Detection of three-dimensional patterns of atoms in chemical structures

Abstract

An algorithm for detecting occurrences of a three-dimensional pattern of objects within a larger structure is presented. The search technique presented uses the geometric structure of the pattern to define characteristics demanded of candidates for matching. This is useful in cases where the properties of each atom, considered individually, do not adequately limit the number of sets of possible matchings. Several applications of this technique in the field of chemistry are: (1) in pharmacology: searching for a common constellation of atoms in molecules possessing similar biological activities; (2) in X-ray crystallography: fitting a structure or a structural fragment to a set of peaks in the electron-density distribution of a Fourier map; (3) in chemical documentation: retrieving from a file the structures containing specified substructures.