Molecular geometry and BULL!

Abstract

Geometric properties are critical for the function of molecules consisting of atoms which are usually modeled as a set of spheres in 3D. We propose 'Molecular Geometry' which is a theoretical framework of computational understanding of the geometry of molecules in the claim that most, hopefully all, molecular structure problems can be effectively and efficiently facilitated by the 'geometrization' of the problem at hand. We also report BULL!, the molecular geometry engine based on the Voronoi diagram of spheres, the quasi-triangulation, and the beta-complex. Being a program implemented in C++, application programmers can simply call API-functions of BULL! to create application programs correctly, efficiently, and conveniently. The BULL! engine, which will be freely available from the Voronoi Diagram Research Center at Hanyang University, is designed so that application programs are completely independent of future modifications and improvements.