├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── demo.py ├── molopt ├── __init__.py ├── base.py ├── gpbo │ ├── README.md │ ├── __init__.py │ ├── bo │ │ ├── README.md │ │ ├── __init__.py │ │ ├── acquisition_funcs.py │ │ └── gp_bo.py │ ├── fingerprints.py │ ├── function_utils.py │ ├── gp │ │ ├── README.md │ │ ├── __init__.py │ │ ├── gp_utils.py │ │ └── tanimoto_gp.py │ ├── graph_ga │ │ ├── README.md │ │ ├── __init__.py │ │ ├── crossover.py │ │ ├── graph_ga.py │ │ └── mutate.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── mol_funcs │ │ ├── SA_Score │ │ │ ├── __init__.py │ │ │ └── sascorer.py │ │ └── simple_funcs.py │ ├── mol_opt │ │ ├── __init__.py │ │ ├── mol_opt.py │ │ ├── run_bo_gp_exact_subset_ucb4.py │ │ ├── run_graph_ga.py │ │ └── run_selfies_ga.py │ ├── results │ │ └── results_gp_bo_qed_0.yaml │ └── run.py ├── graph_ga │ ├── __init__.py │ ├── crossover.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── mutate.py │ └── run.py ├── graph_mcts │ ├── __init__.py │ ├── analyze_dataset.py │ ├── goal_directed_params.json │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── p1.p │ ├── p_ring.p │ ├── r_s1.p │ ├── rs_make_ring.p │ ├── rs_ring.p │ ├── run.py │ ├── sa.py │ ├── size_stats.p │ └── stats.py ├── jt_vae │ ├── README.md │ ├── __init__.py │ ├── data │ │ ├── moses │ │ │ ├── train_5k.txt │ │ │ ├── train_validity_5k.txt │ │ │ └── vocab.txt │ │ └── zinc │ │ │ └── vocab.txt │ ├── fast_jtnn │ │ ├── __init__.py │ │ ├── chemutils.py │ │ ├── datautils.py │ │ ├── jtmpn.py │ │ ├── jtnn_dec.py │ │ ├── jtnn_enc.py │ │ ├── jtnn_vae.py │ │ ├── mol_tree.py │ │ ├── mpn.py │ │ ├── nnutils.py │ │ └── vocab.py │ ├── fast_molvae │ │ ├── README.md │ │ ├── preprocess.py │ │ ├── sample.py │ │ ├── vae_train.py │ │ └── vocab.pkl │ ├── gen_latent.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── molopt │ │ ├── README.md │ │ ├── optimize.py │ │ ├── pretrain.py │ │ ├── sascorer.py │ │ └── vaetrain.py │ ├── preprocess.py │ ├── print_result.py │ ├── run.py │ └── upload.sh ├── mimosa │ ├── __init__.py │ ├── chemutils.py │ ├── clean.py │ ├── data │ │ ├── substructure.txt │ │ └── vocabulary.txt │ ├── download.py │ ├── dpp.py │ ├── evaluate.py │ ├── gnn_layer.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── inference_utils.py │ ├── module.py │ ├── online_train.py │ ├── pretrained_model │ │ └── GNN.ckpt │ ├── run.py │ ├── train.py │ ├── utils.py │ └── vocabulary.py ├── moldqn │ ├── README.md │ ├── __init__.py │ ├── agents │ │ ├── __init__.py │ │ ├── agent.py │ │ ├── configs │ │ │ ├── bootstrap_dqn.json │ │ │ ├── naive_dqn.json │ │ │ ├── prioritized_dqn.json │ │ │ ├── synth.json │ │ │ ├── test.json │ │ │ ├── zaleplon.json │ │ │ └── zinc_space.json │ │ └── generator.py │ ├── environments │ │ ├── __init__.py │ │ ├── environments.py │ │ └── synth_env.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── networks │ │ ├── __init__.py │ │ ├── distributional_net.py │ │ ├── features.py │ │ ├── mlp.py │ │ ├── mpnn.py │ │ ├── nn_utils.py │ │ └── noisy_net.py │ ├── run.py │ └── utils │ │ ├── __init__.py │ │ ├── get_available_features_generators.py │ │ ├── parsing.py │ │ └── utils.py ├── reinvent │ ├── .DS_Store │ ├── README.md │ ├── Vizard │ │ ├── main.py │ │ ├── run.sh │ │ ├── templates │ │ │ ├── index.html │ │ │ └── styles.css │ │ └── theme.yaml │ ├── __init__.py │ ├── data │ │ └── Voc │ ├── data_structs.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── model.py │ ├── multiprocess.py │ ├── pretrain.py │ ├── results │ │ └── results_reinvent_qed_0.yaml │ ├── run.py │ ├── scoring_functions.py │ ├── train_agent.py │ ├── upload.sh │ ├── utils.py │ └── vizard_logger.py ├── reinvent_selfies │ ├── .DS_Store │ ├── README.md │ ├── Vizard │ │ ├── main.py │ │ ├── run.sh │ │ ├── templates │ │ │ ├── index.html │ │ │ └── styles.css │ │ └── theme.yaml │ ├── __init__.py │ ├── data.py │ ├── data │ │ └── Voc │ ├── data_structs.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── model.py │ ├── multiprocess.py │ ├── pretrain.py │ ├── run.py │ ├── scoring_functions.py │ ├── train_agent.py │ ├── upload.sh │ ├── utils.py │ └── vizard_logger.py ├── screening │ ├── __init__.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ └── run.py ├── selfies_ga │ ├── __init__.py │ ├── dataset_prop_calculator.py │ ├── datasets │ │ └── convert_smiles_dataset.py │ ├── discriminator.py │ ├── evolution_functions.py │ ├── generation_props.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ └── run.py ├── smiles_ga │ ├── __init__.py │ ├── cfg_util.py │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ ├── run.py │ └── smiles_grammar.py ├── stoned │ ├── README.md │ ├── __init__.py │ ├── data │ │ └── triplets.pickle │ ├── hparams_default.yaml │ ├── hparams_tune.yaml │ └── run.py ├── utils │ ├── __init__.py │ ├── chem.py │ ├── chem_utils.py │ ├── eval_utils.py │ ├── jtvae_data_utils.py │ ├── nn_utils.py │ ├── preprocess.py │ ├── script_utils.py │ ├── smiles_data_utils.py │ └── vocab.py 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