Merge upstream #4
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Also add web app code for simple gradio app. Refine requirements.txt/environment.yml. Automatically download models if not present.
Version 1.1
…nference-args Rename `inference_args.yaml` to `default_inference_args.yaml` in `README.md`
Meant to rename it earlier, accidentally just removed it.
* Change many print statements to logging statements, for better control * Save log file to web app zip file for easier debugging
* 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
fix a typo in readme
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.
…in some cases, when project not in root directory without own virtual env
Add __init__ files to all python modules
Upated docker commands instructions in README.md
Fixing bug leading to atom graph containing a lot of incorrect atoms
Install prody with conda and not pip.
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Closed in favor of #5 |
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