By default, we infer the graph representation of crystal structures and chemical fragments from their labeled point cloud representations provided in a crystallographic information file (.cif) and XYZ file (.xyz), respectively. We assign a bond between a pair of atoms if the (periodic, in the case of crystal structures) distance between them is less than the sum of their covalent radii taken from Refs. . PoreMatMod.jl allows (i) alteration of the bonding rules and/or (ii) manual bond assignment.