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RetroSynthesisAgent
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RetroSynthesisAgent
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# RetroSynthesisAgent This project aims to conduct retrosynthesis planning for macromolecular based on literature, utilizing an LLM agent and knowledge graphs. Please cite the following work: ``` @article{ma2025automated, title={Automated Retrosynthesis Planning of Macromolecules Using Large Language Models and Knowledge Graphs}, author={Ma, Qinyu and Zhou, Yuhao and Li, Jianfeng}, journal={Macromolecular Rapid Communications}, pages={2500065}, year={2025}, publisher={Wiley Online Library} } ``` ## Requirements ``` conda create -n retrosyn python=3.11 conda activate retrosyn pip install rdkit requests python-dotenv PyMuPDF scholarly openai networkx graphviz pubchempy Pillow fastapi pydantic uvicorn pyvis loguru ``` ## Data + eMolecules download URL: https://downloads.emolecules.com/free/ + for this project, version: 2024-07-01 + Download it and turn it to a set as a format of json ## `env.` File Setting + Set your OpenAI API key (`API_KEY`) and optional `BASE_URL` to use the LLM. + Set the `HEADERS` and `COOKIES` from your browser for web scraping of literatures in JSON + an example: ``` API_KEY=xxx BASE_URL=xxx HEADERS={"user-agent": "xxx"} COOKIES={"xxx": "xxx", "xxx": "xxx"} ``` ## Run the demo ``` sh runRetroSynAgent.sh ``` Parameter Description: + `--material`: Specifies the material to be processed. + `--num_results`: Defines the number of PDF to be processed. + `--alignment`: Determines whether to align entities. + `--expansion`: Determines whether to expand the tree with additional literature. + `--filtration`: Determines whether to apply filtration to the reactions. We provide a demo video of its automated operation process: [](assets/demo-video.mp4) + After constructing the chemical retrosynthetic pathway tree for the target substance, a URL will be generated. You can open it directly in your local browser. + **When you hover over a node in the tree, the name of the substance represented by that node will be displayed.**
