Commits · 9aebc203b0f3176a65b2b42494cb0c5d173d554a · OpenDAS / OpenFold

28 Sep, 2023 4 commits
- update the returned features when it's not training mode in multimer input pipeline · 9aebc203
  Geoffrey Yu authored Sep 28, 2023
  
  9aebc203
- update permutation logic so that it check all valid anchor pairs · 68389359
  Geoffrey Yu authored Sep 28, 2023
  
  68389359
- fixed the return issue in np_example_to_features when training monomer · 2da285aa
  Geoffrey Yu authored Sep 28, 2023
  
  2da285aa
- anchor selection funciton now returns a list of possible pred anchors · cb43a5b3
  Geoffrey Yu authored Sep 28, 2023
  
  cb43a5b3
26 Sep, 2023 4 commits
- added logging infor about filtering results;revert filtering criteria back to default · f6cc4a16
  Geoffrey Yu authored Sep 26, 2023
  
  f6cc4a16
- update anchor selection function logic · 51f3325f
  Geoffrey Yu authored Sep 26, 2023
  
  51f3325f
- update np_example_to_features · 986d1f67
  Geoffrey Yu authored Sep 26, 2023
  
  986d1f67
- update groundtruth_transforms · 9a97d0d7
  Geoffrey Yu authored Sep 26, 2023
  
  9a97d0d7
25 Sep, 2023 4 commits
- update trainining code with new input from new multimer pipeline · 3aaf0ca8
  Geoffrey Yu authored Sep 25, 2023
  
  3aaf0ca8
- update input pipeline multimer · 74670a88
  Geoffrey Yu authored Sep 25, 2023
  
  74670a88
- update input pipeline · 324b2ea6
  Geoffrey Yu authored Sep 25, 2023
  
  324b2ea6
- update loss to accomodate new input data pipeline · fd748a0d
  Geoffrey Yu authored Sep 25, 2023
  
  fd748a0d
24 Sep, 2023 3 commits
- fixed error when selected anchor_aysm is not in the cropped input features · 02ce77c5
  Geoffrey Yu authored Sep 24, 2023
  
  02ce77c5
- updated optimal transform function now · 67f873e7
  Geoffrey Yu authored Sep 24, 2023
  
  67f873e7
- added common features that need to be preserved for both gt and input features · bd82338e
  Geoffrey Yu authored Sep 24, 2023
  
  bd82338e
23 Sep, 2023 1 commit
- update multimer data input pipeline · 093603ee
  Geoffrey Yu authored Sep 23, 2023
  
  093603ee
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 1 commit
- Minor model test fix · 3de188e9
  Christina Floristean authored Aug 10, 2023
  
  3de188e9