├── .codecov.yml ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── CI.yaml │ └── deploy.yaml ├── .gitignore ├── .lgtm.yml ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools ├── conda-envs │ ├── gninatorch-CI.yaml │ └── gninatorch.yaml └── scripts │ └── create_conda_env.py ├── docs ├── Makefile ├── README.md ├── requirements.yaml └── source │ ├── GNINA.rst │ ├── _static │ └── README.md │ ├── _templates │ └── README.md │ ├── api.rst │ ├── api │ ├── gninatorch.dataloaders.rst │ ├── gninatorch.gnina.rst │ ├── gninatorch.inference.rst │ ├── gninatorch.losses.rst │ ├── gninatorch.metrics.rst │ ├── gninatorch.models.rst │ ├── gninatorch.rst │ ├── gninatorch.setup.rst │ ├── gninatorch.training.rst │ ├── gninatorch.transforms.rst │ └── gninatorch.utils.rst │ ├── conf.py │ ├── getting_started.rst │ ├── index.rst │ └── references.bib ├── examples ├── Francoeur2020 │ ├── 00_download.sh │ ├── PDBbind2016-Crystal │ │ ├── 01_train.sh │ │ ├── 02_predict.sh │ │ ├── 03_analysis.sh │ │ ├── README.md │ │ ├── assets │ │ │ ├── pearson-box.png │ │ │ └── rmse-box.png │ │ └── plot.py │ └── PDBbind2016-Docked │ │ ├── 01_train.sh │ │ ├── 02_predict.sh │ │ ├── 03_analysis.sh │ │ ├── README.md │ │ ├── assets │ │ ├── pearson-box.png │ │ └── rmse-box.png │ │ └── plot.py └── Ragoza2017 │ ├── 00_cleanup.sh │ ├── 00_download.sh │ ├── 01_train.sh │ ├── 02_analysis.sh │ ├── README.md │ ├── assets │ └── ROC-AUC.png │ └── plot.py ├── gninatorch ├── __init__.py ├── _version.py ├── data │ ├── intro │ └── logo ├── dataloaders.py ├── gnina.py ├── inference.py ├── losses.py ├── metrics.py ├── models.py ├── setup.py ├── training.py ├── transforms.py ├── utils.py └── weights │ ├── crossdock_default2018.pt │ ├── crossdock_default2018_1.pt │ ├── crossdock_default2018_2.pt │ ├── crossdock_default2018_3.pt │ ├── crossdock_default2018_4.pt │ ├── default2017.pt │ ├── 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