Jacob Silterra
3e80ffd7a0
Merge pull request #241 from bamattsson/fixing_bug_in_atom_preprocessing
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Fixing bug leading to atom graph containing a lot of incorrect atoms
2024-09-03 15:57:25 -04:00
Bjorn Mattsson
8c0b943f1b
changing zero to nan to allow filtering of nan in new_extract_receptor_structure
2024-07-15 15:17:36 +01:00
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
561f70a897
Various bugfixes
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* 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
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* 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
Gabriele Corso
001c4fa46e
first commit v1.1
2024-02-28 11:21:46 -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
HannesStark
b1b9b46541
improve logging
2022-10-26 08:35:32 -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
Gabriele Corso
f6094e7471
remove unwanted raise #13
2022-10-07 18:33:34 -04:00
HannesStark
0b3a1f8d1a
fix lm embedding preparation file if protein was not preprocessed
2022-10-07 09:06:37 -04:00
Gabriele Corso
addd0e9756
avoid failure in case of unreadable molecules
2022-10-06 19:00:20 -04:00
Simon Duerr
6f19de8af4
Update process_mols.py
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This fixes #3 by providing a clearer error message.
The program should exit because it will throw an error when `RemoveAllConformers()` is called on `None`
2022-10-06 13:13:37 -07:00
Gabriele Corso
ac5612da4f
first commit
2022-10-04 20:11:55 -04:00
