Commits · 2dbc8c0eeb66addb0fb17e92d6b209382c6de713 · OpenDAS / OpenFold

21 Mar, 2024 2 commits
- added comments · 2dbc8c0e
  Geoffrey Yu authored Mar 21, 2024
  
  2dbc8c0e
- fixed typing errors; added more comments · 8dfe77e6
  Geoffrey Yu authored Mar 21, 2024
  
  8dfe77e6
20 Feb, 2024 1 commit
- make sure no padded features are going to be selected as anchors · 170d9c55
  Geoffrey Yu authored Feb 20, 2024
  
  170d9c55
16 Feb, 2024 1 commit
- added typing hints and fixed some comments · 7df201e5
  Geoffrey Yu authored Feb 16, 2024
  
  7df201e5
15 Feb, 2024 4 commits
- restore to the verison on main · 2c565664
  Geoffrey Yu authored Feb 15, 2024
  
  2c565664
- remove unnecessary lines · aa18a56b
  Geoffrey Yu authored Feb 15, 2024
  
  aa18a56b
- fixed bugs in unittests for multi-chain permutation. now working on extra subtests · d74b09cc
  Geoffrey Yu authored Feb 15, 2024
  
  d74b09cc
- make sure padded asym_id won't affect permutation steps · df96b586
  Geoffrey Yu authored Feb 15, 2024
  
  df96b586
08 Feb, 2024 1 commit
- Merge pull request #405 from aqlaboratory/multimer · bb3f51e5
  Christina Floristean authored Feb 07, 2024
```
Full multimer merge
```
  bb3f51e5
07 Feb, 2024 14 commits
- Merge branch 'main' into multimer · c33a0bd6
  Christina Floristean authored Feb 07, 2024
  
  c33a0bd6
- Fixed learning rate scheduler issue, returned to original msa file parsing · 6275091c
  Christina Floristean authored Feb 07, 2024
  
  6275091c
- Merge pull request #404 from jnwei/multimer-small-edits · bc075004
  Jennifer Wei authored Feb 07, 2024
```
Type fixes and README changes for multimer branch
```
  bc075004
- Merge branch 'multimer' into multimer-small-edits · a2adb147
  jnwei authored Feb 07, 2024
  
  a2adb147
- edit starting sequence in notebook · 1165d9eb
  jnwei authored Feb 07, 2024
  
  1165d9eb
- Adding multimer support to OpenFold notebook · d4acbe6e
  jnwei authored Jan 30, 2024
  
  d4acbe6e
- Update README.md · 81d817fe
  Jennifer Wei authored Jan 31, 2024
```
fixed a typo in the readme for soloseq params path
```
  81d817fe
- edit starting sequence in notebook · 5e0616b6
  jnwei authored Feb 07, 2024
  
  5e0616b6
- Adding multimer support to OpenFold notebook · 94a3b18e
  jnwei authored Jan 30, 2024
  
  94a3b18e
- update setup.py file for version number · 3c5233bd
  jnwei authored Feb 07, 2024
  
  3c5233bd
- adds cutlass directory to .gitignore · 396fd44a
  Jennifer authored Feb 07, 2024
  
  396fd44a
- Add fixes to permutation test after refactor · 0fe5ea31
  Jennifer authored Feb 07, 2024
  
  0fe5ea31
- fix deepspeed_evo_attention to work in both monomer and multimer settings. · 0aa69474
  Jennifer authored Feb 07, 2024
  
  0aa69474
- create separate test configs for multimer and monomer · 204ed191
  Jennifer authored Feb 07, 2024
  
  204ed191
06 Feb, 2024 6 commits
- debugging for permutation test · bf8788c7
  Jennifer authored Feb 06, 2024
  
  bf8788c7
- Fix Miniforge3 download link in Dockerfile · de12c0ea
  controny authored Feb 05, 2024
  
  de12c0ea
- suporting newer numpy · 15b1bbd6
  yoel shoshan authored Apr 23, 2023
  
  15b1bbd6
- Bump actions/setup-python from 4 to 5 · 51d6a41d
  dependabot[bot] authored Dec 06, 2023
```
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5

)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
```
  51d6a41d
- Updates to setup.py and README · e94c97ec
  Jennifer authored Feb 06, 2024
  
  e94c97ec
- Fix Miniforge3 download link in Dockerfile · ce211367
  controny authored Feb 05, 2024
  
  ce211367
02 Feb, 2024 6 commits
- Change parse_fasta to split on whitespace or '|' character · 790267e3
  Jennifer authored Feb 02, 2024
  
  790267e3
- remove nested definition of local_alignmnet_dir in run_pretrained_openfold.py · 0cf8b928
  Jennifer authored Feb 02, 2024
  
  0cf8b928
- readme and small updates for soloseq support on multimer · 26d555d5
  Jennifer authored Jan 29, 2024
  
  26d555d5
- Adds absolute error comparison function with better messaging. · 30195c4a
  Jennifer authored Jan 24, 2024
  
  30195c4a
- update deprecated jax.numpy.DeviceArray to jax.Array · 8f8b537d
  Jennifer authored Jan 23, 2024
  
  8f8b537d
- np type update in openfold.np.relax · 2120ce37
  Jennifer authored Jan 16, 2024
  
  2120ce37
30 Jan, 2024 1 commit
- Update README.md · 81ca652e
  Jennifer Wei authored Jan 31, 2024
```
fixed a typo in the readme for soloseq params path
```
  81ca652e
23 Jan, 2024 1 commit
- Additional fix for multimer deepspeed test · 40d9e7d7
  Christina Floristean authored Jan 23, 2024
  
  40d9e7d7
17 Jan, 2024 2 commits
- Fix deepspeed test for multimer · 9a07b7f9
  Christina Floristean authored Jan 17, 2024
  
  9a07b7f9
- Merge pull request #396 from aqlaboratory/deepspeed-mean-test · 9e057b7a
  Christina Floristean authored Jan 17, 2024
```
Change test_compare_model in deepspeed test to use mean instead of max
```
  9e057b7a
11 Jan, 2024 1 commit
- Change test_compare_model in deepspeed test to use mean instead of max · 39f9958b
  jnwei authored Jan 11, 2024
  
  39f9958b