Commits · 3de188e9d0f54bb40ebdd3a3e630941e0f4d9539 · OpenDAS / OpenFold

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10 Aug, 2023 3 commits
- Minor model test fix · 3de188e9
  Christina Floristean authored Aug 10, 2023
  
  3de188e9
- Seed fixes for multimer data pipeline · a18f98cf
  Christina Floristean authored Aug 10, 2023
  
  a18f98cf
- Merge branch 'main' into multimer · 44b0bf76
  Christina Floristean authored Aug 10, 2023
  
  44b0bf76
09 Aug, 2023 4 commits
- Additional changes to seeding · 1dc2748c
  Christina Floristean authored Aug 09, 2023
  
  1dc2748c
- Make seeding more consistent · 39d0ef43
  Gustaf Ahdritz authored Aug 09, 2023
  
  39d0ef43
- Fix another seeding bug · 410e1829
  Gustaf Ahdritz authored Aug 09, 2023
  
  410e1829
- Fix seeding bug · 451642c8
  Gustaf Ahdritz authored Aug 09, 2023
  
  451642c8
04 Aug, 2023 5 commits
- Merge pull request #337 from dingquanyu/fix-multimer-boolean-tensor-error · 959b3f25
  Christina Floristean authored Aug 04, 2023
```
Fix multimer boolean tensor error
```
  959b3f25
- remove unfinished test file · e84df271
  Geoffrey Yu authored Aug 04, 2023
  
  e84df271
- revert to 08afe382 config · 4de6b1a3
  Geoffrey Yu authored Aug 04, 2023
  
  4de6b1a3
- fixed TypeError: enabled must be a bool (got Tensor) when training multimer · d7f3d622
  Geoffrey Yu authored Aug 04, 2023
  
  d7f3d622
- Refactored multimer config update · 82bda2d6
  Christina Floristean authored Aug 03, 2023
  
  82bda2d6
03 Aug, 2023 12 commits
- Minor fixes/reformatting for recent multimer training PR · 30764cf9
  Christina Floristean authored Aug 03, 2023
  
  30764cf9
- Merge pull request #336 from dingquanyu/permutation · 31051cf2
  Christina Floristean authored Aug 03, 2023
```
Added multi-chain permutation steps, multimer datamodule, and training code for multimer
```
  31051cf2
- update train_mmcifs_cache so that now only use one structure for testing · e963726b
  Geoffrey Yu authored Aug 03, 2023
  
  e963726b
- removed old data and script for permutation unittest. now working on the new permutation unittest · 139ea9a6
  Geoffrey Yu authored Aug 03, 2023
  
  139ea9a6
- removed unused alignment files · e2193f77
  Geoffrey Yu authored Aug 03, 2023
  
  e2193f77
- Merge branch 'multimer' into permutation · 08afe382
  Dingquan Yu authored Aug 03, 2023
  
  08afe382
- reverse the early stop check back to originl now but the 'enabled must be a... · f44e9830
  Geoffrey Yu authored Aug 03, 2023
```
reverse the early stop check back to originl now but the 'enabled must be a bool (got Tensor)' error still persists
```
  f44e9830
- fixed the error where the iterface backbone loss falsely used intra_chain backbone weights · 0caffd57
  Geoffrey Yu authored Aug 03, 2023
  
  0caffd57
- fixed the confilcts in reading alignment files · bc35ef17
  Geoffrey Yu authored Aug 03, 2023
  
  bc35ef17
- move recycle_early_stop_tolerance into 'model' · 43bab151
  Geoffrey Yu authored Aug 03, 2023
  
  43bab151
- put multimer_model_config_update inside a 'model' key in the config dict · 833c100b
  Geoffrey Yu authored Aug 03, 2023
  
  833c100b
- reverse README back to original · b8d00692
  Geoffrey Yu authored Aug 03, 2023
  
  b8d00692
02 Aug, 2023 2 commits
- Merge branch 'multimer' of https://github.com/aqlaboratory/openfold into multimer · 4ca64437
  Christina Floristean authored Aug 02, 2023
  
  4ca64437
- Bug fixes for multimer inference and monomer training · fdcb72e8
  Christina Floristean authored Aug 02, 2023
  
  fdcb72e8
21 Jul, 2023 6 commits
- Update README.md · 3a2c1480
  Dingquan Yu authored Jul 21, 2023
  
  3a2c1480
- Merge pull request #6 from dingquanyu/multimer-dataloader · 6f78792d
  Dingquan Yu authored Jul 21, 2023
```
Added Multimer dataloader and training scripts
```
  6f78792d
- Update README.md · 5fc80134
  Dingquan Yu authored Jul 21, 2023
  
  5fc80134
- added train_mmcifs_cache.json · a1ef4c8f
  Geoffrey Yu authored Jul 21, 2023
  
  a1ef4c8f
- remove some print statements · 4e382310
  Geoffrey Yu authored Jul 21, 2023
  
  4e382310
- update test files · d7162be4
  Geoffrey Yu authored Jul 21, 2023
  
  d7162be4
20 Jul, 2023 4 commits
- update train_openfold.py to accomodate training multimer · 4b354151
  Geoffrey Yu authored Jul 20, 2023
  
  4b354151
- remove train_multimer script and use the updated train_openfold.py now · d886a7be
  Geoffrey Yu authored Jul 20, 2023
  
  d886a7be
- updated data_module · e482a269
  Geoffrey Yu authored Jul 20, 2023
  
  e482a269
- update kabsch rotation calculation to avoid svd not converge error · 7f2a3267
  Geoffrey Yu authored Jul 20, 2023
  
  7f2a3267
19 Jul, 2023 3 commits
- now update get_optimal_transform · 5348936a
  Geoffrey Yu authored Jul 19, 2023
  
  5348936a
- fixed the overflow problems while slicing matrices · 9f24ebf0
  Geoffrey Yu authored Jul 19, 2023
  
  9f24ebf0
- Merge pull request #331 from dingquanyu/multimer · 8332aa0e
  Christina Floristean authored Jul 18, 2023
```
Batch size fix for tm computation
```
  8332aa0e
18 Jul, 2023 1 commit
- added an example training script for training openfold multimer · d2eae833
  Geoffrey Yu authored Jul 18, 2023
  
  d2eae833