Given a protein, it is often necessary to study its geometric and physicochemical properties for studying its structure and predicting funtions of a protein. In this case, a connolly surface of a protein plays important roles for these purpose. A protein consists of a set of amino acids and a set of atoms comprise an amino acide. Since an atom can be represented by a hard 3D sphere in van der Waals model, a protein is usually modeled as a set of 3D spheres. In this paper, we present the algorithm for computing a connolly surface using Euclidean Voronoi diagram atoms of a protein. The algorithm initially locates the exterior aotms of a protein where connolly surface patches exist and computes the patches by tracking their boundary curves. Since a Euclidean Voronoi diagram is uniquely defined independent of probe radius different from other geometric structures, the connolly surfaces defined by probes of different radii can be computed without re-computing the Euclidean Voronoi diagram.

Euclidean Voronoi diagram of spheres in 3D has not been explored as much as it deserves even though it has significant potential impacts on diverse applications in both science and engineering. In addition, studies on the data structure for its topology have not been reported yet. Presented in this paper is the topological representation for Euclidean Voronoi diagram of spheres which is represented as a cell structure as one of typical non-manifold models. The topological representation is a variation of radial edge data structure with a consideration on the topological characteristics of Euclidean Voronoi diagram of spheres distinguished from general non-manifold models and Euclidean Voronoi diagram of points. Various topological queries in the Voronoi diagram are also presented and analyzed.