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

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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
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article

Orthonym: verified IUPAC names for chemical structures

Kohulan Rajan, Christoph Steinbeck, Markus Nietfeld, Achim Zielesny
1 links
Zenodo (CERN European Organization for Nuclear Research)
Chemistry and Stereochemistry Studies
article

Orthonym: verified IUPAC names for chemical structures

Kohulan Rajan, Christoph Steinbeck, Markus Nietfeld, Achim Zielesny
article en

Abstract

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

Zenodo (CERN European Organization for Nuclear Research)
Beilstein-Institut (DE), Westfälische Hochschule (DE), Friedrich Schiller University Jena (DE)
Openalex Percentile: Top 26%
Chemistry and Stereochemistry Studies
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