Commits · 32765d20a149a3966508492e5551dd353e3b1573 · OpenDAS / OpenFold · GitLab

11 May, 2024 12 commits
- Update test_permutation.py · 32765d20
  Jennifer Wei authored May 11, 2024
```
Fixed a small typo in permutation unit test docstring
```
  32765d20
- fixed typing error of anchor_gt_residue · d9680984
  Dingquan Yu authored May 10, 2024
  
  d9680984
- Update tests and comments · 6f1329ef
  Dingquan Yu authored May 10, 2024
  
  6f1329ef
- update comments;fixed typos · 9a6eb649
  Dingquan Yu authored May 10, 2024
  
  9a6eb649
- added comments · bc240326
  Geoffrey Yu authored Mar 21, 2024
  
  bc240326
- fixed typing errors; added more comments · 04d63782
  Geoffrey Yu authored Mar 21, 2024
  
  04d63782
- make sure no padded features are going to be selected as anchors · 6d418384
  Geoffrey Yu authored Feb 20, 2024
  
  6d418384
- added typing hints and fixed some comments · f7571e25
  Geoffrey Yu authored Feb 16, 2024
  
  f7571e25
- restore to the verison on main · 77cb4135
  Geoffrey Yu authored Feb 15, 2024
  
  77cb4135
- remove unnecessary lines · d1a32aa3
  Geoffrey Yu authored Feb 15, 2024
  
  d1a32aa3
- fixed bugs in unittests for multi-chain permutation. now working on extra subtests · 0df04f33
  Geoffrey Yu authored Feb 15, 2024
  
  0df04f33
- make sure padded asym_id won't affect permutation steps · 17b8c142
  Geoffrey Yu authored Feb 15, 2024
  
  17b8c142
06 May, 2024 1 commit
- adds mpi4py to environment and removes stray print statements from test · af457b95
  Jennifer Wei authored May 06, 2024
  
  af457b95
02 May, 2024 27 commits
- Updates environment.yml to unpin wandb version · 9b6c1dac
  Jennifer authored May 02, 2024
  
  9b6c1dac
- Updates organization of command line flags for pl.Trainer · 142c5e65
  Jennifer authored May 02, 2024
  
  142c5e65
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 2eda3215
  Jennifer authored Apr 02, 2024
  
  2eda3215
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 3a4ed753
  Jennifer authored Apr 02, 2024
  
  3a4ed753
- Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold... · e4f9af23
  Jennifer authored May 02, 2024
```
Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements
```
  e4f9af23
- updates Bio.PDBData call and environment.yml · 02cb7711
  Jennifer authored Apr 22, 2024
  
  02cb7711
- adds deepspeed_evoformer flag to inference script. · c4cccb6b
  Jennifer authored Apr 30, 2024
  
  c4cccb6b
- changes required for pytorch2 · 19525826
  Jennifer Wei authored Apr 12, 2024
  
  19525826
- DNS: Local profiler changes · 226c7bac
  Jennifer authored Mar 29, 2024
  
  226c7bac
- adds config recording to wandb · eba00d85
  Jennifer authored Mar 13, 2024
  
  eba00d85
- Adds `experiment_config_json` for setting custom configurations with a json. · 870e0db3
  Jennifer authored Mar 13, 2024
  
  870e0db3
- removes outputs from OpenFold.ipynb · 0ba7e7f9
  jnwei authored Feb 21, 2024
  
  0ba7e7f9
- Add log statement to weight conversion script · d4ed0b0c
  Jennifer authored Feb 13, 2024
  
  d4ed0b0c
- bugfixes and adds a section to convert optim files · 67454c39
  Jennifer authored Feb 12, 2024
  
  67454c39
- Updates commit value for OpenFold notebook. · 638fbaf6
  jnwei authored Feb 21, 2024
  
  638fbaf6
- fix path error in scripts/utils.py and logging fix · 2dd481e1
  Jennifer authored Apr 29, 2024
  
  2dd481e1
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cfb4c19c
  jnwei authored Apr 23, 2024
  
  cfb4c19c
- clear up some space for docker ci · f4e54ec7
  Jennifer authored Apr 22, 2024
  
  f4e54ec7
- changes required for pytorch2 · 60fbe539
  Jennifer Wei authored Apr 12, 2024
  
  60fbe539
- DNS: Local profiler changes · ec6058cd
  Jennifer authored Mar 29, 2024
  
  ec6058cd
- update license file · 2a4818a3
  jnwei authored Mar 21, 2024
  
  2a4818a3
- adds config recording to wandb · 6b77062d
  Jennifer authored Mar 13, 2024
  
  6b77062d
- Adds `experiment_config_json` for setting custom configurations with a json. · 0f2b2929
  Jennifer authored Mar 13, 2024
  
  0f2b2929
- Changes resume_model_weights_only flag in train_openfold to reload weights... · 5bfad074
  Jennifer authored Feb 22, 2024
```
Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.
```
  5bfad074
- removes outputs from OpenFold.ipynb · 521bc6e9
  jnwei authored Feb 21, 2024
  
  521bc6e9
- changes reloading weights to account for possible state_dict headers. · a7216c73
  Jennifer authored Feb 14, 2024
  
  a7216c73
- Add log statement to weight conversion script · 711ba0ab
  Jennifer authored Feb 13, 2024
  
  711ba0ab