OpenFold Files

With this release, we include a new home for OpenFold documentation located at: https://openfold.readthedocs.io/.

We hope that the guides provided in the documentation will help users with common workflows, as well as issues that commonly occur.

A few quality of life changes are also included:

• Adds scripts for creating the OpenFold training set from the datasets that are stored on RODA. We will aim to host the processed datasets on RODA as well in the near future.
• Adds a script for converting OpenFold v1 weights into OpenFold v2 weights, see this page for more info
• Adds --experiment_config_json option to both run_pretrained_openfold.py and train_openfold.py to more easily edit model config settings in openfold/config.py

What's Changed

• Fix distributed seeding behavior by @ljarosch in https://github.com/aqlaboratory/openfold/pull/418
• Fix resolution field in mmcif_parsing by @ljarosch in https://github.com/aqlaboratory/openfold/pull/420
• Adds mkl version to environment.yml by @jnwei in https://github.com/aqlaboratory/openfold/pull/437
• Update multi-chain permutation and permutation unittest by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/406
• Duplicate expansion support by @ljarosch in https://github.com/aqlaboratory/openfold/pull/419
• Fix Colab by using OF commit from pl_upgrades by @vaclavhanzl in https://github.com/aqlaboratory/openfold/pull/432
• Adds Documentation and minor quality of life fixes by @jnwei in https://github.com/aqlaboratory/openfold/pull/439

New Contributors

• @ljarosch made their first contribution in https://github.com/aqlaboratory/openfold/pull/418

Full Changelog: https://github.com/aqlaboratory/openfold/compare/v2.0.0...v.2.1.0