├── .gitignore ├── LICENSE ├── README.md ├── applications └── virtual_screening │ ├── README.md │ ├── vs_example │ ├── ligand │ │ └── 2qbr_docked.sdf │ ├── pocket │ │ └── 2qbr_pocket.pdb │ └── uff │ │ └── 2qbr_uff.sdf │ └── vs_inference.sh ├── docking ├── README.md ├── __init__.py ├── envfile_conda_base.yml ├── envfile_conda_env_for_obabel.yml ├── examples │ ├── complex │ │ ├── 1bcu_complex.pdb │ │ ├── 2qbq_complex.pdb │ │ ├── 3arp_complex.pdb │ │ └── 4e5w_complex.pdb │ ├── gaussian_predict │ │ ├── 1bcu_G.pkl │ │ ├── 2qbq_G.pkl │ │ ├── 3arp_G.pkl │ │ └── 4e5w_G.pkl │ ├── ligand │ │ ├── 1bcu_docked.sdf │ │ ├── 2qbq_docked.sdf │ │ ├── 3arp_docked.sdf │ │ └── 4e5w_docked.sdf │ └── uff │ │ ├── 1bcu_uff.sdf │ │ ├── 2qbq_uff.sdf │ │ ├── 3arp_uff.sdf │ │ └── 4e5w_uff.sdf ├── merge_summary_input.py ├── pdbqt_ligand │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── atoms │ │ │ ├── __init__.py │ │ │ ├── pdb_atom │ │ │ │ ├── __init__.py │ │ │ │ └── pdb_atom.py │ │ │ └── pdbqt_atom │ │ │ │ ├── __init__.py │ │ │ │ └── pdbqt_atom.py │ │ ├── complexes │ │ │ ├── __init__.py │ │ │ └── pdb_complex │ │ │ │ ├── __init__.py │ │ │ │ └── pdb_complex.py │ │ ├── evaluators │ │ │ ├── __init__.py │ │ │ ├── evaluator_base │ │ │ │ ├── __init__.py │ │ │ │ └── evaluator_base.py │ │ │ └── evaluator_normalscore │ │ │ │ ├── __init__.py │ │ │ │ └── evaluator_normalscore.py │ │ ├── ligands │ │ │ ├── __init__.py │ │ │ └── _pdbqt_ligand │ │ │ │ ├── __init__.py │ │ │ │ └── _pdbqt_ligand.py │ │ ├── minimizers │ │ │ ├── __init__.py │ │ │ ├── minimizer_base │ │ │ │ ├── __init__.py │ │ │ │ └── minimizer_base.py │ │ │ └── minimizer_bfgs │ │ │ │ ├── __init__.py │ │ │ │ └── minimizer_bfgs.py │ │ ├── receptors │ │ │ ├── __init__.py │ │ │ └── pdbqt_receptor │ │ │ │ ├── __init__.py │ │ │ │ └── pdbqt_receptor.py │ │ └── samplers │ │ │ ├── __init__.py │ │ │ ├── sampler_base │ │ │ ├── __init__.py │ │ │ └── sampler_base.py │ │ │ └── sampler_monte_carlo │ │ │ ├── __init__.py │ │ │ └── sampler_monte_carlo.py │ ├── wrappers_for_io │ │ ├── __init__.py │ │ └── iowrappers_dir │ │ │ ├── __init__.py │ │ │ └── iowrapper_dir_newly_created.py │ └── wrappers_for_third_party_tools │ │ ├── __init__.py │ │ ├── wrapper_rdkitmol │ │ ├── __init__.py │ │ └── wrapper_rdkitmol.py │ │ └── wrappers_for_openbabel │ │ ├── __init__.py │ │ └── wrapper_obabel.py ├── pyvina │ └── core │ │ ├── .gitignore │ │ ├── array.cpp │ │ ├── array.hpp │ │ ├── atom.cpp │ │ ├── atom.hpp │ │ ├── bindings.cpp │ │ ├── bkp.scoring_function.cpp │ │ ├── common │ │ ├── common.cc │ │ ├── common.h │ │ ├── format_convert.cc │ │ └── format_convert.h │ │ ├── conformation.hpp │ │ ├── constants │ │ └── common.h │ │ ├── differentiation │ │ ├── coord_differentiation.cc │ │ └── coord_differentiation.h │ │ ├── evaluator │ │ ├── core_evaluator_distancemap_grid.cc │ │ ├── core_evaluator_distancemap_grid.h │ │ ├── eval_vina.cc │ │ ├── eval_vina.h │ │ ├── evaluator_vina_formula_derivative.cc │ │ ├── evaluator_vina_formula_derivative.h │ │ ├── evaluator_vina_vanilla.cc │ │ └── evaluator_vina_vanilla.h │ │ ├── evaluators │ │ ├── core_evaluator_base.cc │ │ ├── core_evaluator_base.h │ │ └── grid_4d │ │ │ ├── core_evaluator_distancemap.cc │ │ │ ├── core_evaluator_distancemap.h │ │ │ ├── core_evaluator_grid_4d.cc │ │ │ ├── core_evaluator_grid_4d.h │ │ │ ├── core_evaluator_normalscore.cc │ │ │ ├── core_evaluator_normalscore.h │ │ │ ├── core_evaluator_vinascore.cc │ │ │ ├── core_evaluator_vinascore.h │ │ │ ├── core_grid_4d.cc │ │ │ └── core_grid_4d.h │ │ ├── grid.cc │ │ ├── grid.h │ │ ├── io_service_pool.cpp │ │ ├── io_service_pool.hpp │ │ ├── ligand.cpp │ │ ├── ligand.hpp │ │ ├── main.cpp │ │ ├── matrix.hpp │ │ ├── minimizer │ │ ├── bfgs_formula_derivative.cc │ │ ├── bfgs_formula_derivative.h │ │ ├── bfgs_torch.cc │ │ └── bfgs_torch.h │ │ ├── minimizers │ │ ├── core_minimizer_base.cc │ │ ├── core_minimizer_base.h │ │ ├── core_minimizer_bfgs.cc │ │ └── core_minimizer_bfgs.h │ │ ├── quaternion │ │ ├── quaternion_torch.cc │ │ ├── quaternion_torch.h │ │ ├── quaternion_vanilla.cc │ │ └── quaternion_vanilla.h │ │ ├── random_forest.cpp │ │ ├── random_forest.hpp │ │ ├── random_forest_x.cpp │ │ ├── random_forest_y.cpp │ │ ├── receptor.cpp │ │ ├── receptor.hpp │ │ ├── result.cpp │ │ ├── result.hpp │ │ ├── safe_counter.cpp │ │ ├── safe_counter.hpp │ │ ├── samplers │ │ ├── core_sampler_base.cc │ │ ├── core_sampler_base.h │ │ ├── core_sampler_monte_carlo.cc │ │ └── core_sampler_monte_carlo.h │ │ ├── scoring_function.cpp │ │ ├── scoring_function.hpp │ │ ├── scoring_function │ │ ├── scoring_function_base_1.cc │ │ ├── scoring_function_base_1.h │ │ ├── vina_scoring_function.cc │ │ ├── vina_scoring_function.h │ │ ├── x_score_scoring_function.cc │ │ └── x_score_scoring_function.h │ │ ├── tests │ │ ├── tensor_tests.cc │ │ └── tensor_tests.h │ │ ├── utils.cpp │ │ ├── wrappers_for_exceptions │ │ ├── common.cc │ │ └── common.h │ │ └── wrappers_for_random │ │ ├── common.cc │ │ └── common.h ├── reconstruct_1_ligand.py ├── reconstruct_ligands.py └── setup.py ├── eda ├── README.md ├── affinity │ ├── affinity_benchmark_test.ipynb │ ├── affinity_pose_sensitive.ipynb │ ├── eval_affinity.py │ └── wet_pearson_figure.ipynb ├── docking │ ├── 2qbr.pse │ ├── eval_docking_ac.py │ ├── interaction-aware_eda.ipynb │ ├── pose2inter_stats.ipynb │ ├── pose2inter_stats.py │ ├── posebuster │ │ ├── check_uff_ligands.py │ │ ├── posebuster_check.py │ │ ├── posebuster_convert_files.py │ │ ├── posebuster_minimum_dis2protein.py │ │ ├── posebuster_performance_plot.ipynb │ │ ├── posescore2sdf.py │ │ └── posescore_eda.ipynb │ └── splits │ │ ├── coresetlist │ │ ├── diff_test+core │ │ ├── posebusters_pdb_ccd_ids.txt │ │ ├── timesplit_no_lig_overlap_train │ │ ├── timesplit_no_lig_overlap_val │ │ ├── timesplit_test │ │ ├── timesplit_test_no_rec_overlap │ │ └── timesplit_test_sanitizable ├── simiarity │ ├── README.md │ ├── ligand_similarity │ │ ├── simiarity_by_ligands.py │ │ └── similarity_box_plot.ipynb │ └── sequence │ │ ├── create_homology_statistic.py │ │ └── homology_docking_ac.py ├── stats_OOD_pdbbind.ipynb └── virtual_screening │ ├── review_5qay.ipynb │ └── review_5qay_vs_input.ipynb ├── environment.yml ├── examples ├── demo_dock.csv ├── ligand │ └── 2qbr_docked.sdf ├── pocket │ └── 2qbr_pocket.pdb ├── raw │ ├── 2qbr.pdb │ └── 2qbr_ligand.sdf └── uff │ └── 2qbr_uff.sdf ├── inference.py ├── interformer ├── constant.py ├── data │ ├── collator │ │ ├── collate_fn.py │ │ ├── inter_collate_fn.py │ │ ├── point_collate_fn.py │ │ └── ppi_collate_fn.py │ ├── data_process.py │ ├── data_stucture │ │ ├── lmdb_dataset.py │ │ └── shard_dataset.py │ ├── data_utils.py │ ├── dataset │ │ ├── bindingdata.py │ │ ├── common_dataset.py │ │ └── ppi_dataset.py │ └── sampler.py ├── feats │ ├── angle_feat.py │ ├── gnina_types │ │ ├── feat_utils.py │ │ ├── gnina_featurizer.py │ │ └── obabel_api.py │ ├── residue │ │ └── residue_featurizer.py │ └── third_rd_lib.py ├── model │ ├── __init__.py │ ├── loss_utils.py │ ├── mixup.py │ ├── model_utils.py │ ├── ppi_model │ │ ├── ppi_model.py │ │ └── ppi_rescorer.py │ ├── sbdd_model.py │ └── transformer │ │ ├── __init__.py │ │ └── graphormer │ │ ├── __init__.py │ │ ├── graphformer_utils.py │ │ └── interformer.py ├── pre.py ├── tests │ ├── __init__.py │ ├── differential_evolution_test.py │ ├── lmdb_data_check.py │ ├── nndocking │ │ ├── __init__.py │ │ └── torsion_align.py │ ├── obabel_example.py │ ├── obabel_feat.py │ ├── test_loading_complex.py │ └── test_pipline.py └── utils │ ├── cluster.py │ ├── configure.py │ ├── eval.py │ ├── parser.py │ └── train_utils.py ├── prepare_input_folder_from_raw.py ├── scripts ├── infer │ ├── affinity.sh │ ├── docking_posebuster.sh │ ├── docking_timesplit.sh │ └── redock_train.sh └── train │ ├── preprocess.sh │ └── train.sh ├── start.sh ├── tools ├── common │ ├── clear_sdf_property.py │ ├── read_smiles_from_sdf.py │ └── rm_similar_smiles.py ├── deepDock │ ├── deepDock_infer.py │ ├── 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