible with JAX custom PRNG

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Commits on Jun 1, 2023

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

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Commits on Jun 16, 2023

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

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• Update Conda in Colab and fix dependency issues

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• Downgrade to pyopenssl 22.0.0 to fix compatibility issue

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• Bump jax to 0.4.14 and haiku to 0.0.10.

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• Add Conda lib path to LD_LIBRARY_PATH.

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• Fix: return correct renaming mask.

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• Remove unused imports.

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Commits on Sep 6, 2023

• Add a cast to prevent future Pandas typing issues.

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Commits on Sep 15, 2023

• Replace deprecated PRNGKeyArray isinstance checks

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Commits on Sep 25, 2023

• Add assertion to aid type checking.

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Commits on Oct 23, 2023

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

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Commits on Nov 1, 2023

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

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Commits on Nov 15, 2023

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

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Commits on Dec 15, 2023

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

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Commits on Jan 31, 2024

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

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Commits on Feb 29, 2024

• Update conda to 24.1.2.

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Commits on Mar 21, 2024

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

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Commits on Apr 10, 2024

• Update jax, haiku and chex versions.

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• Remove deprecated PRNGKeyArray.

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Commits on Apr 12, 2024

• Update requirements:

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Commits on Apr 15, 2024

• Update openmm in AlphaFold colab.

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Commits on May 8, 2024

• Add documentation for AlphaFold Server JSON file format.

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Commits on May 15, 2024

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

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Commits on Jul 1, 2024

• Inline SCOPData to be compatible with future Biopython versions.

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Commits on Jul 25, 2024

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

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Commits on Aug 7, 2024

• Pin setuptools on a version smaller than 72.0.0.

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Commits on Aug 20, 2024

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

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Commits on Nov 14, 2024

• Update the disclaimer to match AlphaFold 3 + run mdformat.

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Commits on Nov 26, 2024

• Automated Code Change: Suppress pytype errors

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Commits on Dec 18, 2024

• Update Conda to 24.11.1 to fix Docker build failure and small improvements to the Dockerfile.

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Commits on Jan 14, 2025

• jax.numpy.clip: update use of deprecated arguments.

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  Jake VanderPlas

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Commits on Jan 23, 2025

• Bump Python in Colab to 3.11.

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Commits on Jan 24, 2025

• Do not use jnp.clip arguments which are not supported in the pinned JAX version.

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Commits on Jan 27, 2025

• Update JSON format docs with new template on/off, cutoff date fields.

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Commits on Jan 29, 2025

• Deprecate the AlphaFold 2 notebook

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