Commits · e28c28281aac8918ec8f23c6f1df9a564b143529 · OpenDAS / OpenFold · GitLab

08 Oct, 2021 15 commits
- Added feature transformations for creating pseudo-beta position for glycine. · e28c2828
  Sachin Kadyan authored Oct 08, 2021
  
  e28c2828
- Added feature transformations related to MSA clustering and summarization. · f7bb6999
  Sachin Kadyan authored Oct 08, 2021
  
  f7bb6999
- Add feature transformations related to MSAs: MSA sampling, handling extra_msa, and block_delete_msa · 62e820fc
  Sachin Kadyan authored Oct 08, 2021
  
  62e820fc
- Added some miscellaneous feature transformations, as well as some others for... · d54d5c55
  Sachin Kadyan authored Oct 08, 2021
```
Added some miscellaneous feature transformations, as well as some others for fixing and correcting residue types.
```
  d54d5c55
- Updated config with configurations required for the feature processing pipeline. · ede37f70
  Sachin Kadyan authored Oct 08, 2021
  
  ede37f70
- Added wrapper DataPipeline class responsible for running the alignment tools... · a48fcf58
  Sachin Kadyan authored Oct 08, 2021
```
Added wrapper DataPipeline class responsible for running the alignment tools and assembling the input features.
```
  a48fcf58
- Added functions for getting templates and calculating template features. · 41f856cd
  Sachin Kadyan authored Oct 08, 2021
  
  41f856cd
- Added parser for parsing mmCIF files for generating templates. · 63e0a247
  Sachin Kadyan authored Oct 08, 2021
  
  63e0a247
- Added functions for parsing various file formats. · 2654fcce
  Sachin Kadyan authored Oct 08, 2021
  
  2654fcce
- Moved all execution wrappers into a separate package directory. · 87740d2f
  Sachin Kadyan authored Oct 08, 2021
  
  87740d2f
- Added Kalign execution wrapper for aligning template sequences. · 857aa321
  Sachin Kadyan authored Oct 08, 2021
  
  857aa321
- Added Jackhmmer execution wrapper for finding MSAs of the input query sequence. · ede3d507
  Sachin Kadyan authored Oct 08, 2021
  
  ede3d507
- Added HHSearch execution wrapper for searching homologous protein in PDB70. · d615ddd4
  Sachin Kadyan authored Oct 08, 2021
  
  d615ddd4
- Added HHBlits execution wrapper. · 7c1fcd6f
  Sachin Kadyan authored Oct 08, 2021
```
Also added utils for execution wrappers.
```
  7c1fcd6f
- Fix circular import · 0a0a741f
  Gustaf Ahdritz authored Oct 07, 2021
  
  0a0a741f
07 Oct, 2021 1 commit
- Add DRMSD computation · 1a341511
  Gustaf Ahdritz authored Oct 07, 2021
  
  1a341511
06 Oct, 2021 1 commit
- Fix another FP16 overflow, finish tests, update util scripts · 9f6b67f3
  Gustaf Ahdritz authored Oct 06, 2021
  
  9f6b67f3
05 Oct, 2021 1 commit
- Get FP16 training working · 893fe372
  Gustaf Ahdritz authored Oct 05, 2021
  
  893fe372
04 Oct, 2021 1 commit
- Add barebones EMA · dd06b323
  Gustaf Ahdritz authored Oct 04, 2021
  
  dd06b323
02 Oct, 2021 3 commits
- Update type checks in tensor_tree_map · ff969b98
  Gustaf Ahdritz authored Oct 02, 2021
  
  ff969b98
- Sidestep AMP bug · f34bef8e
  Gustaf Ahdritz authored Oct 02, 2021
  
  f34bef8e
- Begin to spruce up unit tests, fix config · 304b5ff7
  Gustaf Ahdritz authored Oct 02, 2021
  
  304b5ff7
01 Oct, 2021 2 commits
- Work on import infrastructure · abd78418
  Gustaf Ahdritz authored Sep 30, 2021
  
  abd78418
- Correct commands in README · bb5b4b5c
  Gustaf Ahdritz authored Sep 30, 2021
  
  bb5b4b5c
30 Sep, 2021 3 commits
- Add pTM config options, spruce up pretrained script, add test script · 54317fe4
  Gustaf Ahdritz authored Sep 30, 2021
  
  54317fe4
- Add draft setup.py · 3fb44548
  Gustaf Ahdritz authored Sep 30, 2021
  
  3fb44548
- Finish purge of in-place ops, get grads working, add TM · eb49136d
  Gustaf Ahdritz authored Sep 30, 2021
  
  eb49136d
28 Sep, 2021 1 commit
- Finish accommodating FP16. FAPE does not decrease · 1d47c1e7
  Gustaf Ahdritz authored Sep 28, 2021
  
  1d47c1e7
27 Sep, 2021 8 commits
- Remove vestigial unit tests · 3d9d977a
  Gustaf Ahdritz authored Sep 27, 2021
  
  3d9d977a
- Fix tensor casting, improve TorchScript compatibility · de0fa7b1
  Gustaf Ahdritz authored Sep 27, 2021
  
  de0fa7b1
- Update pretrained runner · 7d53297c
  Gustaf Ahdritz authored Sep 27, 2021
  
  7d53297c
- Add missing license notice · 2065a6ca
  Gustaf Ahdritz authored Sep 27, 2021
  
  2065a6ca
- Add DeepSpeed config script · cc6ba534
  Gustaf Ahdritz authored Sep 27, 2021
  
  cc6ba534
- Fix IPA bug, add missing dtype specs · e98c202d
  Gustaf Ahdritz authored Sep 27, 2021
  
  e98c202d
- Fix OPM bug · ad2e5c97
  Gustaf Ahdritz authored Sep 27, 2021
  
  ad2e5c97
- Refactor certain modules for TorchScript, fix recycling bug · b2d102cb
  Gustaf Ahdritz authored Sep 27, 2021
  
  b2d102cb
26 Sep, 2021 3 commits
- Add first attempt at scripting attention · 4bd4ad93
  Gustaf Ahdritz authored Sep 26, 2021
  
  4bd4ad93
- Add missing config values · dd8e44b3
  Gustaf Ahdritz authored Sep 26, 2021
  
  dd8e44b3
- Continue debugging loss functions, remove in-place ops · ab0c6977
  Gustaf Ahdritz authored Sep 26, 2021
  
  ab0c6977
24 Sep, 2021 1 commit
- Disable activation checkpointing during inference · 85c0a9a9
  Gustaf Ahdritz authored Sep 24, 2021
  
  85c0a9a9