  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.
