PATTY - A PROGRAMMABLE ATOM TYPER AND LANGUAGE FOR AUTOMATIC CLASSIFICATION OF ATOMS IN MOLECULAR DATABASES

PATTY (Programmable ATom TYper) is an algorithm for assigning ''atom types'' to a molecule based on its connection table of atoms and bonds. Its operation is controlled entirely by a rules file created by the user. Each rule contains a ''pattern'', a description in linear notation of a class of chemical substructures which may contain branches or rings. Rules are of two sorts: those which define properties to be used in subsequent rules and those which assign the final atom types. As an example, we present rules for classifying atoms into seven broad types based on their physical properties (e.g. cation, H-bond donor, hydrophobe). This classification has been applied to large databases of three-dimensional modes of druglike compounds. PATTY is very rapid and operates on a variety of hardware platforms.