├── .gitignore ├── 1_route_planning ├── .DS_Store ├── analysis │ ├── .DS_Store │ ├── .gitkeep │ ├── 01_create_chembl200k.ipynb │ ├── 02_1_extract_caspyrus_results.py │ ├── 02_2_extract_chembl_results.py │ └── 03_analyse_results.ipynb ├── led3 │ ├── .DS_Store │ ├── caspyrus_50k │ │ ├── results │ │ │ └── README.md │ │ ├── runs │ │ │ ├── README.md │ │ │ └── part1 │ │ │ │ └── 0_alice_short.slurm │ │ └── splitted │ │ │ ├── README.md │ │ │ └── splitted_datasets.txt │ ├── chembl_200k │ │ ├── results │ │ │ └── README.md │ │ ├── runs │ │ │ └── first_run │ │ │ │ ├── README.md │ │ │ │ └── alice_0.slurm │ │ └── splitted │ │ │ ├── README.md │ │ │ └── splitted_datasets.txt │ └── led3_azf_config.yml └── zinc │ ├── caspyrus_50k │ ├── results │ │ └── README.md │ ├── runs │ │ ├── README.md │ │ └── alice_short │ │ │ └── 0_alice_short.slurm │ └── splitted │ │ ├── README.md │ │ ├── calculation_time.json │ │ └── splitted_datasets.txt │ ├── chembl_200k │ ├── results │ │ └── README.md │ ├── runs │ │ ├── README.md │ │ └── first_run │ │ │ └── alice_0.slurm │ └── splitted │ │ ├── README.md │ │ ├── calculation_time.json │ │ └── splitted_datasets.txt │ └── zinc_azf_config.yml ├── 2_synthesis_score ├── .gitkeep ├── 0_test_set_generation │ ├── 0_chembl200k_test_set_generation.py │ ├── 1_verify_test_set.ipynb │ ├── 2_extract_chembl_results.py │ ├── 3_check_differences.ipynb │ ├── extract_results.txt │ ├── led3 │ │ ├── chembl_200k_test_set │ │ │ ├── runs │ │ │ │ └── run_1 │ │ │ │ │ └── alice_0.slurm │ │ │ └── splitted │ │ │ │ ├── calculation_time.json │ │ │ │ └── splitted_datasets.txt │ │ └── led3_azf_config.yml │ └── zinc │ │ ├── chembl_200k_test_set │ │ ├── runs │ │ │ └── run_1 │ │ │ │ └── alice_0.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ │ └── zinc_azf_config.yml ├── 1_hyperparameter_optimization │ ├── 0_split_datasets.ipynb │ ├── led3_building_blocks │ │ ├── chembl200k_random_hist_xgboost │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ │ ├── led3_caspyrus10k_hist_xgboost │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ │ ├── led3_caspyrus1k_hist_xgboost │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ │ ├── led3_caspyrus20k_hist_xgboost │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ │ ├── led3_caspyrus50k_hist_xgboost │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ │ └── template │ │ │ ├── Makefile │ │ │ ├── alice_0.slurm │ │ │ ├── train.py │ │ │ └── wandb_config.yaml │ └── zinc_building_blocks │ │ ├── Makefile │ │ ├── template │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml │ │ ├── zinc_caspyrus10k_hist_xgboost │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml │ │ ├── zinc_caspyrus1k_hist_xgboost │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml │ │ ├── zinc_caspyrus20k_hist_xgboost │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml │ │ ├── zinc_caspyrus50k_hist_xgboost │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml │ │ └── zinc_chembl200k_random_hist_xgboost │ │ ├── Makefile │ │ ├── alice_0.slurm │ │ ├── train.py │ │ └── wandb_config.yaml └── 2_evaluation │ ├── evaluate_models.ipynb │ └── visualize_results.ipynb ├── 3_molecular_generation ├── .gitkeep ├── 1_generate_molecules │ ├── .gitignore │ ├── .gitkeep │ ├── FT.ipynb │ ├── FT_analysis.ipynb │ ├── README.md │ ├── RL.ipynb │ ├── RL_analysis_overall.ipynb │ ├── RL_generate.ipynb │ ├── RL_initial.ipynb │ ├── RL_run.py │ ├── env.yml │ ├── filtering.ipynb │ ├── predictors.py │ ├── qsub.sh │ ├── requirements.txt │ ├── settings.py │ ├── start.sh │ ├── stop.sh │ └── utils.py └── 2_evaluate_molecules │ └── full_model │ ├── led3_building_blocks │ ├── Q99685_Led3score_caspyrus_10k │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0_alice.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_Led3score_chembl_200k │ │ ├── 00_akh_transform_data.ipynb │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0_alice.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_Zincscore_caspyrus_10k │ │ ├── 00_akh_transform_data.ipynb │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0_alice.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_baseline_qsar_only │ │ ├── 00_akh_transform_data.ipynb │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_chembl_200k_zincscore │ │ ├── 00_akh_transform_data.ipynb │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_known_ligands │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── analyze_data.ipynb │ │ ├── runs │ │ │ └── 0_alice.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ ├── Q99685_sascore │ │ ├── 00_akh_transform_data.ipynb │ │ ├── 01_akh_molecule_analysis.ipynb │ │ ├── runs │ │ │ └── 0.slurm │ │ └── splitted │ │ │ ├── calculation_time.json │ │ │ └── splitted_datasets.txt │ └── led3_azf_config.yml │ └── zinc_building_blocks │ ├── Q99685_Led3_caspyrus_10k │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0_alice.slurm │ ├── Q99685_Led3score_chembl_200k │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0_alice.slurm │ ├── Q99685_Zincscore_caspyrus_10k │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 1000_alice.slurm │ ├── Q99685_baseline_qsar_only │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0.slurm │ ├── Q99685_chembl_200k_zincscore │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0.slurm │ ├── Q99685_known_ligands │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0_alice.slurm │ ├── Q99685_sascore │ ├── 01_akh_molecule_analysis.ipynb │ └── runs │ │ └── 0.slurm │ └── zinc_azf_config.yml ├── 4_wetlab └── evaluate_possible_ligands │ └── led3_building_blocks │ ├── Q99685_Led3Score_Caspyrus_10k_selected_ligands │ └── runs │ │ └── 0_alice.slurm │ └── led3_azf_config.yml ├── 5_paper ├── .DS_Store ├── cluster_size_analysis │ └── analysis.ipynb ├── paper_supplementary.ipynb ├── paper_visualization_1.ipynb ├── paper_visualization_2.ipynb ├── paper_visualization_3.ipynb ├── pdfs │ ├── .DS_Store │ ├── experiment_1_route_length_distributions_with_mean.pdf │ ├── experiment_1_route_planning_results_new.pdf │ ├── experiment_2_synthesizability_score_new.pdf │ ├── experiment_3_QSAR_MODEL_F1.pdf │ ├── experiment_3_closest_ligand_similarity_shorstlist.pdf │ ├── experiment_3_closest_ligand_similarity_short_list_solved.pdf │ ├── experiment_3_denovo_design.pdf │ ├── experiment_3_denovo_design_new_double_patch.pdf │ ├── experiment_3_led3caspyurs_pareto_candidates.pdf │ ├── experiment_3_model_fine_tuning.pdf │ ├── experiment_3_out_of_distribution.pdf │ ├── experiment_3_out_of_distribution_new.pdf │ ├── experiment_3_out_of_distribution_new_2.pdf │ ├── experiment_3_out_of_distribution_new_final.pdf │ ├── experiment_3_out_of_distribution_new_final_absolute.pdf │ ├── experiment_3_rl_summary_desirability.pdf │ ├── experiment_3_rl_summary_qsar.pdf │ ├── experiment_3_selected_candidates_vs_ligand_space.pdf │ ├── experiment_3_selected_canidates_vs_known_ligands_plot_new.pdf │ ├── experiment_3_solved_space_ALL_SCORES_led3_zinc_scatter_plot_new_2.pdf │ ├── experiment_3_solved_space_CHEMBL200k_led3_zinc_scatter_plot_new_2.pdf │ ├── experiment_3_solved_space_Caspyrus10k_led3_zinc_scatter_plot_new_2.pdf │ ├── experiment_3_solved_space_led3_zinc_contour_plot_new_2.pdf │ └── experiment_3_solved_space_led3_zinc_scatter_plot_new_2.pdf └── svgs │ ├── .DS_Store │ ├── candidate │ ├── experiment_3_candidate_1_closest_ligands_new.svg │ ├── experiment_3_candidate_2_closest_ligands_new.svg │ └── experiment_3_candidate_3_closest_ligands_new.svg │ ├── experiment_1_route_length_distributions.svg │ ├── experiment_1_route_length_distributions_with_mean.svg │ ├── experiment_1_route_planning_results_with_1k.svg │ ├── experiment_1_route_planning_results_with_1k_new.svg │ ├── experiment_2_synthesizability_score.svg │ ├── experiment_2_synthesizability_score_new.svg │ ├── experiment_3_QSAR_MODEL_F1.svg │ ├── experiment_3_closest_ligand_similarity_short_list_solved.svg │ ├── experiment_3_closest_ligand_similarity_shortlist.svg │ ├── experiment_3_denovo_design.svg │ ├── experiment_3_denovo_design_new_double_patch.svg │ ├── experiment_3_led3caspyurs_pareto_candidates.svg │ ├── experiment_3_model_fine_tuning.svg │ ├── experiment_3_out_of_distribution.svg │ ├── experiment_3_out_of_distribution_new.svg │ ├── experiment_3_out_of_distribution_new_2.svg │ ├── experiment_3_out_of_distribution_new_final.svg │ ├── experiment_3_out_of_distribution_new_final_absolute.svg │ ├── experiment_3_rl_summary_desirability.svg │ ├── experiment_3_rl_summary_qsar.svg │ ├── experiment_3_selected_candidates_vs_ligand_space.svg │ ├── experiment_3_selected_canidates_vs_known_ligands_plot_new.svg │ ├── experiment_3_solved_space_ALL_SCORES_led3_zinc_scatter_plot_new_2.svg │ ├── experiment_3_solved_space_CHEMBL200k_led3_zinc_scatter_plot_new_2.svg │ ├── experiment_3_solved_space_Caspyrus10k_led3_zinc_scatter_plot_new_2.svg │ ├── experiment_3_solved_space_led3_zinc_contour_plot_new_2.svg │ └── experiment_3_solved_space_led3_zinc_scatter_plot_new_2.svg ├── Makefile ├── README.md ├── condaenvironment.yaml ├── poetry.lock ├── pyproject.toml └── src └── led3_score └── fingerprints ├── __init__.py ├── fingerprint_generator.py ├── 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