├── .gitignore ├── LICENSE ├── README.md ├── REPRODUCE.md ├── data ├── ROBIN.csv ├── map_files │ └── edges_and_nodes_map.pickle ├── rmscores │ └── systems.txt ├── rnamigos2_data.tar.gz ├── sample_files │ ├── 3ox0.cif │ └── test_smiles.txt └── train_test_75.p ├── figs └── rnamigos2.png ├── pretrained ├── R_1_16 │ ├── config.yaml │ └── model.pth ├── R_1_16_undirected.tar.gz ├── R_1_16_undirected │ ├── config.yaml │ └── model.pth ├── R_1_64 │ ├── config.yaml │ └── model.pth ├── R_iso_16 │ ├── config.yaml │ └── model.pth ├── R_iso_64 │ ├── config.yaml │ └── model.pth ├── hungarian_16 │ ├── config.yaml │ └── model.pth ├── hungarian_64 │ ├── config.yaml │ └── model.pth └── optimol │ ├── params.json │ └── weights.pth ├── pyproject.toml ├── requirements.txt ├── results └── trained_models │ ├── dock │ └── dock_42 │ │ ├── config.yaml │ │ └── model.pth │ └── is_native │ └── native_42 │ ├── config.yaml │ └── model.pth ├── rnamigos ├── conf │ ├── data │ │ └── default.yaml │ ├── evaluate.yaml │ ├── inference.yaml │ ├── model │ │ ├── default.yaml │ │ └── default_fp.yaml │ ├── paths │ │ └── default.yaml │ ├── pretrain.yaml │ ├── pretrain │ │ └── default.yaml │ ├── tokens │ │ └── default.yaml │ ├── train.yaml │ └── train │ │ └── default.yaml ├── data_processor │ ├── binding_pocket_analyse.py │ ├── binding_pocket_filter.py │ ├── build_dataset.py │ ├── graph_process.py │ ├── lig_dict_cluster.py │ └── rnafm_pockets.py ├── evaluate.py ├── inference.py ├── learning │ ├── attn.py │ ├── dataloader.py │ ├── dataset.py │ ├── learn.py │ ├── ligand_encoding.py │ └── models.py ├── pretrain.py ├── train.py └── utils │ ├── graph_utils.py │ ├── learning_utils.py │ ├── mixing_utils.py │ └── virtual_screen.py ├── rnamigos_inference.ipynb ├── scripts_fig ├── dock_vs_migos.py ├── fig_2.py ├── fig_3a.py ├── inspect_embeddings.py ├── lig_tsne.py ├── panel_1.py ├── panel_2.py ├── panel_3.py ├── perturbations │ ├── compute_perturbed_results.py │ ├── get_perturbed_pockets.py │ └── pertub_plot_utils.py ├── plot_utils.py ├── pose_picker.py ├── rm_mar.py ├── robin_OT.py ├── robin_analyse.py ├── robin_fig.py ├── robin_knn.py ├── table_2.py ├── time_ef.py ├── time_ef_keep.csv └── violins.py ├── scripts_prepare ├── build_csvs.py ├── build_ligand_cache.py ├── build_screen_data.py ├── decoy_finder.py ├── export_migos_data.py ├── get_ligands_encoding.py ├── get_pocket_graphs.py ├── ligand_ids.py └── split.py ├── scripts_run ├── chembl_inference.py ├── old │ ├── fig_3_screen_launch.sh │ ├── grid_search.sh │ ├── grid_search_table_2.sh │ ├── grid_table_gen.py │ ├── launch_pretrain.sh │ ├── python_launcher.py │ ├── vincent_launcher_chembl.sh │ ├── vincent_launcher_dock.sh │ ├── vincent_launcher_dock_2.sh │ ├── vincent_launcher_fp.sh │ ├── vincent_launcher_fp_pre.sh │ ├── vincent_launcher_native.sh │ ├── vincent_launcher_native_pre.sh │ ├── vincent_launcher_optimol_dock.sh │ ├── vincent_launcher_optimol_dock_quantiles.sh │ └── vincent_launcher_optimol_native.sh ├── old_2 │ ├── paper_run.sh │ ├── 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