├── .gitignore ├── LICENSE ├── README.md ├── bioscore_data.sh ├── bioscore_train.sh ├── data ├── converter │ ├── atom_blocks_to_frag_blocks.py │ ├── mol2_to_blocks.py │ ├── pdb_to_list_blocks.py │ └── sdf_to_blocks.py ├── dataset.py ├── pdb_utils.py ├── split.py └── tokenizer │ ├── mol_bpe.py │ ├── molecule.py │ └── tokenize_3d.py ├── datasets ├── Carbohydrate │ └── Carbohydrate_finetune │ │ └── bioscore │ │ └── version_0 │ │ └── checkpoint │ │ ├── final.ckpt │ │ └── namespace.json ├── PLI+PPI │ ├── PLI+PPI_pretrain │ │ └── bioscore │ │ │ └── version_0 │ │ │ └── checkpoint │ │ │ ├── final.ckpt │ │ │ ├── final_results.jsonl │ │ │ └── namespace.json │ ├── PLI_finetune │ │ └── bioscore │ │ │ └── version_0 │ │ │ └── checkpoint │ │ │ ├── final.ckpt │ │ │ └── namespace.json │ └── PPI_finetune │ │ └── bioscore │ │ └── version_0 │ │ └── checkpoint │ │ ├── final.ckpt │ │ └── namespace.json ├── PNI │ └── PNI-finetune │ │ └── version_0 │ │ └── checkpoint │ │ ├── final.ckpt │ │ └── namespace.json └── SAbDab │ └── SAbDab_finetune │ └── bioscore │ └── version_0 │ └── checkpoint │ ├── final.ckpt │ └── namespace.json ├── environment.yml ├── example ├── data │ ├── BioScore_data │ │ ├── PLI_example_10A.pkl │ │ ├── PPI_example_6A.BlockGeoAffDataset_processed.pkl │ │ └── PPI_example_6A.pkl │ ├── PLI │ │ ├── metadata │ │ │ └── example_affinities.json │ │ ├── processed_data │ │ │ └── 3prs │ │ │ │ ├── 3prs_ligand.sdf │ │ │ │ └── 3prs_protein_pocket_10.0.pdb │ │ └── raw_data │ │ │ └── 3prs │ │ │ ├── 3prs_ligand.sdf │ │ │ └── 3prs_protein.pdb │ └── PPI │ │ ├── example_index.csv │ │ └── pdb_files │ │ └── 2uyz.pdb ├── data_preprocess.sh ├── inference_example.sh └── results │ ├── PLI_example_docking_screening_results.jsonl │ ├── PLI_example_scoring_ranking_results.jsonl │ ├── PPI_example_docking_screening_results.jsonl │ └── PPI_example_scoring_ranking_results.jsonl ├── figures └── bioscore.png ├── inference.py ├── models ├── GET │ ├── encoder.py │ ├── model.py │ ├── modules │ │ ├── get.py │ │ ├── radial_basis.py │ │ └── tools.py │ └── pool_encoder.py ├── __init__.py ├── affinity_predictor.py └── score_model.py ├── requirements.txt ├── scripts ├── data_process │ ├── extract_pocket.py │ ├── process_CASF2016_docking_pocket.py │ ├── process_CASF2016_scoring_pocket.py │ ├── process_CASF2016_screening_pocket.py │ ├── process_PDBbind_NL_all.py │ ├── process_PDBbind_PN_all.py │ ├── process_PDBbind_PP_docking.py │ ├── process_PDBbind_PP_others+scoring.py │ ├── process_PDBbind_PP_screening.py │ ├── process_PLI_pocket.py │ └── process_PPI.py ├── exps │ ├── BioScore_data_preprocess.py │ ├── configs │ │ ├── PLI+PPI │ │ │ ├── mix-PLI-PPI-pretrain.json │ │ │ ├── mix-PLI-finetune.json │ │ │ └── mix-PPI-finetune.json │ │ ├── PLI │ │ │ └── Carbohydrate-finetune.json │ │ ├── PNI │ │ │ └── PNI-finetune.json │ │ └── PPI │ │ │ └── SAbDab-finetune.json │ └── exps.py ├── test │ ├── docking_power_all.py │ ├── docking_power_all.sh │ ├── evaluate_docking_pli.py │ ├── evaluate_docking_ppi.py │ ├── evaluate_ranking_all.py │ ├── evaluate_scoring_all.py │ ├── evaluate_screening_all.py │ ├── evaluate_screening_casf.py │ ├── evaluate_screening_ppi.py │ ├── ranking_power_all.sh │ ├── scoring_power_all.py │ ├── scoring_power_all.sh │ ├── screening_power_all.py │ ├── screening_power_all_evaluate.sh │ └── screening_power_all_predict.sh └── train │ └── train.sh ├── train.py ├── trainers ├── __init__.py ├── abs_trainer.py └── affinity_trainer.py └── utils ├── __init__.py ├── chem_utils.py ├── convert.py ├── io.py ├── logger.py ├── mol_atom_match.py ├── neighbors.py ├── network.py ├── nn_utils.py ├── protein_init.py ├── random_seed.py ├── singleton.py ├── sorted_segment_ops.py ├── time_sign.py └── unsorted_segment_ops.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChemloverYuchen/BioScore/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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