├── .gitignore ├── README.md ├── atom2d ├── MasifLigand │ ├── config.json │ ├── config.yaml │ ├── data.py │ ├── main.py │ ├── metrics.py │ ├── models.py │ ├── predict.py │ ├── pronet_bench.py │ ├── splits │ │ ├── test-list.txt │ │ ├── train-list.txt │ │ └── val-list.txt │ └── trainer.py ├── atom2d_utils │ ├── atom3dutils.py │ ├── callbacks.py │ ├── learning_utils.py │ └── naming_utils.py ├── base_nets │ ├── __init__.py │ ├── architectures.py │ ├── diffusion_net │ │ ├── geometry.py │ │ ├── layers.py │ │ └── utils.py │ ├── gvp.py │ ├── pesto.py │ ├── pronet.py │ ├── pronet_updated.py │ └── utils.py ├── data_processing │ ├── Atom3DDataset.py │ ├── add_seq_embs.py │ ├── data_module.py │ ├── df_utils.py │ ├── get_operators.py │ ├── hmr_min.py │ ├── io_atomsurf.py │ ├── main.py │ ├── point_cloud_utils.py │ ├── preprocessor_dataset.py │ ├── pronet_processer.py │ ├── surface_utils.py │ └── transforms.py ├── executables │ ├── atmtypenumbers │ ├── msms │ └── pdb_to_xyzr ├── holoprot │ ├── config.yaml │ ├── create_operators.py │ ├── datasets.py │ ├── pl_module.py │ └── train.py ├── masif_site │ ├── config.yaml │ ├── load_data.py │ ├── models.py │ ├── pl_module.py │ ├── preprocess.py │ ├── readme.md │ └── train.py ├── msp_task │ ├── config.yaml │ ├── data_loader.py │ ├── main.py │ ├── models.py │ ├── pl_module.py │ ├── preprocess_data.py │ └── train.py ├── pip_task │ ├── config.yaml │ ├── data_loader.py │ ├── debug.py │ ├── figure.py │ ├── models.py │ ├── old_train.py │ ├── pl_module.py │ ├── preprocess_data.py │ ├── reprocess_data.py │ ├── test.py │ ├── toy.yaml │ └── train.py └── psr_task │ ├── config.yaml │ ├── data_loader.py │ ├── main.py │ ├── models.py │ ├── pl_module.py │ ├── preprocess_data.py │ ├── test.py │ └── train.py ├── data └── example_files │ ├── 4kt3.pdb │ ├── from_biopython.pdb │ └── from_db.pdb ├── exclude.txt └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 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