Unique Ring Families:
A Chemically Meaningful Description of Molecular Ring Topologies
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Abstract
The perception of a set of rings forms the basis for
a number of chemoinformatics applications, e.g. the systematic naming
of compounds, the calculation of molecular descriptors, the matching
of SMARTS expressions, and the generation of atomic coordinates. We
introduce the concept of unique ring families (URFs) as an extension
of the concept of relevant cycles (RCs)., URFs are consistent
for different atom orders and represent an intuitive description of
the rings of a molecular graph. Furthermore, in contrast to RCs, URFs
are polynomial in number. We provide an algorithm to efficiently calculate
URFs in polynomial time and demonstrate their suitability for real-time
applications by providing computing time benchmarks for the PubChem
Database. URFs combine three important
properties of chemical ring descriptions, for the first time, namely
being unique, chemically meaningful, and efficient to compute. Therefore,
URFs are a valuable alternative to the commonly used concept of the
smallest set of smallest rings (SSSR) and would be suited to become
the standard measure for ring topologies of small molecules