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OpenFold v1.0.1

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@gahdritz gahdritz released this 23 Nov 20:46
· 672 commits to main since this release

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

What's Changed

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

New Contributors

Full Changelog: v1.0.0...v1.0.1