Commits · cfd0fc6eb55c0287257c9e3860c0be330c0a6020 · OpenDAS / OpenFold

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
15 Nov, 2021 1 commit
- Fix bug in alignment precomputation script · 6e5c619c
  Gustaf Ahdritz authored Nov 15, 2021
  
  6e5c619c
10 Nov, 2021 4 commits
- Update documention for ProteinNet use case · 8c95493f
  Gustaf authored Nov 10, 2021
  
  8c95493f
- Add missing variable · e7b239c9
  Gustaf authored Nov 10, 2021
  
  e7b239c9
- Add more ProteinNet functionality · 2c7ce956
  Gustaf authored Nov 10, 2021
  
  2c7ce956
- Begin to add ProteinNet support (WIP) · 22cc45a8
  Gustaf authored Nov 09, 2021
  
  22cc45a8
09 Nov, 2021 1 commit
- Add MMseqs2 MSA generation · 36f317be
  Gustaf authored Nov 09, 2021
  
  36f317be
02 Nov, 2021 1 commit
- add dllogger to conda env · 6c14c76a
  Marta authored Nov 02, 2021
  
  6c14c76a
30 Oct, 2021 1 commit
- Speed up template featurizer · 9d4c9357
  Gustaf Ahdritz authored Oct 29, 2021
  
  9d4c9357
26 Oct, 2021 3 commits
- Fix model checkpointing bug · a9a19b78
  Gustaf Ahdritz authored Oct 26, 2021
  
  a9a19b78
- 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
24 Oct, 2021 1 commit
- minor fixes · 04fa3548
  sft-managed authored Oct 24, 2021
  
  04fa3548
22 Oct, 2021 2 commits
- Add script for installing the HH-suite · 5b9cfdaf
  Gustaf Ahdritz authored Oct 22, 2021
  
  5b9cfdaf
- Add gradient clipping to DeepSpeed config generator · 872787b9
  Gustaf Ahdritz authored Oct 21, 2021
  
  872787b9
20 Oct, 2021 1 commit
- Bring tests up to speed · 49767099
  Gustaf Ahdritz authored Oct 19, 2021
  
  49767099
19 Oct, 2021 1 commit
- Prettyprint mmCIF cache · a6f56d16
  Gustaf Ahdritz authored Oct 19, 2021
  
  a6f56d16
18 Oct, 2021 1 commit
- Add mmCIF cache generation script, remove verbose warnings · 23886619
  Gustaf Ahdritz authored Oct 18, 2021
  
  23886619
15 Oct, 2021 2 commits
- Fix faulty symlink command in install script · 5497655c
  Gustaf Ahdritz authored Oct 15, 2021
  
  5497655c
- Add training parsers · d48c052c
  Gustaf Ahdritz authored Oct 15, 2021
  
  d48c052c
09 Oct, 2021 1 commit
- Tweak run script args, roll back repo to Python 3.7 (for Colab) · f4150fa1
  Gustaf Ahdritz authored Oct 08, 2021
  
  f4150fa1