├── .coveragerc ├── .github ├── azure_pipelines │ └── code-security-analysis.yml └── workflows │ ├── ci.yml │ ├── docs.yml │ └── release.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── DEVELOPMENT.md ├── LICENSE ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── docs ├── cli │ ├── eval_single_step.md │ └── search.md ├── images │ ├── logo.png │ └── logo.svg ├── index.md ├── installation.md ├── single_step.md └── tutorials │ ├── .gitignore │ ├── custom_model.ipynb │ ├── paroutes_benchmark.ipynb │ └── quick_start.ipynb ├── environment.yml ├── environment_full.yml ├── mkdocs.yml ├── pyproject.toml └── syntheseus ├── __init__.py ├── cli ├── __init__.py ├── eval_single_step.py ├── main.py ├── search.py └── search_config.yml ├── interface ├── __init__.py ├── bag.py ├── models.py ├── molecule.py └── reaction.py ├── py.typed ├── reaction_prediction ├── __init__.py ├── chem │ ├── __init__.py │ └── utils.py ├── data │ ├── __init__.py │ ├── dataset.py │ └── reaction_sample.py ├── environment_gln │ ├── Dockerfile │ └── environment.yml ├── inference │ ├── __init__.py │ ├── base.py │ ├── chemformer.py │ ├── config.py │ ├── default_checkpoint_links.yml │ ├── gln.py │ ├── graph2edits.py │ ├── local_retro.py │ ├── megan.py │ ├── mhnreact.py │ ├── retro_knn.py │ ├── root_aligned.py │ └── toy_models.py ├── models │ ├── __init__.py │ └── retro_knn.py └── utils │ ├── __init__.py │ ├── config.py │ ├── downloading.py │ ├── inference.py │ ├── metrics.py │ ├── misc.py │ ├── model_loading.py │ ├── parallel.py │ └── testing.py ├── search ├── __init__.py ├── algorithms │ ├── __init__.py │ ├── base.py │ ├── best_first │ │ ├── __init__.py │ │ ├── base.py │ │ └── retro_star.py │ ├── breadth_first.py │ ├── mcts │ │ ├── __init__.py │ │ ├── base.py │ │ └── molset.py │ ├── mixins.py │ ├── pdvn.py │ └── random.py ├── analysis │ ├── __init__.py │ ├── diversity.py │ ├── route_extraction.py │ └── solution_time.py ├── graph │ ├── __init__.py │ ├── and_or.py │ ├── base_graph.py │ ├── message_passing │ │ ├── __init__.py │ │ ├── run.py │ │ └── update_functions.py │ ├── molset.py │ ├── node.py │ ├── route.py │ └── standardization.py ├── mol_inventory.py ├── node_evaluation │ ├── __init__.py │ ├── base.py │ └── common.py ├── utils │ ├── __init__.py │ └── misc.py └── visualization.py └── tests ├── __init__.py ├── cli ├── __init__.py ├── test_cli.py ├── test_eval_single_step.py └── test_search.py ├── conftest.py ├── interface ├── __init__.py ├── test_bag.py ├── test_models.py ├── test_molecule.py ├── test_reaction.py └── test_toy_models.py ├── reaction_prediction ├── __init__.py ├── chem │ ├── __init__.py │ └── test_utils.py ├── data │ ├── __init__.py │ └── test_dataset.py ├── inference │ ├── __init__.py │ └── test_models.py └── utils │ ├── __init__.py │ ├── test_misc.py │ └── test_parallel.py └── search ├── __init__.py ├── algorithms ├── __init__.py ├── test_base.py ├── test_best_first.py ├── test_breadth_first.py ├── test_mcts.py ├── test_pdvn.py └── test_random.py ├── analysis ├── __init__.py ├── conftest.py ├── test_diversity.py ├── test_route_extraction.py └── test_solution_time.py ├── conftest.py ├── graph ├── __init__.py ├── test_andor.py ├── test_base.py ├── test_message_passing.py ├── test_molset.py ├── test_route.py └── test_standardization.py ├── node_evaluation ├── __init__.py └── test_common.py ├── test_mol_inventory.py └── test_visualization.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/syntheseus/HEAD/.coveragerc -------------------------------------------------------------------------------- /.github/azure_pipelines/code-security-analysis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/syntheseus/HEAD/.github/azure_pipelines/code-security-analysis.yml -------------------------------------------------------------------------------- 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