Commits · f3c1af45564e74fea8a658205230bbe907556be0 · OpenDAS / OpenFold

21 Sep, 2023 5 commits
- fixed error with anchor selections; updated permutation unittest · f3c1af45
  Geoffrey Yu authored Sep 21, 2023
  
  f3c1af45
- cleaned up and split into smaller functions · 15f1fa63
  Geoffrey Yu authored Sep 21, 2023
  
  15f1fa63
- fixed merge_labels index error. Now working on cleaning up · ea7fcced
  Geoffrey Yu authored Sep 21, 2023
  
  ea7fcced
- fixed the index error. Now working on updating greedy_align · fe01bb0c
  Geoffrey Yu authored Sep 21, 2023
  
  fe01bb0c
- revert back to e097da95 for now · 2184eff0
  Geoffrey Yu authored Sep 21, 2023
  
  2184eff0
20 Sep, 2023 1 commit
- fixed inference script · 01ef215e
  Geoffrey Yu authored Sep 20, 2023
  
  01ef215e
19 Sep, 2023 2 commits
- further cleaned up functions · d909c707
  Geoffrey Yu authored Sep 19, 2023
  
  d909c707
- split multi_chain_perm_align into multiple smaller functions · faca088f
  Geoffrey Yu authored Sep 19, 2023
  
  faca088f
18 Sep, 2023 2 commits
- revert back to e097da95 · be127915
  Geoffrey Yu authored Sep 18, 2023
  
  be127915
- protect necessary tensors by moving them to cpu memory · 0d98466d
  Geoffrey Yu authored Sep 18, 2023
  
  0d98466d
13 Sep, 2023 1 commit
- update data_transforms_multimer to the latest version of multimer branch · bc49758a
  Geoffrey Yu authored Sep 13, 2023
  
  bc49758a
10 Sep, 2023 3 commits
- Update train_openfold.py · da92663d
  Dingquan Yu authored Sep 10, 2023
  
  da92663d
- remove debugging statement · 2d09f801
  Geoffrey Yu authored Sep 10, 2023
  
  2d09f801
- fixed index error in cropping · 4a215372
  Geoffrey Yu authored Sep 10, 2023
  
  4a215372
08 Sep, 2023 1 commit
- update train_openfold to handle val_mmcif_cache;update datamodule to handle if... · dc5d43d7
  Geoffrey Yu authored Sep 08, 2023
```
update train_openfold to handle val_mmcif_cache;update datamodule to handle if validation mmcif cache is not provided
```
  dc5d43d7
06 Sep, 2023 1 commit
- check if it's a monomer first; add permutate_chains back to forward() · e097da95
  Geoffrey Yu authored Sep 06, 2023
  
  e097da95
03 Sep, 2023 2 commits
- added test3 to test if permutated tensors end up as expected · cec5a426
  Geoffrey Yu authored Sep 03, 2023
  
  cec5a426
- update permutation unittest · c5f16efc
  Geoffrey Yu authored Sep 03, 2023
  
  c5f16efc
31 Aug, 2023 2 commits
- check if the strucutre is a monomer first before applying multi-chain permutation · 20586e4e
  Geoffrey Yu authored Aug 31, 2023
  
  20586e4e
- update AlphaFoldMultimerLoss to accomodate new way of data_module loading procudure · 2a1028f0
  Geoffrey Yu authored Aug 31, 2023
  
  2a1028f0
30 Aug, 2023 1 commit
- update get_least_asym_entity_or_longest_length and added split_ground_truth_labels · dff973ab
  Geoffrey Yu authored Aug 30, 2023
  
  dff973ab
28 Aug, 2023 1 commit
- Fixes for memory usage in multimer dataloader, spatial cropping, and tensor... · ab09ded4
  Christina Floristean authored Aug 28, 2023
```
Fixes for memory usage in multimer dataloader, spatial cropping, and tensor type conversions within model.
```
  ab09ded4
16 Aug, 2023 1 commit
- Fixes for multimer config features and cropping · da5d0e7d
  Christina Floristean authored Aug 16, 2023
  
  da5d0e7d
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 5 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