aqlaboratory/openfold: OpenFold v1.0.1

OpenFold as of the release of our manuscript. Many new features, including FP16 training + more stable training.

• use multiple models for inference by @decarboxy in https://github.com/aqlaboratory/openfold/pull/117
• Update input processing by @brianloyal in https://github.com/aqlaboratory/openfold/pull/116
• adding a caption to the image in the readme by @decarboxy in https://github.com/aqlaboratory/openfold/pull/133
• Properly handling file outputs when multiple models are evaluated by @decarboxy in https://github.com/aqlaboratory/openfold/pull/142
• Fix for issue in download_mgnify.sh by @josemduarte in https://github.com/aqlaboratory/openfold/pull/166
• Fix tag-sequence mismatch when predicting for multiple fastas by @sdvillal in https://github.com/aqlaboratory/openfold/pull/164
• Support openmm >= 7.6 by @sdvillal in https://github.com/aqlaboratory/openfold/pull/163
• Fixing issue in download_uniref90.sh by @josemduarte in https://github.com/aqlaboratory/openfold/pull/171
• Fix propagation of use_flash for offloaded inference by @epenning in https://github.com/aqlaboratory/openfold/pull/178
• Update deepspeed version to 0.5.10 by @NZ99 in https://github.com/aqlaboratory/openfold/pull/185
• Fixes errors when processing .pdb files by @NZ99 in https://github.com/aqlaboratory/openfold/pull/188
• fix incorrect learning rate warm-up after restarting from ckpt by @Zhang690683220 in https://github.com/aqlaboratory/openfold/pull/182
• Add opencontainers image-spec to Dockerfile by @SauravMaheshkar in https://github.com/aqlaboratory/openfold/pull/128
• Write inference and relaxation timings to a file by @brianloyal in https://github.com/aqlaboratory/openfold/pull/201
• Minor fixes in setup scripts by @timodonnell in https://github.com/aqlaboratory/openfold/pull/202
• Minor optimizations & fixes to support ESMFold by @nikitos9000 in https://github.com/aqlaboratory/openfold/pull/199
• Drop chains that are missing (structure) data in training by @timodonnell in https://github.com/aqlaboratory/openfold/pull/210
• adding a script for threading a sequence onto a structure by @decarboxy in https://github.com/aqlaboratory/openfold/pull/206
• Set pin_memory to True in default dataloader config. by @NZ99 in https://github.com/aqlaboratory/openfold/pull/212
• Fix missing subtract_plddt argument in prep_output call by @mhrmsn in https://github.com/aqlaboratory/openfold/pull/217
• fp16 fixes by @beiwang2003 in https://github.com/aqlaboratory/openfold/pull/222
• Set clamped vs unclamped FAPE for each sample in batch independently by @ar-nowaczynski in https://github.com/aqlaboratory/openfold/pull/223
• Fix probabilities type (int -> float) by @atgctg in https://github.com/aqlaboratory/openfold/pull/225
• Small fix for prep_mmseqs_dbs. by @jonathanking in https://github.com/aqlaboratory/openfold/pull/232

• @brianloyal made their first contribution in https://github.com/aqlaboratory/openfold/pull/116
• @josemduarte made their first contribution in https://github.com/aqlaboratory/openfold/pull/166
• @sdvillal made their first contribution in https://github.com/aqlaboratory/openfold/pull/164
• @epenning made their first contribution in https://github.com/aqlaboratory/openfold/pull/178
• @NZ99 made their first contribution in https://github.com/aqlaboratory/openfold/pull/185
• @Zhang690683220 made their first contribution in https://github.com/aqlaboratory/openfold/pull/182
• @SauravMaheshkar made their first contribution in https://github.com/aqlaboratory/openfold/pull/128
• @timodonnell made their first contribution in https://github.com/aqlaboratory/openfold/pull/202
• @nikitos9000 made their first contribution in https://github.com/aqlaboratory/openfold/pull/199
• @mhrmsn made their first contribution in https://github.com/aqlaboratory/openfold/pull/217
• @beiwang2003 made their first contribution in https://github.com/aqlaboratory/openfold/pull/222
• @ar-nowaczynski made their first contribution in https://github.com/aqlaboratory/openfold/pull/223
• @atgctg made their first contribution in https://github.com/aqlaboratory/openfold/pull/225
• @jonathanking made their first contribution in https://github.com/aqlaboratory/openfold/pull/232

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