├── LICENSE ├── MO_virtual_screening ├── optimization_dataset_oracle_screening.py └── optimization_dataset_shape_screening.py ├── README.md ├── RUN_ME.ipynb ├── dataset_generation ├── MOSES2_training_val_arrays.py ├── MOSES2_training_val_dataset_generation.py ├── READ_ME.md ├── combine_generation_data_MOSES2.py ├── combine_maxFutureRocs_MOSES2.py ├── combine_scorer_data_MOSES2.py ├── create_test_mols_MOSES2.py ├── generate_artificial_mols_MOSES2.py └── get_max_future_rocs_artificial_MOSES2.py ├── environment.yml ├── models ├── EGNN.py ├── decoder.py ├── egnn_vn_point_cloud.py ├── encoder.py ├── fragment_encoder.py ├── models.py └── vnn │ └── models │ ├── utils │ ├── __init__.py │ ├── dgcnn_util.py │ ├── pointnet_util.py │ └── vn_dgcnn_util.py │ └── vn_layers.py ├── shape_conditioned_generation_dataset_baseline.py ├── shape_conditioned_generation_evaluations.py ├── shape_constrained_optimization_evaluations.py ├── train_graph_generator.py ├── train_scorer.py ├── trained_models ├── graph_generator.pt ├── graph_generator_ablateEqui.pt ├── scorer.pt └── scorer_ablateEqui.pt └── utils ├── general_utils.py ├── graph_generator_datasets_and_loaders.py ├── openeye_utils.py ├── scorer_datasets_and_loaders.py └── shaep_utils.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/keiradams/SQUID/HEAD/LICENSE -------------------------------------------------------------------------------- /MO_virtual_screening/optimization_dataset_oracle_screening.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/keiradams/SQUID/HEAD/MO_virtual_screening/optimization_dataset_oracle_screening.py -------------------------------------------------------------------------------- /MO_virtual_screening/optimization_dataset_shape_screening.py: -------------------------------------------------------------------------------- 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