Orthonym: verified IUPAC names for chemical structures
The 2013 IUPAC recommendations define one preferred IUPAC name (PIN) per structure; naming by hand is slow and error-prone. Most structure-to-name software is proprietary, so a wrong name cannot be traced to its rule. Neural translators can give a valid name for the wrong molecule, and nothing in the name signals the error. Open rule-based tools do not refuse to answer when they cannot verify a name. Orthonym is an open-source, rule-based engine that generates IUPAC names in four stages: perception (RDKit), rules (2013 IUPAC recommendations), assembly and checks. A name must pass three validation checks before it is emitted: atom coverage, a round trip through OPSIN, and an InChIKey match with the input. If any check fails, the engine declines and states the reason. A name counts as correct only if OPSIN reads it back to a structure with the same full InChIKey as the input; a decline counts as a failure. Across HOLDOUT2000, QM9, ChEBI, PubChem (500,000) and ZINC22 (500,000), Orthonym reaches a 97.15–99.98% round-trip rate and emits zero names for the wrong molecule in all test sets, compared with Openclatura 0.3.2 and NISPO 0.1.6. MIT licence. Engine version measured: 1.0.8, available on PyPI and conda-forge (pip install orthonym). Web application: orthonym.decimer.ai
Authors
- Kohulan Rajan (ORCID: https://orcid.org/0000-0003-1066-7792)
- Christoph Steinbeck (ORCID: https://orcid.org/0000-0001-6966-0814)
- Markus Nietfeld (ORCID: https://orcid.org/0000-0001-7786-3005)
- Achim Zielesny (ORCID: https://orcid.org/0000-0003-0722-4229)
Institutions
- Beilstein-Institut (DE)
- Westfälische Hochschule (DE)
- Friedrich Schiller University Jena (DE)
Publication Details
- Journal
- Zenodo (CERN European Organization for Nuclear Research)
- Published
- 2026-10-30
- DOI
- https://doi.org/10.5281/zenodo.23803834
- Primary Topic
- Chemistry and Stereochemistry Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00