Try CCP4mg molecular-graphics software for some of the features. Matter of the fact, nearly all chemistry software providing optimization, docking, distance and figure/pictorial as well as structure superimposition analyses uses the theory in one or other ways. Try the basic topological and inter-relational applications by the Randic, Hosoya, and Wiener indices, as the case may be, first on a mathematical-chemical platform to develop further. This is where the Chemistry meets the Mathematics at the structural levels.