Commits · 585136e4a4de81d3de5f30d7f2e51028be6a90a7 · OpenDAS / OpenFold

30 Jun, 2023 7 commits
- Update README.md · 585136e4
  Dingquan Yu authored Jun 30, 2023
  
  585136e4
- Update README.md · 02b008dc
  Dingquan Yu authored Jun 30, 2023
  
  02b008dc
- change it back to unittest testunit · 7e969e48
  Geoffrey Yu authored Jun 30, 2023
  
  7e969e48
- update test codes so that it generates correct structure of input data · 1e268fd5
  Geoffrey Yu authored Jun 30, 2023
  
  1e268fd5
- finished constructing AlphaFoldMultimerLoss and other necessary changes in the losses calculations · 6eb1afe7
  Geoffrey Yu authored Jun 30, 2023
  
  6eb1afe7
- remove some the printed out messages · 30d50a18
  Geoffrey Yu authored Jun 30, 2023
  
  30d50a18
- fixed the input data generation so that true_msa and bert_mask shapes are... · 1b4fc115
  Geoffrey Yu authored Jun 30, 2023
```
fixed the input data generation so that true_msa and bert_mask shapes are correct otherwise crashes in loss calculations
```
  1b4fc115
29 Jun, 2023 12 commits
- Merge branch 'permutation' of github.com:henrywotton/openfold into permutation · 4f50aadc
  Geoffrey Yu authored Jun 29, 2023
  
  4f50aadc
- updated the loss config so that the masked msa dim is 22 instead of 23 · 9ebb1e1a
  Geoffrey Yu authored Jun 29, 2023
  
  9ebb1e1a
- start working on masked_msa_loss error · 07421c47
  Geoffrey Yu authored Jun 29, 2023
  
  07421c47
- Update README.md · 33a55033
  Dingquan Yu authored Jun 29, 2023
  
  33a55033
- fixed lddt_loss nan error · 1df55b4e
  Geoffrey Yu authored Jun 29, 2023
  
  1df55b4e
- Merge branch 'permutation' of github.com:henrywotton/openfold into permutation · edb4858e
  Geoffrey Yu authored Jun 29, 2023
  
  edb4858e
- Update README.md · 76e55250
  Dingquan Yu authored Jun 29, 2023
  
  76e55250
- update test code · c8a3f35e
  Geoffrey Yu authored Jun 29, 2023
  
  c8a3f35e
- fixed the fape and backbone loss errors · bbf42cc5
  Geoffrey Yu authored Jun 29, 2023
  
  bbf42cc5
- update config so that it will update multimer loss otherwise fape loss calculation crashes · b22bd4e3
  Geoffrey Yu authored Jun 29, 2023
  
  b22bd4e3
- fix the aatype indexing error. now move all tensors to cpu and run calculations first · beccaa4b
  Geoffrey Yu authored Jun 29, 2023
  
  beccaa4b
- update greedy_align just in case there are nan in rmsd calculation · 80b32a3a
  Geoffrey Yu authored Jun 29, 2023
  
  80b32a3a
28 Jun, 2023 6 commits
- solved cuda error just for now by moving the 2 tensors to cpu · 80f0d617
  Geoffrey Yu authored Jun 28, 2023
  
  80f0d617
- move some tensors back to gpu · 3ab9da6e
  Geoffrey Yu authored Jun 28, 2023
  
  3ab9da6e
- now check the batch_size in compute_tm function · a420160f
  Geoffrey Yu authored Jun 28, 2023
  
  a420160f
- update the compue_tm function · 5e1af36e
  Geoffrey Yu authored Jun 28, 2023
  
  5e1af36e
- added batch_size dimension · c69053e5
  Geoffrey Yu authored Jun 28, 2023
  
  c69053e5
- added batch_size dimesion to compute_tm · 15105078
  Geoffrey Yu authored Jun 28, 2023
  
  15105078
27 Jun, 2023 4 commits
- Update README.md · a3ea7c65
  Dingquan Yu authored Jun 27, 2023
  
  a3ea7c65
- Merge pull request #3 from dingquanyu/modify-assignment-stage · 3d87ef2f
  Dingquan Yu authored Jun 27, 2023
```
Modify assignment stage
```
  3d87ef2f
- start working on loss part · eeb035c2
  Geoffrey Yu authored Jun 27, 2023
  
  eeb035c2
- remove shuffling · 24e470be
  Geoffrey Yu authored Jun 27, 2023
  
  24e470be
26 Jun, 2023 6 commits
- handel NaN and Inf in test output to avoid crashes · 2a70e080
  Geoffrey Yu authored Jun 26, 2023
  
  2a70e080
- switch optimal alignment method to procustes package · 458a62f7
  Geoffrey Yu authored Jun 26, 2023
  
  458a62f7
- swtich to scipy's kabsch algorithm · 82895ec3
  Geoffrey Yu authored Jun 26, 2023
  
  82895ec3
- update the test input to be A2B3 · 5621ac05
  Geoffrey Yu authored Jun 26, 2023
  
  5621ac05
- update codes · 4666e15e
  Geoffrey Yu authored Jun 26, 2023
  
  4666e15e
- Update README.md · 938782e0
  Dingquan Yu authored Jun 26, 2023
  
  938782e0
24 Jun, 2023 5 commits
- added example label files · a741b42a
  Geoffrey Yu authored Jun 24, 2023
  
  a741b42a
- remove unnecessary extra file · 50abc1a7
  Geoffrey Yu authored Jun 24, 2023
  
  50abc1a7
- Merge pull request #2 from dingquanyu/cleanup-permutation · 697ac82a
  Dingquan Yu authored Jun 24, 2023
```
added multi-chain permutation to AlphaFoldMultimerLoss
```
  697ac82a
- added multi-chain permutation to AlphaFoldMultimerLoss · a49e4896
  Geoffrey Yu authored Jun 24, 2023
  
  a49e4896
- revert data_utils and remove all the changes in this file · 85cd91f6
  Geoffrey Yu authored Jun 24, 2023
  
  85cd91f6