├── .gitattributes ├── .gitignore ├── 1.cpp_baselines.ipynb ├── 1.cpp_dist.ipynb ├── 1.cpp_step_plot.ipynb ├── 1.eval_cpp_pred.ipynb ├── 2.kras_dist.ipynb ├── 2.kras_pred_model.ipynb ├── 2.kras_step_plot.ipynb ├── 3.cpl_loss_effect.ipynb ├── 3.kras_perm_cpps.ipynb ├── LICENSE.txt ├── README.md ├── agent ├── __init__.py ├── agent_trainer.py ├── scoring │ ├── kras.py │ ├── kras_ic50.py │ ├── permeability.py │ └── transformation.py └── scoring_functions.py ├── data ├── cpp │ ├── X_dps.npy │ ├── X_fps.npy │ ├── all.csv.gz │ ├── pred_cpp_perm.pkl │ ├── regression_rf.pkl │ └── scaffold_k_fold_idxes.pkl ├── kras_kd │ └── kras_xgboost_reg.pkl └── prior │ ├── CycPeptMPDB │ ├── CycPeptMPDB_Monomer_All.csv │ └── CycPeptMPDB_Peptide_All.csv │ ├── chembl32 │ ├── biotherapeutics_dict_prot.csv │ ├── biotherapeutics_dict_prot_flt.csv │ └── chembl_32_monomer_library.xml │ ├── monomer_library.csv │ └── prior_data.csv ├── environment.yml ├── figures ├── cpp │ └── agent_add_cpl_llh_vs_perm.png ├── kras_kd │ └── agent_perm_dist.png └── kras_perm │ └── pass_both_filter.png ├── generate.py ├── helm-gpt.png ├── model ├── model.py └── sampler.py ├── prior └── trainer.py ├── requirements.txt ├── result ├── agent │ ├── cpp │ │ ├── cpp_agent_permeability.pkl │ │ ├── likelihoods.pkl │ │ └── pep_perm_5.1_reinvent_cpl_a1_bs100_3000s │ │ │ └── all_step_aa_seqs_300_valid.csv │ └── kras_kd │ │ ├── kras_5.1_reinvent_cpl-a1_bs100_3000s_v2 │ │ └── all_step_aa_seqs_step300_valid.csv │ │ ├── kras_kd_agent.pkl │ │ └── kras_kd_pred_eval.pkl └── prior │ ├── cpp_permeability.pkl │ ├── kras_kd_priors.pkl │ ├── loss_chembl_5.0.csv │ ├── loss_cycpeptpdb_tune_5.0.csv │ ├── loss_kras_tune_5.0.csv │ ├── valid_chembl_5.0.csv │ ├── valid_cycpeptpdb_tune_5.0.csv │ └── valid_kras_tune_5.0.csv ├── run_scripts.sh ├── train_agent.py ├── train_prior.py └── utils ├── bpe.py ├── dataset.py ├── helm_utils.py ├── metrics_utils.py ├── plot_style_utils.py ├── sascore ├── SA_score_prediction.pkl.gz ├── __init__.py ├── 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