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Author SHA1 Message Date
Christina Floristean
6275091c96 Fixed learning rate scheduler issue, returned to original msa file parsing 2024-02-07 15:47:24 -05:00
Jennifer Wei
bc07500422 Merge pull request #404 from jnwei/multimer-small-edits 
Type fixes and README changes for multimer branch
 2024-02-07 23:25:00 +07:00
jnwei
a2adb14748 Merge branch 'multimer' into multimer-small-edits 2024-02-07 23:19:27 +07:00
jnwei
1165d9ebef edit starting sequence in notebook 2024-02-07 23:02:23 +07:00
jnwei
d4acbe6ef8 Adding multimer support to OpenFold notebook 2024-02-07 23:02:23 +07:00
Jennifer Wei
81d817fe68 Update README.md 
fixed a typo in the readme for soloseq params path
 2024-02-07 23:02:19 +07:00
jnwei
5e0616b641 edit starting sequence in notebook 2024-02-07 22:57:37 +07:00
jnwei
94a3b18e23 Adding multimer support to OpenFold notebook 2024-02-07 22:57:37 +07:00
jnwei
3c5233bdaf update setup.py file for version number 2024-02-07 22:54:16 +07:00
Jennifer
396fd44afa adds cutlass directory to .gitignore 2024-02-07 01:04:12 -05:00
Jennifer
0fe5ea3168 Add fixes to permutation test after refactor 2024-02-07 01:03:40 -05:00
Jennifer
0aa694741c fix deepspeed_evo_attention to work in both monomer and multimer settings. 2024-02-07 00:07:58 -05:00
Jennifer
204ed19105 create separate test configs for multimer and monomer 2024-02-07 00:07:29 -05:00
Jennifer
bf8788c7c7 debugging for permutation test 2024-02-06 03:49:53 -05:00
controny
de12c0eada Fix Miniforge3 download link in Dockerfile 2024-02-06 03:48:27 -05:00
yoel shoshan
15b1bbd667 suporting newer numpy 2024-02-06 03:48:27 -05:00
dependabot[bot]
51d6a41d5a Bump actions/setup-python from 4 to 5 
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>
 2024-02-06 03:48:27 -05:00
Jennifer
e94c97ec2d Updates to setup.py and README 2024-02-06 02:50:59 -05:00
controny
ce21136785 Fix Miniforge3 download link in Dockerfile 2024-02-06 10:30:10 +07:00
Jennifer
790267e344 Change parse_fasta to split on whitespace or '|' character 2024-02-02 01:31:11 -05:00
Jennifer
0cf8b928e1 remove nested definition of local_alignmnet_dir in run_pretrained_openfold.py 2024-02-02 01:29:21 -05:00
Jennifer
26d555d5b0 readme and small updates for soloseq support on multimer 2024-02-01 22:53:13 -05:00
Jennifer
30195c4abb Adds absolute error comparison function with better messaging. 2024-02-01 22:53:12 -05:00
Jennifer
8f8b537da8 update deprecated jax.numpy.DeviceArray to jax.Array 2024-02-01 22:53:12 -05:00
Jennifer
2120ce3796 np type update in openfold.np.relax 2024-02-01 22:53:12 -05:00
Jennifer Wei
81ca652ec7 Update README.md 
fixed a typo in the readme for soloseq params path
 2024-01-31 00:30:46 +07:00
Christina Floristean
40d9e7d72d Additional fix for multimer deepspeed test 2024-01-23 12:17:40 -05:00
Christina Floristean
9a07b7f976 Fix deepspeed test for multimer 2024-01-17 10:21:24 -05:00
Christina Floristean
9e057b7a34 Merge pull request #396 from aqlaboratory/deepspeed-mean-test 
Change test_compare_model in deepspeed test to use mean instead of max
 2024-01-17 10:15:51 -05:00
jnwei
39f9958b4a Change test_compare_model in deepspeed test to use mean instead of max 2024-01-11 15:05:37 +07:00
yoel shoshan
447670c03d suporting newer numpy 2024-01-08 16:25:18 +07:00
Jennifer Wei
561333f2e8 Merge pull request #389 from aqlaboratory/readme-changes 
Readme changes
 2023-12-20 16:43:43 -05:00
jnwei
40f98ff075 Adds an outline to the README 2023-12-20 16:40:54 -05:00
Jennifer Wei
6a4b9f395a Merge pull request #380 from aqlaboratory/dependabot/github_actions/actions/setup-python-5 
Bump actions/setup-python from 4 to 5
 2023-12-20 16:25:31 -05:00
Jennifer Wei
f200562821 Update README.md 
small edits to headers
 2023-12-19 17:19:01 -05:00
jnwei
cd54c029f9 [README] Updates inference section to highlight subsections. 2023-12-19 17:09:08 -05:00
Christina Floristean
a475ad11a7 Merge pull request #385 from dingquanyu/update-data-pipeline 
Update data pipeline
 2023-12-18 10:55:38 -05:00
Dingquan Yu
989f2d9335 Update data_pipeline.py 2023-12-15 20:12:42 +01:00
Dingquan Yu
8d8584acc0 get rid of parsing tar.gz2 files for now 2023-12-15 20:05:12 +01:00
Dingquan Yu
c5a69771f4 added back cpu_count import 2023-12-15 20:04:53 +01:00
Dingquan Yu
ffa812e4f2 remove unnecessary imports 2023-12-15 20:04:32 +01:00
Dingquan Yu
de28d842a6 added steps of reading in compressed msa files 2023-12-15 20:04:13 +01:00
Dingquan Yu
e9287b491c added steps to read zipped msa files 2023-12-15 20:03:53 +01:00
Christina Floristean
9d6127cbc4 Fix missing import in tests 2023-12-15 11:49:25 -05:00
Christina Floristean
fe8869c3b6 Bug fixes for multi-chain permutation alignment 2023-12-14 16:29:47 -05:00
Christina Floristean
4f38c82601 Added alignment indexing to multimer pipeline and fixed jackhmmer query return type 2023-12-11 17:16:04 -05:00
Christina Floristean
bcabb8e344 Fix bug from deepspeed upgrade, do not use uniprot_hits in msa feats 2023-12-11 12:00:17 -05:00
Christina Floristean
f861ff396a Merge pull request #376 from dingquanyu/speedup-dataloader 
Speed up data loading process
 2023-12-11 11:52:18 -05:00
Christina Floristean
1606ac0834 Merge branch 'main' into multimer 2023-12-11 10:48:16 -05:00
Christina Floristean
67a00a6cd4 Remove env restart from setup script 2023-12-08 16:50:23 -05:00