├── .gitignore ├── LICENSE ├── README.md ├── environment.yml ├── examples ├── amd │ ├── baselines │ │ ├── 01_get_routes_for_each.py │ │ ├── 02_baseline_results.py │ │ ├── 03_compare_costs.py │ │ ├── baseline_curves.csv │ │ └── price_comparison.csv │ ├── cmd_list.txt │ ├── config_opt.ini │ ├── config_opt_diversity.ini │ ├── constant_reward.csv │ ├── targets.csv │ └── trees_w_info.json ├── automoldesigner │ ├── README.md │ ├── chkpts │ │ └── neutral_smiles.csv │ ├── configs │ │ ├── config_bo.ini │ │ ├── config_diversity.ini │ │ ├── config_namerxn.ini │ │ ├── config_namerxn_diversity.ini │ │ └── config_nonlinear.ini │ ├── data │ │ ├── enamine_per_g_122024.csv │ │ ├── enamine_to_inventory.ipynb │ │ ├── staph_targets_raw.csv │ │ └── trees_w_costs.json.gz │ ├── figures │ │ ├── figures.ipynb │ │ └── plot_utils.py │ ├── scripts │ │ ├── 01_v2_treebuild.py │ │ ├── 02_conditions.py │ │ ├── 03_scores.py │ │ ├── 04_route_graph.py │ │ ├── 05_costs_and_prune.py │ │ ├── cmd_list.txt │ │ ├── run_cmds.batch │ │ ├── run_cmds.py │ │ ├── screen_lambda_rew.py │ │ └── vary_lambda_rew.batch │ └── targets.csv ├── button_alectinib │ ├── alectinib_rewards.csv │ ├── config.ini │ ├── config_opt.ini │ ├── config_opt_diversity.ini │ ├── constant_reward.csv │ └── trees_w_info.json ├── garibsingh │ ├── baselines │ │ ├── 01_get_routes_for_each.py │ │ ├── 02_baseline_results.py │ │ ├── 03_compare_costs.py │ │ ├── baseline_curves.csv │ │ ├── fpscores.pkl.gz │ │ └── price_comparison.csv │ ├── cmd_list.txt │ ├── config.ini │ ├── config_opt.ini │ ├── constant_reward.csv │ ├── targets.csv │ └── trees_w_info.json ├── swanson │ ├── configs │ │ ├── config_bo.ini │ │ ├── config_diversity.ini │ │ ├── config_namerxn.ini │ │ └── config_nonlinear.ini │ ├── data │ │ ├── targets_raw.csv │ │ └── trees_w_costs.json.gz │ ├── figures │ │ ├── figures.ipynb │ │ └── plot_utils.py │ ├── scripts │ │ ├── 01_v2_treebuild.py │ │ ├── 02_conditions.py │ │ ├── 03_scores.py │ │ ├── 04_route_graph.py │ │ ├── cmd_list.txt │ │ ├── run_cmds.batch │ │ ├── screen_lambda_rew.py │ │ └── vary_lambda_rew.batch │ └── targets.csv └── templates │ ├── inventory.csv │ ├── reaction_classes.csv │ └── tree.json ├── keys.py ├── notebooks ├── linear │ ├── analyze_results.ipynb │ ├── figs_amd │ │ ├── costs.txt │ │ ├── fig4_baselines.csv │ │ ├── fig4_sparrow.csv │ │ ├── latex_table.txt │ │ ├── latex_table_baselines.txt │ │ └── latex_table_rxn.txt │ └── figs_garibsingh │ │ ├── costs.csv │ │ ├── costs.txt │ │ ├── fig1_baselines.csv │ │ ├── fig1_sparrow.csv │ │ ├── latex_sparrow.txt │ │ ├── latex_table.txt │ │ ├── latex_table_baselines.txt │ │ ├── latex_table_cost.txt │ │ ├── latex_table_reward.txt │ │ └── latex_table_rxn.txt └── plot_utils.py ├── requirements.txt ├── scripts ├── optimize_preprint.py ├── optimize_single_constr.py └── run_from_config.py ├── setup.cfg ├── setup.py └── src └── sparrow ├── __init__.py ├── cli ├── __init__.py ├── args.py ├── main.py └── run.py ├── condition_recommender.py ├── coster.py ├── nodes.py ├── path_finder.py ├── route_graph.py ├── rxn_classifier.py ├── scorer.py ├── selector ├── __init__.py ├── base.py ├── bayesian.py ├── linear.py └── nonlinear.py ├── utils ├── __init__.py ├── api_utils.py ├── cluster_utils.py ├── json_utils.py └── parallel_utils.py └── visualizer.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/coleygroup/sparrow/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/coleygroup/sparrow/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/coleygroup/sparrow/HEAD/README.md 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