├── .DS_Store ├── GraphINVENT_Protac ├── graphinvent │ ├── Analyzer.py │ ├── BlockDatasetLoader.py │ ├── DataProcesser.py │ ├── GraphGenerator.py │ ├── GraphGeneratorRL.py │ ├── MolecularGraph.py │ ├── ProtacScoringFunction.py │ ├── ScoringFunction.py │ ├── Workflow.py │ ├── __init__.py │ ├── data │ │ ├── fine-tuning │ │ │ └── README.md │ │ ├── pre-training │ │ │ └── MOSES │ │ │ │ └── README.md │ │ └── protac │ │ │ └── README.md │ ├── gnn │ │ ├── aggregation_mpnn.py │ │ ├── edge_mpnn.py │ │ ├── modules.py │ │ ├── mpnn.py │ │ └── summation_mpnn.py │ ├── main.py │ ├── parameters │ │ ├── args.py │ │ ├── constants.py │ │ ├── defaults.py │ │ └── load.py │ ├── training_stats.py │ └── util.py └── tools │ ├── analyze_final_epoch.py │ ├── atom_types.py │ ├── combine_HDFs.py │ ├── combine_generation_batches.py │ ├── formal_charges.py │ ├── max_n_nodes.py │ ├── split_filter_protac.py │ ├── submit-split-preprocessing-supercloud.py │ ├── tdc-create-dataset.py │ ├── utils.py │ └── visualization.py ├── LICENSE.md ├── README.md ├── binary_label_metrics.py ├── features.pkl ├── molecule_metrics.ipynb ├── surrogate_model.ipynb └── surrogate_model.pkl /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/divnori/Protac-Design/HEAD/.DS_Store -------------------------------------------------------------------------------- /GraphINVENT_Protac/graphinvent/Analyzer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/divnori/Protac-Design/HEAD/GraphINVENT_Protac/graphinvent/Analyzer.py -------------------------------------------------------------------------------- /GraphINVENT_Protac/graphinvent/BlockDatasetLoader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/divnori/Protac-Design/HEAD/GraphINVENT_Protac/graphinvent/BlockDatasetLoader.py 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