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dev_v1.1
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Author SHA1 Message Date
Jacob Silterra
d9114a44ae Add Dockerfile for creating container. 
Also add web app code for simple gradio app.
Refine requirements.txt/environment.yml.
Automatically download models if not present.
 2024-02-28 11:37:18 -05:00
Gabriele Corso
001c4fa46e first commit v1.1 2024-02-28 11:21:46 -05:00
Gabriele Corso
bc6b515145 Update README.md v1.0 2023-10-12 14:25:03 -07:00
Gabriele Corso
600a23fa23 Fix ckpt path #85 2023-07-18 01:40:55 -07:00
Gabriele Corso
2782769ccd added code to align apo with holo structures 2023-07-03 09:13:10 +02:00
Gabriele Corso
7dc84c9269 Update environment #74 2023-06-16 02:05:26 -07:00
Gabriele Corso
3d45728415 fix inference_utils.py #90 2023-06-08 05:13:04 -07:00
Hannes Stärk
1b9a9cb09b Update inference_utils.py for issue #90 2023-05-12 13:58:25 -04:00
Hannes Stärk
6c3d8ceb6e Update evaluate.py to non-hardcoded split path 2023-05-12 13:44:27 -04:00
Hannes Stärk
81ff501e20 Update evaluate_files.py with non-hard coded paths 2023-05-12 13:41:34 -04:00
Gabriele Corso
c1abe25540 Update README.md 2023-04-13 13:16:51 -07:00
Gabriele Corso
3c3c728cf2 Merge pull request #93 from duerrsimon/patch-1 
Remove hyperparameter notice
 2023-03-27 15:37:02 -04:00
Simon Duerr
23e1dba5d0 Remove hyperparameter notice 
Due to a runtime error I had to update the space to pin pytorch geometric to 2.1.0 and also updated the space to run with the same default options as described here, so I think this notice can be removed. I keep the number of samples at 10 for now due to runtime constraints but people can set it higher if they want. 

I think the colab notebook also needs to fix the dependency, it threw a few errors when I tried it earlier: `pip install git+https://github.com/pyg-team/pytorch_geometric.git@2.1.0
`
 2023-03-26 22:58:54 +02:00
Gabriele Corso
f135e3baa7 Update README.md 2023-03-25 12:15:55 -07:00
Gabriele Corso
2c7d438516 Fix path in model parameters #80 2023-03-09 15:12:47 -08:00
Gabriele Corso
73ef67ffcf fix testset csv and removed raise #77 2023-03-04 14:16:35 -05:00
Gabriele Corso
3829a23af8 Update README.md 2023-02-20 11:10:19 -08:00
Gabriele Corso
dde480d709 small fix 2023-02-11 12:39:27 -05:00
Gabriele Corso
b7259b9584 add example 2023-02-11 12:33:49 -05:00
Gabriele Corso
83993e9ee5 remove odd_parity #76 2023-02-11 12:11:18 -05:00
Gabriele Corso
1f63eb8b37 fix new version 2023-02-11 12:07:56 -05:00
Gabriele Corso
510e51690a new version: integrated ESM + ESMFold 2023-02-10 19:56:03 -05:00
Gabriele Corso
47bf7e5e08 added no_aminoacid_identities 2023-02-05 20:17:35 -05:00
Hannes Stärk
fff8f0b5eb Update README.md 2023-01-09 16:32:12 -05:00
Hannes Stärk
382b3f0eb3 Add truncation sequence length in esm embedding generation command since the default is only 1022 2023-01-09 09:47:18 -05:00
Hannes Stärk
8e853d6b14 Update README.md 2022-11-25 16:57:19 -05:00
Hannes Stärk
71c110fd7d Update README.md 
better instructions for conda environment creation
 2022-11-25 16:52:42 -05:00
HannesStark
cd98700f42 add additional logging to avoid confusion that repeatedly occurred 2022-11-20 13:11:19 -05:00
HannesStark
7d1768a505 raise error if no complexes could be preprocessed instead of saving the empty list to the pickle file since users were getting confused 2022-11-20 12:56:24 -05:00
HannesStark
4fb49bbf2b better log messaging 2022-11-18 09:30:18 -05:00
Hannes Stärk
d615844a55 Update README.md 2022-11-18 08:58:36 -05:00
Gabriele Corso
724da9406b logs for cache 2022-11-16 14:40:09 -05:00
Gabriele Corso
5393a8cafc fix confidence ckpt and improve memory 2022-11-16 14:13:42 -05:00
Gabriele Corso
4c60e5b7ee fix center convolution index #34 2022-11-16 14:00:39 -05:00
HannesStark
f8d67b5b2b correct skipping of complexes in inference from files 2022-10-26 08:38:32 -04:00
HannesStark
b1b9b46541 improve logging 2022-10-26 08:35:32 -04:00
HannesStark
c32ec5b433 add logging to eval-files.py 2022-10-26 08:31:49 -04:00
HannesStark
21fadc2a37 skip molecules if preprocessing ligands does not work out. 2022-10-25 17:41:45 -04:00
HannesStark
cdb6a0e8cb skip molecules if preprocessing ligands does not work out. 2022-10-25 17:40:26 -04:00
HannesStark
b60807224f fix user inference mistake that Rachel found 2022-10-25 17:14:28 -04:00
HannesStark
4cd8ee1bb9 add more logging 2022-10-25 16:58:13 -04:00
Gabriele Corso
63f9c33afa raise instead of return #26 2022-10-23 22:22:10 -04:00
HannesStark
a6c527536d remove debugging raise in the inference file 2022-10-14 17:30:46 -04:00
Hannes Stärk
5cf22913e1 correct num predictions in the readme 2022-10-14 17:04:40 -04:00
Gabriele Corso
2221adbeb3 Fixed the inference script 2022-10-13 09:22:36 -07:00
Gabriele Corso
be1dcde594 Update README.md 2022-10-12 11:04:07 -07:00
Hannes Stärk
6795f8f2e2 Remove unnecessary parameters from readme confidence train 2022-10-11 10:01:15 -04:00
Gabriele Corso
7b68ba2483 Update README.md 2022-10-10 14:55:39 -07:00
Gabriele Corso
d935c51c64 Update README.md 2022-10-09 21:05:33 -07:00
HannesStark
1754dfbaf7 fix typo 2022-10-09 20:54:20 -04:00