├── CHANGELOG.md ├── LICENSE ├── README.md ├── aizynthtrain ├── __init__.py ├── data │ ├── __init__.py │ └── uspto.py ├── modelling │ ├── __init__.py │ ├── chemformer │ │ └── create_dataset_split.py │ └── expansion_policy │ │ ├── __init__.py │ │ ├── create_template_lib.py │ │ ├── eval_multi_step.py │ │ ├── eval_one_step.py │ │ ├── featurize.py │ │ ├── split_data.py │ │ └── training.py ├── pipelines │ ├── __init__.py │ ├── chemformer_data_prep_pipeline.py │ ├── chemformer_train_pipeline.py │ ├── data │ │ ├── __init__.py │ │ ├── autotag_data_extraction.yaml │ │ ├── chemformer_data_prep_pipeline.yaml │ │ ├── chemformer_product_tagging_pipeline.yaml │ │ ├── reaction_validation_pipeline.yaml │ │ ├── stereo_checks_pipeline.yaml │ │ └── template_validation_pipeline.yaml │ ├── disconnection_chemformer_data_prep_pipeline.py │ ├── expansion_model_pipeline.py │ ├── notebooks │ │ ├── __init__.py │ │ ├── expansion_model_val.py │ │ ├── reaction_selection.py │ │ ├── stereo_selection.py │ │ ├── stereo_template_selection.py │ │ └── template_selection.py │ ├── stereo_template_pipeline.py │ └── template_pipeline.py └── utils │ ├── __init__.py │ ├── configs.py │ ├── data_utils.py │ ├── files.py │ ├── keras_utils.py │ ├── onnx_converter.py │ ├── reporting.py │ ├── stereo_flipper.py │ └── template_runner.py ├── configs └── uspto │ ├── expansion_model_pipeline_config.yml │ ├── expansion_pipeline.sh │ ├── ringbreaker_model_pipeline_config.yml │ ├── ringbreaker_pipeline.sh │ ├── routes_for_eval.json │ ├── setup_folder.py │ ├── smiles_for_eval.txt │ ├── stock_for_eval_recov.txt │ ├── template_pipeline.sh │ └── template_pipeline_config.yml ├── env-dev.yml ├── poetry.lock ├── pyproject.toml └── tests ├── __init__.py ├── data └── test_keras.hdf5 ├── test_configs.py ├── test_data_utils.py ├── test_file_utils.py └── test_onnx_converter.py /CHANGELOG.md: -------------------------------------------------------------------------------- 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