Commits · 8d8584acc0ee3699730bf07ef2fadd565723a08b · OpenDAS / OpenFold

15 Dec, 2023 6 commits
- get rid of parsing tar.gz2 files for now · 8d8584ac
  Dingquan Yu authored Dec 15, 2023
  
  8d8584ac
- added back cpu_count import · c5a69771
  Dingquan Yu authored Dec 14, 2023
  
  c5a69771
- remove unnecessary imports · ffa812e4
  Dingquan Yu authored Dec 14, 2023
  
  ffa812e4
- added steps of reading in compressed msa files · de28d842
  Dingquan Yu authored Dec 14, 2023
  
  de28d842
- added steps to read zipped msa files · e9287b49
  Dingquan Yu authored Dec 13, 2023
  
  e9287b49
- Fix missing import in tests · 9d6127cb
  Christina Floristean authored Dec 15, 2023
  
  9d6127cb
14 Dec, 2023 1 commit
- Bug fixes for multi-chain permutation alignment · fe8869c3
  Christina Floristean authored Dec 14, 2023
  
  fe8869c3
11 Dec, 2023 4 commits
- Added alignment indexing to multimer pipeline and fixed jackhmmer query return type · 4f38c826
  Christina Floristean authored Dec 11, 2023
  
  4f38c826
- Fix bug from deepspeed upgrade, do not use uniprot_hits in msa feats · bcabb8e3
  Christina Floristean authored Dec 11, 2023
  
  bcabb8e3
- Merge pull request #376 from dingquanyu/speedup-dataloader · f861ff39
  Christina Floristean authored Dec 11, 2023
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Speed up data loading process 
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  f861ff39
- Merge branch 'main' into multimer · 1606ac08
  Christina Floristean authored Dec 11, 2023
  
  1606ac08
08 Dec, 2023 4 commits
- Remove env restart from setup script · 67a00a6c
  Christina Floristean authored Dec 08, 2023
  
  67a00a6c
- Merge pull request #378 from aqlaboratory/deepspeed-evo-attention · a13c0ce5
  Christina Floristean authored Dec 08, 2023
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Deepspeed evoformer attention
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  a13c0ce5
- Minor change to tests · 40d76358
  Christina Floristean authored Dec 08, 2023
  
  40d76358
- Minor test and README changes · 336c899a
  Christina Floristean authored Dec 08, 2023
  
  336c899a
06 Dec, 2023 2 commits
- Updated DeepSpeed version, added inplace_safe for template offloading · cdd97841
  Christina Floristean authored Dec 06, 2023
  
  cdd97841
- Merge branch 'multimer' into speedup-dataloader · 6f26b0ad
  Dingquan Yu authored Dec 06, 2023
  
  6f26b0ad
05 Dec, 2023 8 commits
- Exclude uniprot hits from regular msa feature processing · 58d65692
  Christina Floristean authored Dec 05, 2023
  
  58d65692
- Merge pull request #375 from aqlaboratory/jackhmmer_query_update · 96f46b08
  Jennifer Wei authored Dec 05, 2023
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Adds query_multiple to jackhammer.py
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  96f46b08
- remove unnecessary imports and statements · 78ecfc64
  Dingquan Yu authored Dec 05, 2023
  
  78ecfc64
- reverse back to multimer branch version · 08bfb1ff
  Dingquan Yu authored Dec 05, 2023
  
  08bfb1ff
- moved pase_msa_file into tools subfolder · 28b9e2b6
  Dingquan Yu authored Dec 05, 2023
  
  28b9e2b6
- remove debugging statement · e72e4e62
  Dingquan Yu authored Dec 05, 2023
  
  e72e4e62
- Merge branch 'main' into deepspeed-evo-attention · 9236c1e3
  Christina Floristean authored Dec 05, 2023
  
  9236c1e3
- update config.py for the development for now · 53c03a6a
  Dingquan Yu authored Dec 05, 2023
  
  53c03a6a
04 Dec, 2023 5 commits
- Adds query_multiple to jackhammer.py · 4958683b
  Jennifer authored Dec 04, 2023
  
  4958683b
- Merge pull request #374 from aqlaboratory/msa-block-deletion · 2dc080ce
  Christina Floristean authored Dec 04, 2023
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Fix for MSA block deletion
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  2dc080ce
- Fix bugs in block deletion, disable for soloseq · b935639b
  Christina Floristean authored Dec 04, 2023
  
  b935639b
- now use ThreadPoolExecutor · 4e58a6a0
  Dingquan Yu authored Dec 04, 2023
  
  4e58a6a0
- Fix for MSA block deletion · 616de3df
  Christina Floristean authored Dec 04, 2023
  
  616de3df
02 Dec, 2023 1 commit
- fixed errors when running in subprocess · 2204bbb2
  Dingquan Yu authored Dec 02, 2023
  
  2204bbb2
01 Dec, 2023 1 commit
- now run in a subprocess · c3c627e7
  Dingquan Yu authored Dec 01, 2023
  
  c3c627e7
30 Nov, 2023 4 commits
- Merge pull request #373 from aqlaboratory/soloseq-params · a64f1a29
  Jennifer Wei authored Nov 30, 2023
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Adds Soloseq parameter download script.
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  a64f1a29
- now using multiprocessing style · 2e1941a0
  Dingquan Yu authored Nov 30, 2023
  
  2e1941a0
- now used asynchronised version in parse_msa_data · 6f3e0c0c
  Dingquan Yu authored Nov 30, 2023
  
  6f3e0c0c
- added timing steps · aec12764
  Dingquan Yu authored Nov 30, 2023
  
  aec12764
29 Nov, 2023 2 commits
- Adds Soloseq parameter download script. · 4a50c9c4
  jnwei authored Nov 29, 2023
  
  4a50c9c4
- Fix for issue #367 · 2c36cb8b
  Christina Floristean authored Nov 29, 2023
  
  2c36cb8b
21 Nov, 2023 2 commits
- Merge pull request #372 from aqlaboratory/fix-colab-imports · bc20f02f
  Jennifer Wei authored Nov 21, 2023
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Fixes imports to colab notebook.
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  bc20f02f
- Update OpenFold.ipynb · 4384ac08
  Jennifer Wei authored Nov 21, 2023
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fix small typo on button.
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  4384ac08