RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases.
Many cheminformatics applications like aromaticity detection, SMARTS matching, or the calculation of atomic coordinates require a chemically meaningful perception of the molecular ring topology. The unique ring families (URFs) were recently introduced as a unique, polynomial, and chemically meaningful description of the ring topology. Here we present the first open-source implementation of the URF concept for ring perception. The C library RingDecomposerLib is easy to use, portable, well-documented, and thoroughly tested. Aside from the URFs, other related ring topology descriptions like the relevant cycles (RCs), relevant cycle prototypes (RCPs), and a smallest set of smallest rings (SSSR) can be calculated. We demonstrate the runtime efficiency of the RingDecomposerLib with computing time benchmarks for the complete PubChem Compound Database and thereby show the applicability in large-scale and interactive applications.
Universität Hamburg , ZBH - Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany.
Florian
0000-0001-7051-8719
F
Flachsenberg
Universität Hamburg , ZBH - Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany.
Niek
N
Andresen
Universität Hamburg , ZBH - Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany.
Matthias
0000-0002-9553-6531
M
Rarey
D062313:Databases, Pharmaceutical; D048088:Informatics / Q000379:methods*