OpenFold Files

Major Changes

• SoloSeq inference: Single Sequence Inference using ESM-1b embeddings with template features is now supported. Check out SoloSeq in the README for more information.
• Multimer : Inference in multimer mode using the AlphaFold-Multimer weights is now supported. Check out Multimer in the README for more instructions, or try out multimer inference in the Colab notebook.
• Addition of a custom DeepSpeed DS4Sci_EvoformerAttention kernel for 13X reduced peak device memory requirement, leading to 15% faster training and 4x speedup during inference. Test it out using the use_deepspeed_evo_attention option in openfold/config.py. More information in the README.

All Changes

• add long_sequence_inference option to command line by @decarboxy in https://github.com/aqlaboratory/openfold/pull/253
• Fix for CPU only install by @p-durandin in https://github.com/aqlaboratory/openfold/pull/252
• Obsolete parsing and File not found fix by @l-bick in https://github.com/aqlaboratory/openfold/pull/264
• Load pretrained jax weights by @l-bick in https://github.com/aqlaboratory/openfold/pull/263
• Fix --cpus_per_task argument in README by @awaelchli in https://github.com/aqlaboratory/openfold/pull/278
• Add a .gitignore file by @awaelchli in https://github.com/aqlaboratory/openfold/pull/279
• Add missing warmup_num_steps parameters to DeepSpeed config generation script. by @jonathanking in https://github.com/aqlaboratory/openfold/pull/290
• Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 glitch by @vaclavhanzl in https://github.com/aqlaboratory/openfold/pull/285
• New option to output in ModelCIF format instead of PDB format by @josemduarte in https://github.com/aqlaboratory/openfold/pull/287
• Fix comparison for max_seqlen when downloading CAMEO. by @jonathanking in https://github.com/aqlaboratory/openfold/pull/292
• Resolving torch cuda availability for cpu-only installation by @zrqiao in https://github.com/aqlaboratory/openfold/pull/275
• Improve TriangularMultiplicativeUpdate stability in fp16 mode by @nikitos9000 in https://github.com/aqlaboratory/openfold/pull/295
• Advance python version to 3.9 to build docker in Ubuntu Lunar Lobster by @vaclavhanzl in https://github.com/aqlaboratory/openfold/pull/309
• add comment about the interpretation of ambiguous atoms by @luwei0917 in https://github.com/aqlaboratory/openfold/pull/314
• Fix Colab again after ModelCIF merge and python version change in Colab by @vaclavhanzl in https://github.com/aqlaboratory/openfold/pull/308
• Fix Colab: Install all conda packages together by @vaclavhanzl in https://github.com/aqlaboratory/openfold/pull/320
• Multimer by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/331
• Added multi-chain permutation steps, multimer datamodule, and training code for multimer by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/336
• Fix multimer boolean tensor error by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/337
• Update multi-chain permutation by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/343
• Update validation by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/346
• Fixes cuda/float wrapper error in unit tests by @jnwei in https://github.com/aqlaboratory/openfold/pull/350
• Fixed inference script in multimer mode by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/348
• Update multi-chain permutation and training codes by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/353
• fixed the creation of best_align when permutation is turned off by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/355
• Single-sequence model by @sachinkadyan7 in https://github.com/aqlaboratory/openfold/pull/354
• move the kabsch rotation step to gpu by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/359
• Installation updates by @jnwei in https://github.com/aqlaboratory/openfold/pull/360
• [DNM] Update Docker config by @mattwthompson in https://github.com/aqlaboratory/openfold/pull/361
• Bump actions/checkout from 2 to 4 by @dependabot in https://github.com/aqlaboratory/openfold/pull/366
• Bump actions/setup-python from 2 to 4 by @dependabot in https://github.com/aqlaboratory/openfold/pull/365
• Fixes imports to colab notebook. by @jnwei in https://github.com/aqlaboratory/openfold/pull/372
• Adds Soloseq parameter download script. by @jnwei in https://github.com/aqlaboratory/openfold/pull/373
• Fix for MSA block deletion by @christinaflo in https://github.com/aqlaboratory/openfold/pull/374
• Adds query_multiple to jackhammer.py by @jnwei in https://github.com/aqlaboratory/openfold/pull/375
• Deepspeed evoformer attention by @christinaflo in https://github.com/aqlaboratory/openfold/pull/378
• Speed up data loading process by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/376
• Update data pipeline by @dingquanyu in https://github.com/aqlaboratory/openfold/pull/385
• Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/aqlaboratory/openfold/pull/380
• Readme changes by @jnwei in https://github.com/aqlaboratory/openfold/pull/389
• suporting newer numpy by @YoelShoshan in https://github.com/aqlaboratory/openfold/pull/307
• Change test_compare_model in deepspeed test to use mean instead of max by @jnwei in https://github.com/aqlaboratory/openfold/pull/396
• Fix Miniforge3 download link in Dockerfile by @controny in https://github.com/aqlaboratory/openfold/pull/402
• Adding multimer support to OpenFold notebook by @jnwei in https://github.com/aqlaboratory/openfold/pull/401
• Type fixes and README changes for multimer branch by @jnwei in https://github.com/aqlaboratory/openfold/pull/404
• Full multimer merge by @christinaflo in https://github.com/aqlaboratory/openfold/pull/405

New Contributors

• @p-durandin made their first contribution in https://github.com/aqlaboratory/openfold/pull/252
• @l-bick made their first contribution in https://github.com/aqlaboratory/openfold/pull/264
• @awaelchli made their first contribution in https://github.com/aqlaboratory/openfold/pull/278
• @vaclavhanzl made their first contribution in https://github.com/aqlaboratory/openfold/pull/285
• @zrqiao made their first contribution in https://github.com/aqlaboratory/openfold/pull/275
• @luwei0917 made their first contribution in https://github.com/aqlaboratory/openfold/pull/314
• @dingquanyu made their first contribution in https://github.com/aqlaboratory/openfold/pull/331
• @jnwei made their first contribution in https://github.com/aqlaboratory/openfold/pull/350
• @mattwthompson made their first contribution in https://github.com/aqlaboratory/openfold/pull/361
• @dependabot made their first contribution in https://github.com/aqlaboratory/openfold/pull/366
• @christinaflo made their first contribution in https://github.com/aqlaboratory/openfold/pull/374
• @YoelShoshan made their first contribution in https://github.com/aqlaboratory/openfold/pull/307
• @controny made their first contribution in https://github.com/aqlaboratory/openfold/pull/402

Full Changelog: https://github.com/aqlaboratory/openfold/compare/v1.0.1...v2.0.0