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Updated: Jun 3, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

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Published on: June 27, 2014

Chemical name to structure: OPSIN, an open source solution.

Daniel M Lowe¹, Peter T Corbett, Peter Murray-Rust

¹Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, England.

Journal of Chemical Information and Modeling

|March 10, 2011

Summary

This summary is machine-generated.

We developed Open Parser for Systematic IUPAC Nomenclature (OPSIN), an open-source algorithm for fast and precise interpretation of organic chemical names. OPSIN achieves high accuracy, enabling robust chemical structure reconstruction from nomenclature.

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Area of Science:

Computational chemistry
Cheminformatics
Organic chemistry

Background:

Accurate interpretation of chemical nomenclature is crucial for data exchange and reproducibility.
Existing methods for chemical name parsing can be slow or imprecise.
Developing automated tools for chemical name-to-structure conversion is an ongoing challenge.

Purpose of the Study:

To introduce Open Parser for Systematic IUPAC Nomenclature (OPSIN), a novel open-source algorithm.
To provide a fast and precise method for interpreting organic chemical nomenclature.
To enable accurate reconstruction of chemical structures from their names.

Main Methods:

Development of an algorithm based on a regular grammar approach.
Utilizing the grammar to guide tokenization of chemical names.
Constructing an XML parse tree from the parsed name for stepwise structure reconstruction.

Main Results:

OPSIN demonstrates exceptional precision (99.8%+) in name/structure pair interpretation.
High recall rates (98.7-99.2%) were achieved using general organic chemical nomenclature.
The software successfully reconstructs chemical structures from names.

Conclusions:

OPSIN offers a highly accurate and efficient solution for chemical name parsing.
The open-source nature of OPSIN facilitates future development in chemical informatics.
This algorithm serves as a foundation for advancing automated chemical structure elucidation.