Within constitutional isomerism, the different isomers represent different atom-connectivity patterns or permutations. In recognising that the set of possible atom-connectivity configurations also represents combinatorial structure, each configuration can be treated as an abstract polytope representable as a matrix. These abstract polytope species (henceforth simply called "species"), and their matrix representation, are equivalent to what in cheminformatics is called the adjacency matrix of a simple molecular graph. These encode which atoms in a molecule are connected. Fig. gives some simple examples for the 5-atom class.