├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── e3fp_paper ├── __init__.py ├── config │ ├── best_params.cfg │ └── best_params.fit ├── crossvalidation │ ├── __init__.py │ ├── analysis.py │ ├── methods.py │ ├── run.py │ ├── sample.py │ └── util.py ├── pipeline.py ├── plotting │ ├── __init__.py │ ├── comparison.py │ ├── defaults.py │ ├── experiments.py │ ├── util.py │ └── validation.py └── sea_utils │ ├── __init__.py │ ├── library.py │ ├── run.py │ └── util.py ├── project ├── README.md ├── analysis │ ├── benchmark │ │ └── make_supp_plot_table.py │ ├── comparison │ │ ├── README.md │ │ ├── get_confusion_stats.py │ │ ├── make_cv_summary_table.py │ │ ├── make_pdb_supp_plot.py │ │ ├── make_plots.py │ │ ├── make_rocs_supp_plots.py │ │ └── make_supp_plots.py │ ├── experiments │ │ ├── README.md │ │ ├── make_plots.py │ │ ├── make_supp_mat.py │ │ └── make_supp_plots.py │ ├── optimization │ │ ├── README.md │ │ ├── get_cv_results.py │ │ └── plot_cv_performance.py │ └── visualization │ │ ├── README.md │ │ ├── draw_graph.py │ │ └── make_shell_figures.py ├── benchmark │ ├── README.md │ ├── get_random_subset.py │ └── run_benchmark.py ├── conformer_generation │ └── README.md ├── crossvalidation │ ├── README.md │ ├── classifiers │ │ └── README.md │ ├── classifiers_mean │ │ └── README.md │ └── sea │ │ ├── README.md │ │ ├── e2fp-stereo │ │ └── params.cfg │ │ ├── e2fp │ │ └── params.cfg │ │ ├── e3fp-nostereo │ │ └── params.cfg │ │ ├── e3fp-rdkit │ │ └── params.cfg │ │ └── e3fp │ │ └── params.cfg ├── data │ ├── CHEMBL210990.sdf.bz2 │ ├── CHEMBL2110918.sdf.bz2 │ ├── CHEMBL270807.sdf.bz2 │ ├── available_targets_pdsp_chembl20_map.tab.bz2 │ ├── chembl20_binding_targets.csv.bz2 │ ├── chembl20_proto_smiles.smi.bz2 │ ├── chembl20_zinc_in-stock_mw800_unique_proto.smi.bz2 │ ├── early_params.cfg │ ├── early_params.fit │ ├── ecfp4.fit │ └── examples.txt ├── experiment_prediction │ ├── README.md │ ├── drug_selection │ │ └── README.md │ ├── get_mol_vs_target_tcs.py │ ├── target_drug_search │ │ ├── README.md │ │ └── analyze_search_results.py │ └── target_selection │ │ └── README.md ├── fingerprint_comparison │ ├── README.md │ ├── compare_fingerprints.py │ ├── count_pairwise_tcs.py │ ├── get_fastrocs_tril_tcs.py │ ├── get_fingerprint_tril_tcs.py │ ├── get_pairwise_tcs.py │ ├── get_rmsd.py │ ├── get_triangle_indices.py │ ├── random_conformer_pairs │ │ ├── README.md │ │ ├── get_pair_fastrocs_tcs.py │ │ ├── get_pair_rmsds_tfds_tcs.py │ │ └── get_random_pairs.py │ ├── random_conformers │ │ ├── README.md │ │ └── get_random_confomers.py │ └── sdf_files_to_file.py ├── parameter_optimization │ ├── 1_chembl20_opt │ │ └── config │ │ │ ├── config.pb │ │ │ └── wrapper.py │ ├── 2_chembl20_opt │ │ └── config │ │ │ ├── config.pb │ │ │ └── wrapper.py │ └── README.md ├── pdb_enrichment │ ├── README.md │ ├── create_inputs.py │ └── validate.py └── scripts │ ├── generate_e3fp_fprints.py │ ├── generate_ecfp_fprints.py │ ├── run_cv.py │ ├── search_library.py │ └── 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