├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── dataset ├── README.md ├── download.sh ├── generate_PDA │ ├── README.md │ ├── filter_valid.py │ ├── generate_conformers.py │ ├── local_opt.sh │ ├── run_dockrmsd.sh │ └── score-pdbbind.txt ├── preprocess │ ├── README.md │ ├── compress_data.sh │ ├── generate_data.py │ └── protonate.py └── untar.sh ├── examples ├── case1.txt ├── case2.txt ├── case3.txt ├── ligand1.sdf ├── ligand2.sdf ├── ligand_single_conformation.sdf ├── protein.pdb └── protein_dup.pdb ├── experiments ├── README.md ├── benchmark_scripts │ ├── .git-keep │ ├── casf2016_docking.sh │ ├── casf2016_scoring.sh │ ├── casf2016_screening.sh │ ├── derivative.sh │ ├── dude.sh │ ├── pretrained_casf2016_docking.sh │ ├── pretrained_casf2016_scoring.sh │ ├── pretrained_casf2016_screening.sh │ ├── pretrained_derivative.sh │ └── pretrained_dude.sh └── training_scripts │ ├── .git-keep │ ├── baseline.sh │ ├── only_nda.sh │ ├── only_pda.sh │ └── pda_nda.sh ├── pyproject.toml ├── requirements.txt └── src ├── analyze ├── KL.py └── get_averaged_benchmark.py ├── benchmark ├── CoreSet.dat ├── TargetInfo.dat ├── decoys_docking.tar ├── derivative_benchmark.py ├── derivative_data │ ├── BACE │ │ └── data.txt │ ├── CDK2 │ │ └── data.txt │ ├── Jnk1 │ │ └── data.txt │ ├── MCL1 │ │ └── data.txt │ ├── PTP1B │ │ └── data.txt │ ├── Thrombin │ │ └── data.txt │ ├── Tyk2 │ │ └── data.txt │ └── p38 │ │ └── data.txt ├── docking_power.py ├── dude_screening_power.py ├── ranking_power.py ├── scoring_power.py └── screening_power.py ├── ckpt ├── pda_0.pt ├── pda_1.pt ├── pda_2.pt └── pda_3.pt ├── config ├── config_test.yaml ├── config_train.yaml ├── data │ ├── default │ │ ├── casf2016_docking.yaml │ │ ├── casf2016_scoring.yaml │ │ ├── casf2016_screening.yaml │ │ ├── cross.yaml │ │ ├── derivative.yaml │ │ ├── docking.yaml │ │ ├── dude.yaml │ │ ├── pda.yaml │ │ ├── random.yaml │ │ └── scoring.yaml │ └── messi │ │ ├── baseline.yaml │ │ ├── casf2016_docking.yaml │ │ ├── casf2016_scoring.yaml │ │ ├── casf2016_screening.yaml │ │ ├── cross.yaml │ │ ├── derivative.yaml │ │ ├── docking.yaml │ │ ├── dude.yaml │ │ ├── pda.yaml │ │ ├── random.yaml │ │ └── scoring.yaml ├── model │ ├── pignet.yaml │ └── pignet_morse.yaml └── run │ ├── test.yaml │ └── train.yaml ├── data ├── __init__.py ├── chem.py ├── data.py ├── datamodule.py ├── rmsd │ └── pdbbind-v2020_docking_rmsd.csv └── utils.py ├── exe ├── path.py ├── predict.py ├── set_cuda.py ├── test.py ├── train.py └── utils.py ├── keys ├── DUD-E │ └── test_keys.txt ├── casf2016 │ ├── docking │ │ └── test_keys.txt │ ├── scoring │ │ └── test_keys.txt │ └── screening │ │ └── test_keys.txt ├── derivative │ └── test_keys.txt ├── generate_keys.py └── train │ └── PDBbind_v2020 │ ├── cross │ ├── test_keys.txt │ └── train_keys.txt │ ├── docking │ ├── test_keys.txt │ └── train_keys.txt │ ├── pda │ ├── test_keys.txt │ └── train_keys.txt │ ├── random │ ├── test_keys.txt │ └── train_keys.txt │ └── scoring │ ├── test_keys.txt │ 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