In general, the availability of biomolecular structural data has paved the way for the transition from the traditional qualitative description to quantitative analysis and prediction in biological sciences. An essential ingredient of quantitative biology is geometric, topological and graph theory modeling, analysis and computation. Aided by increasingly powerful high performance computers, geometric, topological and graph theory modeling, analysis and computation have become indispensable apparatuses not only for the visualization of biological data, but also filling the gap between biological data and mathematical models of biological systems [@ZYu:2008; @ZYu:2008b; @XFeng:2012a; @XFeng:2013b; @KLXia:2014a; @MXChen:2012; @Rocchia:2002; @PMach:2011; @XShi:2011; @JLi:2013; @Decherchi:2013; @LiLin:2014].

One of the simplest molecular geometric models, or molecular structural models, is the space-filling Corey-Pauling-Koltun (CPK) theory, which represents an atom by a solid sphere with a van der Waals (VDW) radius [@Koltun:1965]. The outer boundary of CPK model gives rise to the van der Waals (vdW) surface, which is composed of piece-wise unburied sphere surfaces. Solvent accessible surface (SAS) and solvent-excluded surface (SES) have also been introduced to create smooth molecular surfaces by rolling a probe molecule over the vdW surface [@Richards:1977; @Connolly85]. SESs have widely been applied to protein folding [@Spolar], protein surface topography [@Kuhn], protein-protein interactions [@Crowley], DNA binding 