This work is mainly concerned with the comparison of the similarities of the R-groups.Each R-group is based on several descriptors, such as electronegativity, hydrogen-bond acceptor, hydrogen-bond donor etc., which will affect reactions obviously and can be calculated conveniently.Since the environment with very long distance from the reaction core has relatively small effect on the reaction, the comparison partners of R-group can be regarded as some substructures that have through-bond of up to six from the point of substitution on the reaction core.This work proposed a method based on the description of R-group and the constraints of distance to compare the R-group similarities, which represented an R-group with a 45 dimensional vector and converted the comparison of chemical structures into the corresponding multiple vectors.Employing this method, we successfully distinguished a large number of R-group similarities, and realized the goal of predicating the similarity of unknown chemical compounds.

Key words: similarity, descriptor, normalization, barycenter