Abstract
Molecular shape comparison is a complicated undertaking. A graph-based representation of molecular shape is attractive in that it may be possible to leverage preexisting graph-theoretical algorithms to simplify molecular shape comparison. In this paper, we present methodology for deriving topographical graphs, a graph-like, high-level representation of molecular shape, which are considerably simpler than the molecules from which they were derived. The nodes in a topographical graph correspond to surface segments that possess a given topography, while edges denote the adjacency of the surface segments. In addition to the graph-theoretical properties, the nodes have three-dimensional position and the edges have length. We will present examples of topographical graphs generated for a variety of molecules and will illustrate the potential benefits of this representation.