├── .gitignore ├── LICENSE ├── README.md ├── data ├── best_model.pt ├── vocab.csv └── zinc250k.csv ├── examples ├── penalized_logp │ ├── README.md │ ├── analysis.ipynb │ ├── config.yaml │ ├── run_p1_step_nodup.sh │ ├── run_p2_final_dup.sh │ └── run_p3_step_dup.sh ├── pretrain │ ├── run_create_expert_dataset.sh │ └── run_pretrain_policy.sh ├── run_prep_dataset.sh └── similarity │ ├── README.md │ ├── analysis.ipynb │ ├── config_c1.yaml │ ├── config_s1.yaml │ ├── config_sim_tiny.yaml │ ├── run_c1_step_nodup.sh │ ├── run_c2_final_dup.sh │ ├── run_c3_step_dup.sh │ ├── run_ppo_sim.sh │ ├── run_s1_step_nodup.sh │ ├── run_s2_final_dup.sh │ └── run_s3_step_dup.sh ├── png └── graphical_abstract.png ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt ├── results ├── c1 │ └── history │ │ └── results.csv ├── c2 │ └── history │ │ └── results.csv ├── c3 │ └── history │ │ └── results.csv ├── p1 │ └── history │ │ └── results.csv ├── p2 │ └── history │ │ └── results.csv ├── p3 │ └── history │ │ └── results.csv ├── s1 │ └── history │ │ └── results.csv ├── s2 │ └── history │ │ └── results.csv └── s3 │ └── history │ └── results.csv ├── rjt_rl ├── __init__.py ├── _version.py ├── consts.py ├── extensions │ ├── __init__.py │ └── invoke_gc.py ├── nn │ ├── __init__.py │ ├── site_tree │ │ ├── __init__.py │ │ ├── edge_tree_gru.py │ │ ├── embed_site_info.py │ │ └── site_tree_encoder.py │ ├── tree │ │ ├── __init__.py │ │ └── tree_encoder.py │ └── tree_rnn.py ├── rjt │ ├── __init__.py │ ├── assemble_mol.py │ ├── chemutils.py │ ├── consts.py │ ├── mol_tree.py │ ├── mol_tree_node.py │ ├── rdkit_utils.py │ ├── tree_decomp.py │ ├── tree_utils.py │ ├── utils.py │ └── vocab.py ├── rl │ ├── __init__.py │ ├── agents │ │ ├── __init__.py │ │ └── rjt_ppo.py │ ├── consts.py │ ├── datasets │ │ ├── __init__.py │ │ ├── expert_dataset2.py │ │ ├── expert_dataset_builder2.py │ │ └── expert_dataset_collator.py │ ├── envs │ │ ├── __init__.py │ │ ├── actions.py │ │ ├── base_history.py │ │ ├── mol_action_distr.py │ │ ├── mol_env_base.py │ │ ├── moltree_builder.py │ │ ├── rjt_mol_env.py │ │ ├── simple_history.py │ │ └── states.py │ ├── models │ │ ├── __init__.py │ │ ├── policy_pretrain_wrapper.py │ │ └── rjt_policy_net.py │ ├── rewards │ │ ├── __init__.py │ │ ├── base_mol_reward.py │ │ ├── base_reward.py │ │ ├── fpscores.pkl.gz │ │ ├── penalized_logp_reward.py │ │ ├── sa_score.py │ │ └── similarity_reward.py │ └── training │ │ ├── __init__.py │ │ ├── expert_pretrain_utils.py │ │ ├── ppo_trainer.py │ │ ├── rjt_ppo_trainer.py │ │ ├── snapshot.py │ │ └── utils.py └── utils │ ├── __init__.py │ ├── config_wrapper.py │ ├── logger.py │ ├── make_dataset.py │ ├── make_dataset3.py │ ├── mol_utils.py │ └── path_like.py ├── scripts ├── prep_dataset.py └── rl │ ├── create_expert_dataset.py │ ├── pretrain_policy.py │ └── train_ppo.py ├── setup.cfg └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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