Commits · 6f78792dbf181bf55b924d1a9c9daf0bf23c3539 · OpenDAS / OpenFold

"runtime/rust/src/protocols/annotated.rs" did not exist on "4017bd18d0e84b8463bfe381279d4c5a6fd0c6e0"

21 Jul, 2023 5 commits
- 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 2 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
18 Jul, 2023 4 commits
- added an example training script for training openfold multimer · d2eae833
  Geoffrey Yu authored Jul 18, 2023
  
  d2eae833
- added an extra step because sometimes the boolean value will change into a pytorch tensor · 2f2793f4
  Geoffrey Yu authored Jul 18, 2023
  
  2f2793f4
- Merge pull request #5 from dingquanyu/multimer-dataloader · 85185efd
  Dingquan Yu authored Jul 18, 2023
```
added openfold multimer dataloader class and overwrite batch processing
```
  85185efd
- added openfold multimer dataloader class and overwrite batch processing · 566ca1a3
  Geoffrey Yu authored Jul 18, 2023
  
  566ca1a3
16 Jul, 2023 5 commits
- Merge pull request #4 from dingquanyu/multimer-dataloader · e7eadc44
  Dingquan Yu authored Jul 16, 2023
```
created Multimer dataloader and datamodule classes
```
  e7eadc44
- added test alignment files for dataloader unittest · dbc0b085
  Dingquan Yu authored Jul 16, 2023
  
  dbc0b085
- remove unnecessary test files · 39d67ba5
  Dingquan Yu authored Jul 16, 2023
  
  39d67ba5
- update test script · 173f055e
  Dingquan Yu authored Jul 16, 2023
  
  173f055e
- fixed the error when loading a monomeric training object · 0d348792
  Geoffrey Yu authored Jul 16, 2023
  
  0d348792
14 Jul, 2023 5 commits
- update test · caac73c0
  Geoffrey Yu authored Jul 14, 2023
  
  caac73c0
- reduce asym_id in chain_center_of_mass_loss by 1 to avoid torch one_hot error · 64493e08
  Geoffrey Yu authored Jul 14, 2023
  
  64493e08
- remove unecessary print statements · 2c4d4183
  Geoffrey Yu authored Jul 14, 2023
  
  2c4d4183
- need to change ground truth load mode to train to avoid loss error · e4d7f6d2
  Geoffrey Yu authored Jul 14, 2023
  
  e4d7f6d2
- update the merge label functions so that the merging dimension is not hard coded · 08a5be86
  Geoffrey Yu authored Jul 14, 2023
  
  08a5be86
13 Jul, 2023 2 commits
- start modifying mderge_label function to make it compatible with dataloader inputs · 66a60d58
  Geoffrey Yu authored Jul 13, 2023
  
  66a60d58
- remove number of chains filter; no longer hard code is_multimer in multime... · e9794a62
  Geoffrey Yu authored Jul 13, 2023
```
remove number of chains filter; no longer hard code is_multimer in multime classes; remove recycling dimesion in ground truth features
```
  e9794a62
11 Jul, 2023 6 commits
- remove manual processing. now use feature_pipeline instead · 19fe90b2
  Geoffrey Yu authored Jul 11, 2023
  
  19fe90b2
- comment out code that stops multimer feature processing · 55cfb825
  Geoffrey Yu authored Jul 11, 2023
  
  55cfb825
- add ground truth feature processing · ab8f4a5b
  Geoffrey Yu authored Jul 11, 2023
  
  ab8f4a5b
- update test script · ca340ce8
  Geoffrey Yu authored Jul 11, 2023
  
  ca340ce8
- turn all_seq_features from numpy to tensor and move all_seq_featurs to cuda · 753fc31f
  Geoffrey Yu authored Jul 11, 2023
  
  753fc31f
- reverse back to cbcd81fb · 9cab17c4
  Geoffrey Yu authored Jul 11, 2023
  
  9cab17c4
10 Jul, 2023 3 commits
- update test script · 42a89403
  Geoffrey Yu authored Jul 10, 2023
  
  42a89403
- finished constructing multimer dataset object and now return both... · 581411fa
  Geoffrey Yu authored Jul 10, 2023
```
finished constructing multimer dataset object and now return both all_seq_features and ground truth structure
```
  581411fa
- finished constructing OpenFoldMultimerDataset filtering and sampling steps · b55ad675
  Geoffrey Yu authored Jul 10, 2023
  
  b55ad675
09 Jul, 2023 4 commits
- update test scripts · 71fdc063
  Geoffrey Yu authored Jul 09, 2023
  
  71fdc063
- update multimer datasets · b61e99bc
  Geoffrey Yu authored Jul 09, 2023
  
  b61e99bc
- added multimer training filter criteria described in the multimer paper · 33d8de81
  Geoffrey Yu authored Jul 09, 2023
  
  33d8de81
- add OpenFoldMultimerDataModule · d35816e3
  Geoffrey Yu authored Jul 09, 2023
  
  d35816e3