A software tool for visualization of molecular face (VMF) by improving marching cubes algorithm

Visualization of the molecular face (VMF) is a software tool for 3D visualization of the molecular face model in terms of molecular face theory. VMF is achieved on the Linux platform by adopting C language programming and OpenGL graphics standards. The Marching Cubes (MC) algorithm forms an important part of the VMF. We are dedicated to improving the MC algorithm so as to better meet the reconstruction of molecular face. First, signs of vertices in the cell are used to define the configurations. Second, binary digits are used to denote faces, vertices and edges of the cell. Third, configurations are classified into three types, for which different algorithms of triangulation are used. Furthermore, the temporal and spatial efficiencies of the algorithm are improved by using the coherence of the neighbor cells and optimizing storage structure, respectively. Finally, interactive operation functions and visualization of the molecular face model in real time are realized. In this article, details of the improved MC algorithm are described, and the analytical results for several typical datasets of molecular graphics demonstrate the correctness and effectiveness of our software. The surface area and volume of molecular surface are also given in this paper. The VMF can provide technical support to researchers working in related fields of data visualization.