├── .gitignore ├── README.md ├── Supplement.pdf ├── algos.pyx ├── analyses ├── atom_encoder │ ├── graph_embedding │ │ └── graph_embedding_compare.py │ └── kernel_reader.py ├── gt_0.00.csv └── labels_0.00.csv ├── data.py ├── data_split ├── 1798_seed2.pt ├── 1798_seed2.pt.checksum ├── 1843_seed2.pt ├── 1843_seed2.pt.checksum ├── 2258_seed2.pt ├── 2258_seed2.pt.checksum ├── 2689_seed2.pt ├── 2689_seed2.pt.checksum ├── 435008_seed2.pt ├── 435008_seed2.pt.checksum ├── 435034_seed2.pt ├── 435034_seed2.pt.checksum ├── 463087_seed2.pt ├── 463087_seed2.pt.checksum ├── 485290_seed2.pt ├── 485290_seed2.pt.checksum ├── 488997_seed2.pt ├── 488997_seed2.pt.checksum ├── 9999_seed2.pt ├── 9999_seed2.pt.checksum ├── shrink_1798_seed2.pt ├── shrink_1798_seed2.pt.checksum ├── shrink_1843_seed2.pt ├── shrink_1843_seed2.pt.checksum ├── shrink_2258_seed2.pt ├── shrink_2258_seed2.pt.checksum ├── shrink_2689_seed2.pt ├── shrink_2689_seed2.pt.checksum ├── shrink_435008_seed2.pt ├── shrink_435008_seed2.pt.checksum ├── shrink_435034_seed2.pt ├── shrink_435034_seed2.pt.checksum ├── shrink_463087_seed2.pt ├── shrink_463087_seed2.pt.checksum ├── shrink_485290_seed2.pt ├── shrink_485290_seed2.pt.checksum ├── shrink_488997_seed2.pt ├── shrink_488997_seed2.pt.checksum ├── shrink_9999_seed2.pt └── shrink_9999_seed2.pt.checksum ├── dataset_multigenerator.py ├── entry.py ├── evaluation.py ├── lr.py ├── model.py ├── models ├── ChIRoNet │ ├── ChIRoNet.py │ ├── alpha_encoder.py │ ├── datasets_samplers.py │ ├── embedding_functions.py │ ├── gnn_3D │ │ ├── dimenet_pp.py │ │ ├── optimization_functions.py │ │ ├── schnet.py │ │ ├── spherenet.py │ │ ├── train_functions.py │ │ └── train_models.py │ ├── optimization_functions.py │ ├── params_interpreter.py │ ├── train_functions.py │ └── train_models.py ├── DimeNetPP │ └── DimeNetPP.py ├── MolKGNN │ ├── KernelLayer.py │ ├── MolKGNNNet.py │ └── kernels.py ├── SchNet │ ├── SchNet.py │ └── schnet.py └── SphereNet │ └── SphereNet.py ├── monitors.py ├── requirements.txt ├── utils ├── data_split.py ├── new_data_split.py ├── scheduler-barium-kgnn.py ├── scheduler-live-kgnn.py ├── scheduler-ndslab3-kgnn.py ├── test_all-barium-kgnn-new_node_attr.py ├── test_all-barium-kgnn-optimize1.py ├── test_all-barium-kgnn-optimize2.py ├── test_all-barium-kgnn-optimize4.py └── test_all-barium-kgnn.py └── wrapper.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meilerlab/MolKGNN/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/meilerlab/MolKGNN/HEAD/README.md -------------------------------------------------------------------------------- /Supplement.pdf: -------------------------------------------------------------------------------- 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