Triangulating the surface of a molecule

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Abstract

Questions of chemical reactivity can often be cast as questions of molecular geometry. Common geometric models for proteins and other molecules are the space-filling diagram, the solvent accessible surface and the molecular surface. In this paper we present a new approach to triangulating the surface of a molecule under the three models, which is fast, robust, and results in topologically correct triangulations. Our computations are based on a simplicial complex dual to the molecule models. All proposed algorithms are parallelizable.

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The research of both authors is partially supported by the Office of Naval Research. Herbert Edelsbrunner is also supported through the Alan T. Waterman award, grant CCR-9118874.