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 t ypes'' to a molecule based on its connection table of atoms and bonds. Its operation is controlled entirely by a rules file created by the u ser. Each rule contains a ''pattern'', a description in linear notatio n of a class of chemical substructures which may contain branches or r ings. Rules are of two sorts: those which define properties to be used in subsequent rules and those which assign the final atom types. As a n example, we present rules for classifying atoms into seven broad typ es based on their physical properties (e.g. cation, H-bond donor, hydr ophobe). This classification has been applied to large databases of th ree-dimensional modes of druglike compounds. PATTY is very rapid and o perates on a variety of hardware platforms.