Commits · 4e934f7462d19bf94948b785cd93810c2a28fa0e · OpenDAS / OpenFold

21 Jun, 2022 3 commits
- Add SLURM script acknowledgement · 4e934f74
  Gustaf Ahdritz authored Jun 21, 2022
  
  4e934f74
- Add SLURM alignment script · 4a3c3924
  Gustaf Ahdritz authored Jun 21, 2022
  
  4a3c3924
- Update file ID in OpenFold parameter download script · 5fbb0d0d
  Gustaf Ahdritz authored Jun 21, 2022
  
  5fbb0d0d
17 Jun, 2022 3 commits
- Move parameter downloads · f8f74006
  Gustaf Ahdritz authored Jun 17, 2022
  
  f8f74006
- Update link in OpenFold parameter download script · 9d09bdb8
  Gustaf Ahdritz authored Jun 17, 2022
  
  9d09bdb8
- Add OpenFold parameter download script · 233704c5
  Gustaf Ahdritz authored Jun 17, 2022
  
  233704c5
10 Jun, 2022 1 commit
- Vastly lower peak inference memory usage · 6e66b218
  Gustaf Ahdritz authored Jun 10, 2022
  
  6e66b218
30 Mar, 2022 1 commit
- Undo DeepSpeed config change · f362ebff
  Gustaf Ahdritz authored Mar 29, 2022
  
  f362ebff
29 Mar, 2022 1 commit
- Fix DeepSpeed config builder · 9f558178
  Gustaf Ahdritz authored Mar 29, 2022
  
  9f558178
14 Mar, 2022 1 commit
- Fix bug in mmCIF cache script · c83c42e8
  Gustaf Ahdritz authored Mar 14, 2022
  
  c83c42e8
22 Feb, 2022 3 commits
- One last adjustment to generate_chain_data_cache.py · 950b02f0
  Gustaf Ahdritz authored Feb 22, 2022
  
  950b02f0
- Adjust default behavior of generate_chain_data_cache.py · 39860f93
  Gustaf Ahdritz authored Feb 22, 2022
  
  39860f93
- Fix chain data cache script bug, improve logging · 4c7c30b1
  Gustaf Ahdritz authored Feb 22, 2022
  
  4c7c30b1
05 Feb, 2022 2 commits
- Fix bugs in chain data cache script · 70362e4b
  Gustaf Ahdritz authored Feb 05, 2022
  
  70362e4b
- Add chain data cache generator · 3b82ddb7
  Gustaf Ahdritz authored Feb 04, 2022
  
  3b82ddb7
04 Feb, 2022 5 commits
- Revert changes to mmcif cache gen script · a46f1b12
  Gustaf Ahdritz authored Feb 04, 2022
  
  a46f1b12
- Un-comment lines in alignment script · 7f3a48ee
  Gustaf Ahdritz authored Feb 04, 2022
  
  7f3a48ee
- Fix bug in cache script · 84f45ee1
  Gustaf Ahdritz authored Feb 04, 2022
  
  84f45ee1
- Restore cache generation script · 54deee17
  Gustaf Ahdritz authored Feb 04, 2022
  
  54deee17
- Add GPU relaxation · 721e43be
  Gustaf Ahdritz authored Feb 03, 2022
  
  721e43be
03 Feb, 2022 3 commits
- Prep for training · f30d77b7
  Gustaf Ahdritz authored Jan 27, 2022
  
  f30d77b7
- Fixes · 6ce8cfe3
  Gustaf Ahdritz authored Jan 18, 2022
  
  6ce8cfe3
- Beef up alignment script · 02fc4376
  Gustaf Ahdritz authored Jan 10, 2022
  
  02fc4376
01 Feb, 2022 4 commits
- Fix NVIDIA loggier issue in install script · 81ebd4a8
  Gustaf Ahdritz authored Feb 01, 2022
  
  81ebd4a8
- reverting accidental chance to third party dep install script · 4cd2aba7
  Sam DeLuca authored Feb 01, 2022
  
  4cd2aba7
- Update AlphaFold parameter download link · 52a8b8f3
  Gustaf Ahdritz authored Feb 01, 2022
  
  52a8b8f3
- adding a dockerfile build for openfold, along with a fix to the residue_constraints module · 4f2bc2e8
  Sam DeLuca authored Feb 01, 2022
  
  4f2bc2e8
20 Jan, 2022 2 commits
- Source the environment because it is reccomended that this is called via source · ffd15414
  Karl Leswing authored Jan 20, 2022
  
  ffd15414
- Ready For PR · 74675b73
  Karl Leswing authored Jan 20, 2022
  
  74675b73
31 Dec, 2021 1 commit
- Add script for generating sample feature dict · 36b9a8ea
  Gustaf Ahdritz authored Dec 30, 2021
  
  36b9a8ea
20 Dec, 2021 2 commits
- Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py · f4701ffa
  Gustaf Ahdritz authored Dec 20, 2021
  
  f4701ffa
- Make AlignmentRunner more flexible · edffead3
  Gustaf Ahdritz authored Dec 19, 2021
  
  edffead3
19 Dec, 2021 1 commit
- Fix AlphaFold DB download script · f4316dc0
  Gustaf Ahdritz authored Dec 19, 2021
  
  f4316dc0
17 Dec, 2021 1 commit
- Add low-memory attention (still needs to be incorporated) · 96709588
  Gustaf Ahdritz authored Dec 17, 2021
  
  96709588
10 Dec, 2021 2 commits
- Fix mmseqs script bug · 71fabe1e
  Gustaf Ahdritz authored Dec 10, 2021
  
  71fabe1e
- Made initialization consistent for template_featurizer in all modules. · ddf922df
  Sachin Kadyan authored Dec 10, 2021
```
Added obsolete_pdbs_file and release_dates_path in all initialization points.
```
  ddf922df
30 Nov, 2021 1 commit
- Add bfloat16 support to DeepSpeed config script · ca810168
  Gustaf Ahdritz authored Nov 29, 2021
  
  ca810168
29 Nov, 2021 2 commits
- Update precompute_alignments_mmseqs.py · 1bfb1e1b
  yuzhiguo07 authored Nov 29, 2021
  
  1bfb1e1b
- Fix bugs in MMseqs DB script · 78e79962
  Gustaf Ahdritz authored Nov 29, 2021
  
  78e79962
22 Nov, 2021 1 commit
- Add alternative fasta file extension · 52800ff0
  Gustaf Ahdritz authored Nov 22, 2021
  
  52800ff0