Bioinformatics Preprint 03-012
Counterexamples in Chemical Ring Perception
Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold. Peter F. Stadler
Ring information is a large part of the structural topology used to identify and characterize molecular structures. It is hence of crucial importance to obtain this information for a variety of tasks in computational chemistry. Many different approaches for "ring perception", i.e., the extraction of cycles from a molecular graph, have been described. The chemistry literature on this topic, however, reports a surprisingly large number of incorrect statements about the properties of chemically relevant ring sets and, in particular, about the mutual relationships of different sets of cycles in a graph. In part these problems seem to have arisen from a sometimes rather idiosyncratic terminology for notions that are fairly standard in graph theory. In this contribution we translate the definitions of concepts such as the Smallest Set of Smallest Rings, Essential Set of Essential Rings, Extended Set of Smallest Rings, Set of Smallest Cycles at Edges, Set of Elementary Rings, K-rings, and beta-rings into a more widely-used mathematical language. We then outline the basic properties of different cycle sets and provide numerous counterexamples to incorrect claims in the published literature. These counterexamples may have a serious practical impact because at least some of them are molecular graphs of well-known molecules. As a consequence, we propose a catalogue of desirable properties for chemically useful sets of rings.
Chemical Ring Perception, Counterexamples
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Last modified: 2003-06-11 14:48:52 studla