Abstract
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present “Molecular Geometry (MG)” as a theoretical framework accompanied by “MG Operating System (MGOS)” which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering. Program summaryProgram Title: Molecular Geometry Operating System (MGOS)Program Files doi:http://dx.doi.org/10.17632/hp2wmvxsfz.1Licensing provisions: CC By 4.0Programming language: C++Supplementary material: (1) Supplementary Video 1, (2) Supplementary Video 2, (3) Supplementary Video 3, (4) Supplementary Video 4, (5) MGOS manual, and (6) 300 test PDB structure filesNature of problem: For both organic and inorganic molecules, structure determines molecular function and molecular structure is highly correlated with molecular shape or geometry. Hence, many studies were conducted for the analysis and evaluation of the geometry of atomic arrangement. However, most studies were based on Monte Carlo, grid-counting, or approximation methods and a high-quality solution requires heavy computational resources, not to mention its dependency on computation environment. In this paper, we introduce a unified framework of computational library, Molecular Geometry Operating System (MGOS), based on an analytic method for the molecular geometry of atomic arrangements. We believe that the powerful MGOS application programming interface (API) functions will free scientists from developing and implementing complicated geometric algorithms and let them focus on more important scientific problems.Solution method: Molecular Geometry (MG) is a general framework of mathematical/computational methods for solving molecular structure problems using a geometry-priority philosophy and is implemented by MGOS which is a library of callable C++ API functions. MGOS is developed based on the Voronoi diagram of three-dimensional spheres and its two derivative constructs called the quasi-triangulation and beta-complex. Note that this Voronoi diagram is different from the ordinary Voronoi diagram of points where the points are atom centers. Being an analytic method, the solutions of many geometric queries on atomic arrangement, if not all, are obtained correctly and quickly. The MGOS architecture is carefully designed in a three-tier architecture so that future modifications and/or improvements can be reflected in the application programs with no additional programming by users.
Highlights
In physics, chemistry, and materials science, the properties of inorganic molecules result from the arrangement of their atoms [1,2,3]
In physics and materials science, examples include the diffusion of lithium ions through paths closely correlated with geometric channels [1]; the porosity and surface area of metal organic framework (MOF) for hydrogen storage [2,3], water content regulation in polymer membranes through nanocracks which work as nanoscale valves [10], to name a few
Molecular Geometry (MG) Operating System (MGOS) consists of a set of natural-language-like application programming interface (API) functions, callable from application programs and efficiently provides a correct/accurate solution of geometric queries involving the arrangements of spherical objects where the objects are frequently van der Waals atoms
Summary
Chemistry, and materials science, the properties of inorganic molecules result from the arrangement of their atoms [1,2,3]. Molecular volume is commonly estimated by counting the numbers of random points or grid points contained in the molecule [15]; molecular voids are recognized by removing these grid points [16] Another example is the imprecise estimation of solvent accessible surfaces [17], which is critical for solvation models used in the calculation of electrostatic energy. In other words, equipped with MG/MGOS, researchers from diverse disciplines can conveniently and build computational models to solve molecular geometry problems and quickly obtain correct (or accurate) solutions.
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