├── .gitignore ├── LICENSE ├── README.md ├── bootstrapping ├── bootstrapping.py ├── buffer.py └── parsing.py ├── confidence ├── confidence_train.py └── dataset.py ├── data ├── 1a0q │ ├── 1a0q_ligand.mol2 │ ├── 1a0q_ligand.sdf │ └── 1a0q_protein_processed.pdb ├── INDEX_general_PL_data.2020 ├── http_requests.py ├── pdb_file_2019.txt ├── pdbbind_counts.pkl ├── posebusters_sequences.fasta ├── preprocess_PDB.py ├── protein_ligand_example_csv.csv ├── sequences_to_id.fasta ├── smiles_list.csv ├── splits │ ├── MOAD_generalisation_splits.pkl │ ├── PDB_train_local │ ├── PDB_train_max2018 │ ├── PDB_val_max2018 │ ├── astex_diverse_set_ids.txt │ ├── pdbids_2019 │ ├── posebusters_benchmark_set_ids.txt │ ├── structure_train │ ├── timesplit_no_lig_overlap_timesplitToVal_train │ ├── timesplit_no_lig_overlap_timesplitToVal_val │ ├── timesplit_no_lig_overlap_train │ ├── timesplit_no_lig_overlap_val │ ├── timesplit_test │ ├── timesplit_test_no_rec_overlap │ └── timesplit_val_filter └── test_ligands_smiles.txt ├── datasets ├── conformer_matching.py ├── constants.py ├── dataloader.py ├── esm_embedding_preparation.py ├── esm_embeddings_to_pt.py ├── loader.py ├── moad.py ├── moad_lm_embedding_preparation.py ├── moad_lm_embedding_preparation_new.py ├── parse_chi.py ├── pdb.py ├── pdb_lm_embedding_preparation.py ├── pdbbind.py ├── pdbbind_lm_embedding_preparation.py ├── process_mols.py ├── sidechain_esm_embeddings_to_pt.py └── torsional.py ├── dock.py ├── environment.yml ├── finetune_train.py ├── inference.py ├── models ├── all_atom_score_model.py ├── layers.py ├── old_all_atom_score_model.py ├── old_score_model.py ├── score_model.py └── tensor_layers.py ├── spyrmsd ├── __init__.py ├── __main__.py ├── _version.py ├── constants.py ├── due.py ├── exceptions.py ├── graph.py ├── graphs │ ├── __init__.py │ ├── _common.py │ ├── gt.py │ └── nx.py ├── hungarian.py ├── io.py ├── molecule.py ├── optional │ ├── __init__.py │ ├── obabel.py │ └── rdkit.py ├── qcp.py ├── rmsd.py └── utils.py ├── train.py ├── utils ├── diffusion_utils.py ├── geometry.py ├── gnina_utils.py ├── inference_utils.py ├── molecules_utils.py ├── parsing.py ├── sampling.py ├── so3.py ├── torsion.py ├── torus.py ├── training.py ├── utils.py └── visualise.py └── workdir ├── pretrained_confidence ├── best_model.pt └── model_parameters.yml └── pretrained_score ├── best_ema_inference_epoch_model.pt └── model_parameters.yml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LDeng0205/confidence-bootstrapping/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LDeng0205/confidence-bootstrapping/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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