Algorithm for naming molecular equivalence classes represented by labeled pseudographs

The emergence of large chemical databases imposes a need for organizing the compounds in these databases. Mapping the chemical graph in particular, and a molecular equivalence class represented by a labeled pseudograph in general, to a unique number or string facilitates high-throughput browsing, grouping, and searching of the chemical database. Computing this number using a naming adaptation of the Morgan algorithm, we observed a large classification noise in which nonisomorphic graphs were mapped to the same number. Our extensions to that algorithm greatly reduced the classification noise.