15 Commits

Author SHA1 Message Date
Jacob Silterra
5c2e633d22 Merge pull request #236 from burn-in-soul/feat/inits
Add __init__ files to all python modules
2024-09-03 15:53:54 -04:00
Gabriele Corso
6d065cd78c fix issue with different sequences and order 2024-07-08 14:12:59 +02:00
Alexander Schepetilnikov
be0f0f59cf Add __init__ files to all python modules. There were import failures in some cases, when project not in root directory without own virtual env 2024-06-20 17:15:12 +03:00
Jacob Silterra
9d0bf3d884 Set any nans/infs in model scores to a small value.
With some low (but non-trivial) frequency, processing through the convolutional layers diverge and node attributes become a mixture of nan and inf (which seem to all turn to nan). This later throws an exception during the Kabsch transform, which ruins results for the whole complex. Setting these to 0 basically skips an iteration, at worst it ruins one of the sampled complexes, but leaves the others. Note this is only applied to the main model, *not* the confidence model.
2024-06-10 12:44:45 -04:00
Jacob Silterra
561f70a897 Various bugfixes
* Ensure we calculate rotatable bonds on the version of the ligand with no hydrogens. Also fix spelling of rotable -> rotatable. Closes GH-220 (@Nobody-Zhang)

* Vectorize SO3 calculations. Closes PR GH-218 (@tornikeo)

* Pin pytorch-lightning version. Closes GH-193 (@mikael-h-christensen)

* Guard against divide by zero in torus.py. Closes GH-161 (@amorehead)

* Update e3nn version to 0.5.1. Closes GH-155 (@amorehead)

* Add a little more info on docker container to README.md
2024-04-30 10:00:31 -04:00
Jacob Silterra
3995b24fcd Improved logging
* Change many print statements to logging statements, for better control
* Save log file to web app zip file for easier debugging
2024-04-25 11:06:31 -04:00
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
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
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
Gabriele Corso
724da9406b logs for cache 2022-11-16 14:40:09 -05:00
Gabriele Corso
ac5612da4f first commit 2022-10-04 20:11:55 -04:00