├── .gitignore ├── HuggingMolecules.pdf ├── LICENSE ├── README.md ├── examples └── quick_tour.py ├── experiments ├── README.md ├── __init__.py ├── configs │ ├── bases │ │ ├── benchmark.gin │ │ ├── train.gin │ │ └── tune_hyper.gin │ ├── datasets │ │ ├── bbbp.gin │ │ ├── bioavailability.gin │ │ ├── caco2.gin │ │ ├── clearance.gin │ │ ├── freesolv.gin │ │ ├── hia.gin │ │ ├── ppbr.gin │ │ ├── qm7.gin │ │ └── tox21-nr-ar.gin │ ├── models │ │ ├── chemberta.gin │ │ ├── chemprop.gin │ │ ├── grover.gin │ │ ├── mat.gin │ │ ├── molbert.gin │ │ └── rmat.gin │ ├── setup.gin │ └── tasks │ │ ├── classification.gin │ │ └── regression.gin ├── requirements.txt ├── scripts │ ├── benchmark.py │ ├── train.py │ └── tune_hyper.py └── src │ ├── __init__.py │ ├── benchmarking │ ├── __init__.py │ ├── benchmarking_benchmark_results.py │ └── benchmarking_utils.py │ ├── gin │ ├── __init__.py │ ├── gin_parser.py │ ├── gin_parser_utils.py │ └── gin_utils.py │ ├── training │ ├── __init__.py │ ├── training_callbacks.py │ ├── training_lightning_module.py │ ├── training_loss_fn.py │ ├── training_metrics.py │ ├── training_train_model.py │ └── training_utils.py │ ├── tuning │ ├── __init__.py │ ├── tuning_tune_hyper.py │ └── tuning_utils.py │ └── wrappers │ ├── __init__.py │ ├── wrappers_chemberta.py │ ├── wrappers_chemprop.py │ └── wrappers_molbert.py └── src ├── clean_cache.py ├── huggingmolecules ├── __init__.py ├── configuration │ ├── __init__.py │ ├── configuration_api.py │ ├── configuration_grover.py │ ├── configuration_mat.py │ └── configuration_rmat.py ├── downloading │ ├── __init__.py │ └── downloading_utils.py ├── featurization │ ├── __init__.py │ ├── featurization_api.py │ ├── featurization_common_utils.py │ ├── featurization_features_generators.py │ ├── featurization_grover.py │ ├── featurization_grover_utils.py │ ├── featurization_mat.py │ ├── featurization_mat_utils.py │ ├── featurization_rmat.py │ └── featurization_rmat_utils.py └── models │ ├── __init__.py │ ├── models_api.py │ ├── models_common_utils.py │ ├── models_grover.py │ ├── models_grover_utils.py │ ├── models_mat.py │ └── models_rmat.py ├── setup.py └── tests ├── __init__.py ├── common ├── __init__.py ├── api.py └── utils.py ├── configuration ├── __init__.py ├── configuration_base.py ├── test_configuration_api.py ├── test_configuration_grover.py ├── test_configuration_mat.py └── test_configuration_rmat.py ├── downloading ├── __init__.py ├── downloading_base.py ├── test_downloading_grover.py ├── test_downloading_mat.py └── test_downloading_rmat.py ├── featurization ├── __init__.py ├── expected │ ├── featurization_expected_grover.py │ ├── featurization_expected_mat.py │ └── featurization_expected_rmat.py ├── featurization_base.py ├── test_featurization_grover.py ├── test_featurization_mat.py └── test_featurization_rmat.py └── models ├── __init__.py ├── models_base.py ├── test_models_api.py ├── test_models_grover.py ├── test_models_mat.py └── test_models_rmat.py /.gitignore: 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