QTF: Quasi-triangulation file format

Abstract

A quasi-triangulation is the dual structure of the Voronoi diagram of spherical balls and its properties and algorithms are well-studied in three-dimensional space. Quasi-triangulation has been used for efficiently solving various structure/shape related problems for biomolecules. The computation of the quasi-triangulation directly from an input file can take a significant amount of time. If the quasi-triangulation is computed a priori and stored in a file, an application software can directly load the file for solving application problems. In this paper, we propose a neutral file format, called the quasi-triangulation file format QTF, so that users can use the quasi-triangulation more effectively and efficiently by focusing more on his or her own application problems than the Voronoi diagram or the quasi-triangulation itself. The proposed QTF file format was thoroughly validated through an extensive experiment by computing the molecular volumes of one hundred molecular models in the Protein Data Bank. This approach has an important consequence: The QTF file format separates the computation of the Voronoi diagram from its applications.