Commits · 53c03a6a577d030beaaaf4566cb2b7745890e497 · OpenDAS / OpenFold

05 Dec, 2023 1 commit
- update config.py for the development for now · 53c03a6a
  Dingquan Yu authored Dec 05, 2023
  
  53c03a6a
04 Dec, 2023 1 commit
- now use ThreadPoolExecutor · 4e58a6a0
  Dingquan Yu authored Dec 04, 2023
  
  4e58a6a0
02 Dec, 2023 1 commit
- fixed errors when running in subprocess · 2204bbb2
  Dingquan Yu authored Dec 02, 2023
  
  2204bbb2
01 Dec, 2023 1 commit
- now run in a subprocess · c3c627e7
  Dingquan Yu authored Dec 01, 2023
  
  c3c627e7
30 Nov, 2023 3 commits
- now using multiprocessing style · 2e1941a0
  Dingquan Yu authored Nov 30, 2023
  
  2e1941a0
- now used asynchronised version in parse_msa_data · 6f3e0c0c
  Dingquan Yu authored Nov 30, 2023
  
  6f3e0c0c
- added timing steps · aec12764
  Dingquan Yu authored Nov 30, 2023
  
  aec12764
21 Nov, 2023 1 commit
- Fix for issue ##369: Bug in multimer deterministic train filter · cdeb8d1b
  Christina Floristean authored Nov 21, 2023
  
  cdeb8d1b
10 Nov, 2023 1 commit
- Fix naming error in alignment runner, add error message for missing uniprot files. · d8c2a979
  Christina Floristean authored Nov 10, 2023
  
  d8c2a979
06 Nov, 2023 4 commits
- Fix for feature indexing when creating output protein object · 7e2b36e0
  Christina Floristean authored Nov 06, 2023
  
  7e2b36e0
- Add description to dummy msa feats · c05b4674
  Christina Floristean authored Nov 06, 2023
  
  c05b4674
- Another fix for dummy msa feature creation · d0f5531b
  Christina Floristean authored Nov 06, 2023
  
  d0f5531b
- Fix for creating msa dummy features · e67d0417
  Christina Floristean authored Nov 06, 2023
  
  e67d0417
03 Nov, 2023 1 commit
- Fix for loading old OF weights into refactored model · f65b75fe
  Christina Floristean authored Nov 03, 2023
  
  f65b75fe
02 Nov, 2023 3 commits
- Unit test fixes for when AF2 is not installed · 5fcd6ed2
  Christina Floristean authored Nov 02, 2023
  
  5fcd6ed2
- Change order of numpy and pandas dependencies to keep numpy version. · f95d9a57
  jnwei authored Nov 02, 2023
  
  f95d9a57
- Fixes for inference alignment generation · f94ee668
  Christina Floristean authored Nov 02, 2023
  
  f94ee668
30 Oct, 2023 5 commits
- Merge branch 'main' into multimer · 5eacd8b6
  Christina Floristean authored Oct 30, 2023
  
  5eacd8b6
- Added multimer inference to README · 15850092
  Christina Floristean authored Oct 30, 2023
  
  15850092
- Merge pull request #365 from aqlaboratory/dependabot/github_actions/actions/setup-python-4 · 2338b896
  Jennifer Wei authored Oct 30, 2023
```
Bump actions/setup-python from 2 to 4
```
  2338b896
- Bump actions/setup-python from 2 to 4 · dcd809d9
  dependabot[bot] authored Oct 30, 2023
```
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v2...v4

)

---
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>
```
  dcd809d9
- Merge pull request #366 from aqlaboratory/dependabot/github_actions/actions/checkout-4 · 51472e75
  Jennifer Wei authored Oct 30, 2023
```
Bump actions/checkout from 2 to 4
```
  51472e75
27 Oct, 2023 6 commits

Bump actions/checkout from 2 to 4 · 13728b12

dependabot[bot] authored Oct 27, 2023

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v4

)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>

13728b12

Merge pull request #360 from aqlaboratory/installation-updates · f7dba95f
Jennifer Wei authored Oct 27, 2023
```
Merging installation updates and updates
```
f7dba95f
Adds KMP_AFFINITY to conda environment. · e3716118
Jennifer Wei authored Oct 27, 2023

e3716118

Merge branch 'installation-updates' of... · 6df89c76

Jennifer Wei authored Oct 27, 2023

Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates

6df89c76

Adds libgcc and pytorch::pytorch to environment.yml · 13f0f6fe
Jennifer Wei authored Oct 27, 2023

13f0f6fe
Merge branch 'main' into multimer · d7c11537
Christina Floristean authored Oct 27, 2023

d7c11537

25 Oct, 2023 2 commits
- README: Small improvements, info regarding templates · 9e32781f
  Sachin Kadyan authored Oct 25, 2023
  
  9e32781f
- Update readme, also reset flash attention version to 0.2.1 in environment.yml · f68a6c69
  jnwei authored Oct 25, 2023
  
  f68a6c69
24 Oct, 2023 10 commits
- Test docker image nvidia/11.7.1-cudnn8-devel-ubuntu18.04 · a5c69a79
  jnwei authored Oct 24, 2023
  
  a5c69a79
- Change docker image to use cudnn devel environment · e2bb3c4b
  jnwei authored Oct 24, 2023
  
  e2bb3c4b
- Test nvidia image 11.4.3-cudnn8-runtime-unbuntu18.04 · 6fe34248
  jnwei authored Oct 24, 2023
  
  6fe34248
- Fix export statement · 5efba442
  jnwei authored Oct 24, 2023
  
  5efba442
- Update Dockerfile to add conda path to $LD_LIBRARY_PATH · 3817d940
  jnwei authored Oct 24, 2023
  
  3817d940
- update flash-attention-version · a5a86d43
  jnwei authored Oct 24, 2023
  
  a5a86d43
- Add git to environment.yml · f06657fe
  Jennifer Wei authored Oct 24, 2023
  
  f06657fe
- README: Update details about SoloSeq and inference-time embedding generation. · 2d4fe4f4
  Sachin Kadyan authored Oct 24, 2023
  
  2d4fe4f4
- Test flash-attention v0.2.1 on docker CI · a90da395
  jnwei authored Oct 24, 2023
  
  a90da395
- Separate out input parsing code in `EmbeddingGenerator` · 86b990d6
  Sachin Kadyan authored Oct 24, 2023
```
Bugfix: Corrected paths for just-in-time embedding generation
```
  86b990d6