├── .gitignore ├── .idea ├── .gitignore ├── PPB-Affinity.iml ├── deployment.xml ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── BaselineModel ├── datasets │ ├── __init__.py │ └── mixed_dataset.py ├── models │ ├── __init__.py │ └── dg_model.py ├── modules │ ├── common │ │ ├── geometry.py │ │ ├── layers.py │ │ └── topology.py │ └── encoders │ │ ├── attn.py │ │ ├── pair.py │ │ └── single.py └── utils │ ├── data.py │ ├── misc.py │ ├── mixed_dataloader.py │ ├── protein │ ├── constants.py │ ├── icoord.py │ ├── parsers.py │ └── writers.py │ ├── train.py │ └── transforms │ ├── __init__.py │ ├── _base.py │ ├── corrupt_chi.py │ ├── mask.py │ ├── noise.py │ ├── patch.py │ ├── select_atom.py │ └── select_chain.py ├── CrossValidationFigs ├── ATLAS.tiff ├── Affinity Benchmark v5.5.tiff ├── Antibody-Antigen.tiff ├── PDBBind v2020.tiff ├── PPB-Affinity.tiff ├── SAbDab.tiff ├── SKEMPI v2.0.tiff └── TCR-pMHC.tiff ├── PPB-Affinity.xlsx ├── README.md ├── baseline_train_config.yml ├── benchmark.csv ├── checkpoints └── readme.md ├── draw.ipynb ├── environment.yaml ├── example_data ├── example.xlsx ├── predict_dG.csv └── test.pdb ├── inference.py ├── process_data.py ├── train.py └── train_datasplit ├── train_pdb.pkl └── val_pdb.pkl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChenPy00/PPB-Affinity/HEAD/.gitignore -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChenPy00/PPB-Affinity/HEAD/.idea/.gitignore -------------------------------------------------------------------------------- /.idea/PPB-Affinity.iml: -------------------------------------------------------------------------------- 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