Commits · def329b880d890d0707684a3ab4060d4c145bf4f · OpenDAS / OpenFold · GitLab

16 Oct, 2023 5 commits
- Removed references to jax · def329b8
  Christina Floristean authored Oct 16, 2023
  
  def329b8
- Fix multimer sampling · 8470b803
  Christina Floristean authored Oct 16, 2023
  
  8470b803
- Merge branch 'multimer' of https://github.com/aqlaboratory/openfold into multimer · 14853379
  Christina Floristean authored Oct 16, 2023
  
  14853379
- Refactoring multimer data pipeline and permutation alignment. · 0cf1541c
  Christina Floristean authored Oct 16, 2023
  
  0cf1541c
- Merge pull request #359 from dingquanyu/update-kabsch_rotation · ec75fe22
  Christina Floristean authored Oct 16, 2023
```
move the kabsch rotation step to gpu
```
  ec75fe22
12 Oct, 2023 1 commit
- move the kabsch rotation step to gpu · cdfb0c75
  Geoffrey Yu authored Oct 12, 2023
  
  cdfb0c75
04 Oct, 2023 1 commit
- Merge pull request #355 from dingquanyu/fix-non-permutation-codes · 377f854c
  Christina Floristean authored Oct 04, 2023
```
fixed the creation of best_align when permutation is turned off
```
  377f854c
03 Oct, 2023 1 commit
- fixed alignments when permutation is turned off · 058fc74f
  Geoffrey Yu authored Oct 03, 2023
  
  058fc74f
29 Sep, 2023 1 commit
- Merge pull request #353 from dingquanyu/permutation · 0ca66146
  Christina Floristean authored Sep 29, 2023
```
Update multi-chain permutation and training codes
```
  0ca66146
28 Sep, 2023 7 commits
- remove debug statements · a9d65037
  Geoffrey Yu authored Sep 28, 2023
  
  a9d65037
- move ground truth preparation out of process_tensors_from_config · 61c7640c
  Geoffrey Yu authored Sep 28, 2023
  
  61c7640c
- update feature_pipeline accordingly · a9cf892f
  Geoffrey Yu authored Sep 28, 2023
  
  a9cf892f
- 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 5 commits
- Merge pull request #348 from dingquanyu/fix-inference-script · 8820875b
  Christina Floristean authored Sep 25, 2023
```
Fixed inference script in multimer mode
```
  8820875b
- 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 4 commits
- Update run_pretrained_openfold.py · 7f12c2a7
  Dingquan Yu authored Sep 19, 2023
  
  7f12c2a7
- 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
- fixed problem with multimer inference · 9a679b31
  Geoffrey Yu authored Sep 19, 2023
  
  9a679b31
18 Sep, 2023 1 commit
- revert back to e097da95 · be127915
  Geoffrey Yu authored Sep 18, 2023
  
  be127915