Commits · cdc28a07a27e9baf4566c6b9796d0046424f9d14 · OpenDAS / OpenFold

22 Dec, 2021 8 commits
- Added test for make_masked_msa · cdc28a07
  Sachin Kadyan authored Dec 21, 2021
  
  cdc28a07
- Added test for make_hhbits_profile · e683dce3
  Sachin Kadyan authored Dec 21, 2021
  
  e683dce3
- Added test for make_msa_mask · a3b5c162
  Sachin Kadyan authored Dec 21, 2021
  
  a3b5c162
- Added test for nearest_neighbor_clusters · 974fe5a9
  Sachin Kadyan authored Dec 21, 2021
  
  974fe5a9
- Added test for delete_extra_msa · 734ce915
  Sachin Kadyan authored Dec 21, 2021
  
  734ce915
- Added test for crop_extra_msa · 09564595
  Sachin Kadyan authored Dec 21, 2021
  
  09564595
- Added test for sample_msa · 925d56f8
  Sachin Kadyan authored Dec 21, 2021
  
  925d56f8
- Added tests for randomly_replace_msa_with_unknown · 011a6526
  Sachin Kadyan authored Dec 21, 2021
  
  011a6526
21 Dec, 2021 7 commits
- Fixed filepath for the features.pkl pickle file. · cad8de7e
  Sachin Kadyan authored Dec 21, 2021
  
  cad8de7e
- Added tests for squeeze_features. · 8923e536
  Sachin Kadyan authored Dec 21, 2021
  
  8923e536
- Added a pickle file of protein features, for use during tests. · 9e4fb16f
  Sachin Kadyan authored Dec 21, 2021
  
  9e4fb16f
- Added test for correct_msa_restypes · 10fc9ec0
  Sachin Kadyan authored Dec 21, 2021
  
  10fc9ec0
- Added test for fix_templates_aatype · a9c1715b
  Sachin Kadyan authored Dec 21, 2021
  
  a9c1715b
- Added test for make_all_atom_aatype · 02bf2e83
  Sachin Kadyan authored Dec 21, 2021
  
  02bf2e83
- Added flag in protein to indicate if protein comes from distillation dataset. · bc7864b1
  Sachin Kadyan authored Dec 21, 2021
  
  bc7864b1
20 Dec, 2021 5 commits
- Update name of ProteinNet script in README · 0e9aaa63
  Gustaf Ahdritz authored Dec 20, 2021
  
  0e9aaa63
- Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py · f4701ffa
  Gustaf Ahdritz authored Dec 20, 2021
  
  f4701ffa
- Fix version number in setup.py · 6c2d04aa
  Gustaf Ahdritz authored Dec 20, 2021
  
  6c2d04aa
- Add default CPU count to AlignmentRunner · 43116de0
  Gustaf Ahdritz authored Dec 19, 2021
  
  43116de0
- 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
13 Dec, 2021 1 commit
- Reintroduce in-place operation to attention module · c4d9f57f
  Gustaf Ahdritz authored Dec 13, 2021
  
  c4d9f57f
11 Dec, 2021 2 commits
- Make triangular attention test even more sensitive · 6c5cd945
  Gustaf Ahdritz authored Dec 10, 2021
  
  6c5cd945
- Make triangle attention test more sensitive · 80f968fe
  Gustaf Ahdritz authored Dec 10, 2021
  
  80f968fe
10 Dec, 2021 4 commits
- Add MMseqs2 clarification · de91f011
  Gustaf Ahdritz authored Dec 10, 2021
  
  de91f011
- Fix mmseqs script bug · 71fabe1e
  Gustaf Ahdritz authored Dec 10, 2021
  
  71fabe1e
- Added tests for the data_transforms · f9e04aa0
  Sachin Kadyan authored Dec 10, 2021
  
  f9e04aa0
- 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
09 Dec, 2021 1 commit
- Fix validation bugs · 2abd8c1d
  Gustaf Ahdritz authored Dec 09, 2021
  
  2abd8c1d
03 Dec, 2021 4 commits
- Remove unexpected indent · 11cf28f7
  Gustaf Ahdritz authored Dec 02, 2021
  
  11cf28f7
- Add non-distillation PDB option to data module · 56632d44
  Gustaf Ahdritz authored Dec 02, 2021
  
  56632d44
- Add flat chunk slicing · f707a9ea
  Gustaf Ahdritz authored Dec 02, 2021
  
  f707a9ea
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · ebcbaa60
  Gustaf Ahdritz authored Dec 02, 2021
  
  ebcbaa60
02 Dec, 2021 1 commit
- Update README.md · b2310ea6
  Gustaf Ahdritz authored Dec 02, 2021
  
  b2310ea6
30 Nov, 2021 5 commits
- Fix datatypes in PDB parsing · e0c7d445
  Gustaf Ahdritz authored Nov 30, 2021
  
  e0c7d445
- Add option to select chains in PDB files · 699f23fd
  Gustaf Ahdritz authored Nov 30, 2021
  
  699f23fd
- Add non-distillation PDB parsing · 5161c0f6
  Gustaf Ahdritz authored Nov 30, 2021
  
  5161c0f6
- Merge pull request #24 from yuzhiguo07/patch-1 · 57720ec7
  Gustaf Ahdritz authored Nov 29, 2021
```
Update precompute_alignments_mmseqs.py
```
  57720ec7
- Add bfloat16 support to DeepSpeed config script · ca810168
  Gustaf Ahdritz authored Nov 29, 2021
  
  ca810168