Duplicate from insilicomedicine/chemcensor

Co-authored-by: Nikita Bondarev <Nikita-Insilico@users.noreply.huggingface.co>

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ChemCensor-DB-U2-1.0.0.sqlite.zip

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README.md

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+---
+language:
+- en
+tags:
+- retrosynthesis
+- chemistry
+- cheminformatics
+- sqlite
+- chemical-plausibility
+license: other
+---
+
+# ChemCensor DataBase
+
+[![Dataset](https://img.shields.io/badge/Dataset-Hugging%20Face-FFD21F?style=flat-square&logo=huggingface&logoColor=black)](https://huggingface.co/datasets/insilicomedicine/ChemCensor-DataBase)
+[![Paper](https://img.shields.io/badge/Paper-arXiv%3A2602.03554-B31B1B?style=flat-square&logo=arxiv&logoColor=white)](https://arxiv.org/abs/2602.03554)
+[![ChemCensor](https://img.shields.io/badge/github-ChemCensor-blue?logo=github)](https://github.com/insilicomedicine/ChemCensor)
+
+This repository provides the SQLite database used by **ChemCensor**, a precedent-based framework for evaluating the reaction chemical plausibility.
+
+ChemCensor scores a proposed reaction by separating the **reaction center** (what changes during the reaction) from the **functional-group context** (what must be tolerated), and then checking whether similar reaction-center and functional-group compatibility patterns are supported by documented synthetic precedents. The resulting **ChemCensor Score** is an integer confidence level from 0 to 5, where higher values indicate stronger support from precedent chemistry.
+
+The database is distributed as a compressed `.zip` archive containing a `.sqlite` file.
+
+---
+
+## What is inside
+
+The SQLite database stores precomputed ChemCensor knowledge used for reaction plausibility scoring. 
+The knowledge base was constructed from the **USPTO-full** reaction dataset [introduced by D. Lowe](https://figshare.com/articles/dataset/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873) 
+and includes reactions extracted by text-mining from United States patents published between 1976 and September 2016.
+
+The DB is compatible with **`chemcensor>=1.0.0`**.
+
+The database includes:
+
+- reaction-center precedent information;
+- functional-group compatibility information;
+- relational mappings required by the ChemCensor scoring pipeline.
+
+During ChemCensor scoring, the database is queried to determine whether a proposed retrosynthetic step is supported by previously observed reaction-center precedents and functional-group compatibility patterns.
+
+## Download and unpack
+
+Download the archive from this Hugging Face repository and unzip it:
+
+```bash
+unzip ChemCensor-DB-U2-1.0.0.sqlite.zip
+```
+
+After unpacking, you should obtain a SQLite database file, for example:
+
+```text
+ChemCensor-DB-U2-1.0.0.sqlite
+```
+
+---
+
+## Use with ChemCensor
+
+The database is intended to be used together with the ChemCensor source code:
+
+```bash
+git clone https://github.com/insilicomedicine/ChemCensor.git
+cd ChemCensor
+```
+
+Place the unpacked `.sqlite` file in the location expected by the ChemCensor configuration, or provide the database path according to the repository instructions.
+
+A typical workflow is:
+
+1. download this dataset;
+2. unzip the `.sqlite` database;
+3. install ChemCensor from the GitHub repository;
+4. point ChemCensor to the unpacked database file;
+5. run ChemCensor scoring for candidate reactions.
+
+Please refer to the [ChemCensor repository](https://github.com/insilicomedicine/ChemCensor) for the exact command-line or Python API usage.
+
+---
+
+## Citation
+
+If you use this database or ChemCensor in your work, please cite:
+
+```
+@misc{zagribelnyy2026singleanswerenoughrethinking,
+      title={When Single Answer Is Not Enough: Rethinking Single-Step Retrosynthesis Benchmarks for LLMs}, 
+      author={Bogdan Zagribelnyy and Ivan Ilin and Maksim Kuznetsov and Nikita Bondarev and Roman Schutski
+                and Thomas MacDougall and Rim Shayakhmetov and Zulfat Miftakhutdinov
+                and Mikolaj Mizera and Vladimir Aladinskiy and Alex Aliper and Alex Zhavoronkov},
+      year={2026},
+      eprint={2602.03554},
+      archivePrefix={arXiv},
+      primaryClass={cs.LG},
+      url={https://arxiv.org/abs/2602.03554}, 
+}
+```
+
+## License
+
+This database is part of **ChemCensor** and is distributed under the same terms as the ChemCensor software.
+By downloading or using this dataset, you agree to the [ChemCensor License Agreement](https://github.com/insilicomedicine/ChemCensor/blob/main/LICENSE)
+(independent benchmarking and evaluation purposes only).
+
+You may use the database solely to assess, compare, validate, or report the performance of models, algorithms, or methodologies together with ChemCensor, as described in the ChemCensor repository and paper.
+Use in products, automated pipelines, training or fine-tuning of models, redistribution, or incorporation into operational workflows is not permitted without prior written permission from Insilico Medicine AI Limited.
+
+Insilico retains all intellectual property rights in the database.
+For the full definitions, permitted and prohibited uses, and legal terms, see the [LICENSE](https://github.com/insilicomedicine/ChemCensor/blob/main/LICENSE)
+file in the [ChemCensor GitHub repository](https://github.com/insilicomedicine/ChemCensor).