├── .gitignore ├── GCN ├── batch.py ├── dataloader.py ├── feature_extract.py ├── finetune.py ├── finetune_mutag_ptc.py ├── loader.py ├── model.py ├── model_gin │ ├── contextpred.pth │ ├── edgepred.pth │ ├── infomax.pth │ ├── masking.pth │ ├── supervised.pth │ ├── supervised_contextpred.pth │ ├── supervised_edgepred.pth │ ├── supervised_infomax.pth │ └── supervised_masking.pth ├── parse_result.py ├── pretrain_contextpred.py ├── pretrain_deepgraphinfomax.py ├── pretrain_edgepred.py ├── pretrain_masking.py ├── pretrain_supervised.py ├── splitters.py └── util.py ├── LICENSE ├── README.md ├── agent.py ├── assets └── pipeline.png ├── colab.ipynb ├── datasets ├── acrylates.txt ├── chain_extenders.txt ├── isocyanates.txt └── polymers_117.txt ├── environment.yml ├── fuseprop ├── __init__.py ├── chemutils.py ├── dataset.py ├── decoder.py ├── encoder.py ├── gnn.py ├── inc_graph.py ├── mol_graph.py ├── nnutils.py ├── rnn.py └── vocab.py ├── grammar_generation.py ├── main.py ├── private ├── __init__.py ├── grammar.py ├── hypergraph.py ├── metrics.py ├── molecule_graph.py ├── subgraph_set.py ├── symbol.py └── utils.py ├── retro_star ├── alg │ ├── __init__.py │ ├── mol_node.py │ ├── mol_tree.py │ ├── molstar.py │ ├── reaction_node.py │ └── syn_route.py ├── api.py ├── common │ ├── __init__.py │ ├── parse_args.py │ ├── prepare_utils.py │ └── smiles_to_fp.py ├── data_loader │ ├── __init__.py │ └── value_data_loader.py ├── environment.yml ├── model │ ├── __init__.py │ └── value_mlp.py ├── packages │ ├── mlp_retrosyn │ │ ├── mlp_retrosyn.egg-info │ │ │ ├── PKG-INFO │ │ │ ├── SOURCES.txt │ │ │ ├── dependency_links.txt │ │ │ └── top_level.txt │ │ ├── mlp_retrosyn │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ │ └── toy │ │ │ │ │ └── sample.csv │ │ │ ├── extract_template.py │ │ │ ├── mlp_inference.py │ │ │ ├── mlp_policies.py │ │ │ ├── mlp_train.py │ │ │ └── scripts │ │ │ │ ├── run_extract_templates.sh │ │ │ │ ├── run_mlp_inference.sh │ │ │ │ └── run_mlp_train.sh │ │ └── setup.py │ └── rdchiral │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── rdchiral │ │ ├── __init__.py │ │ ├── backup │ │ │ ├── __init__.py │ │ │ ├── bonds.py │ │ │ ├── chiral.py │ │ │ ├── clean.py │ │ │ ├── initialization.py │ │ │ ├── main.py │ │ │ ├── template_extractor.py │ │ │ └── utils.py │ │ ├── bonds.py │ │ ├── chiral.py │ │ ├── clean.py │ │ ├── initialization.py │ │ ├── main.py │ │ ├── old │ │ │ ├── __init__.py │ │ │ ├── chiral.py │ │ │ ├── clean.py │ │ │ ├── initialization.py │ │ │ ├── main.py │ │ │ ├── template_extractor.py │ │ │ └── utils.py │ │ ├── template_extractor.py │ │ ├── test │ │ │ ├── __init__.py │ │ │ └── test_smiles_from_50k_uspto.txt │ │ └── utils.py │ │ ├── setup.py │ │ ├── templates │ │ ├── Examine templates.ipynb │ │ ├── README.md │ │ ├── clean_and_extract_uspto.py │ │ ├── example_template_extractions_bad.json │ │ └── example_template_extractions_good.json │ │ └── test │ │ ├── Test rdchiral notebook.ipynb │ │ ├── test_rdchiral.py │ │ └── test_rdchiral_cases.json 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