Commits · 5a004f04cb5292ea93d3e1787f05fa81d92b3d7a · OpenDAS / OpenFold

29 Oct, 2021 7 commits
- zero out nan components in loss · 5a004f04
  Marta authored Oct 29, 2021
  
  5a004f04
- center coordinates at 0 · 45a98436
  Marta authored Oct 29, 2021
  
  45a98436
- add resources to dockerfile + .dockerignore · 1c4d2c71
  Marta authored Oct 29, 2021
  
  1c4d2c71
- Dockerfile with minimal env needed for training · f86fc334
  Marta authored Oct 29, 2021
  
  f86fc334
- Remove debugging print statement · e69b2a11
  Gustaf Ahdritz authored Oct 29, 2021
  
  e69b2a11
- Remove experimental features committed by mistake · 9df2af52
  Gustaf Ahdritz authored Oct 29, 2021
  
  9df2af52
- Fix horrible in-place operation bug · d5480cbe
  Gustaf Ahdritz authored Oct 29, 2021
  
  d5480cbe
28 Oct, 2021 5 commits
- Make template code use less memory during inference · 2faff451
  Gustaf Ahdritz authored Oct 28, 2021
  
  2faff451
- Add empty template handling to inference pipeline · 407d9924
  Gustaf Ahdritz authored Oct 28, 2021
  
  407d9924
- Add PyTorch Lightning note in README · 8f7e90d6
  Gustaf Ahdritz authored Oct 27, 2021
  
  8f7e90d6
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · 5941d584
  Gustaf Ahdritz authored Oct 27, 2021
  
  5941d584
- Fix empty template feature bug · d71d37ff
  Gustaf Ahdritz authored Oct 27, 2021
  
  d71d37ff
26 Oct, 2021 6 commits
- Fix model checkpointing bug · a9a19b78
  Gustaf Ahdritz authored Oct 26, 2021
  
  a9a19b78
- Make template parsing optional · 81ae777d
  Gustaf Ahdritz authored Oct 26, 2021
  
  81ae777d
- Add section on ProteinNet to README · ea484b71
  Gustaf Ahdritz authored Oct 26, 2021
  
  ea484b71
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · f7ed4a4b
  Gustaf Ahdritz authored Oct 26, 2021
  
  f7ed4a4b
- Add description to ProteinNet MSA script · 98b2c663
  Gustaf Ahdritz authored Oct 26, 2021
  
  98b2c663
- Add ProteinNet support to parser · b5f885d0
  Gustaf Ahdritz authored Oct 26, 2021
  
  b5f885d0
25 Oct, 2021 3 commits
- Tweak README formatting · 0fb5b743
  Gustaf Ahdritz authored Oct 25, 2021
  
  0fb5b743
- Remove a pair of outdated comments · f03be78f
  Gustaf Ahdritz authored Oct 25, 2021
  
  f03be78f
- Fix bug in dummy dataset · 428d90ce
  Gustaf Ahdritz authored Oct 25, 2021
  
  428d90ce
24 Oct, 2021 2 commits
- Merge pull request #1 from aqlaboratory/mpvenkatesh/changes · 94ab346e
  Gustaf Ahdritz authored Oct 24, 2021
```
minor fixes
```
  94ab346e
- minor fixes · 04fa3548
  sft-managed authored Oct 24, 2021
  
  04fa3548
23 Oct, 2021 3 commits
- Fix PDB parsing, add distillation MSA cropping · 6298a3e6
  Gustaf Ahdritz authored Oct 23, 2021
  
  6298a3e6
- Fix bug in MSA loss · 4d40ce80
  Gustaf Ahdritz authored Oct 23, 2021
  
  4d40ce80
- Add training callbacks · 4c9d372d
  Gustaf Ahdritz authored Oct 23, 2021
  
  4c9d372d
22 Oct, 2021 14 commits
- Clarify checkpointing comment · 727e68c2
  Gustaf Ahdritz authored Oct 22, 2021
  
  727e68c2
- Move note on aria2c · f706ace4
  Gustaf Ahdritz authored Oct 22, 2021
  
  f706ace4
- Add note about HH-suite installer · 17f8d7cb
  Gustaf Ahdritz authored Oct 22, 2021
  
  17f8d7cb
- Add script for installing the HH-suite · 5b9cfdaf
  Gustaf Ahdritz authored Oct 22, 2021
  
  5b9cfdaf
- Improve global seeding, clean up training script a little · 1715e3d5
  Gustaf Ahdritz authored Oct 22, 2021
  
  1715e3d5
- Delete old file · 971c41d2
  Gustaf Ahdritz authored Oct 22, 2021
  
  971c41d2
- Remove outdated comment · 4df6457a
  Gustaf Ahdritz authored Oct 22, 2021
  
  4df6457a
- Add DeepSpeed check to checkpointing function · 748a8c50
  Gustaf Ahdritz authored Oct 22, 2021
  
  748a8c50
- Add dummy dataloader, most recent version of training script · fcf9e2f8
  Gustaf Ahdritz authored Oct 22, 2021
  
  fcf9e2f8
- Fix grammar mistake · 6dc8aa7f
  Gustaf Ahdritz authored Oct 21, 2021
  
  6dc8aa7f
- Add gradient clipping to DeepSpeed config generator · 872787b9
  Gustaf Ahdritz authored Oct 21, 2021
  
  872787b9
- Add some more dependencies · ac058f54
  Gustaf Ahdritz authored Oct 21, 2021
  
  ac058f54
- Fix typo in README · 8cb569f2
  Gustaf Ahdritz authored Oct 21, 2021
  
  8cb569f2
- Reformat README again · 01ad794b
  Gustaf Ahdritz authored Oct 21, 2021
  
  01ad794b