GMA: A generic match algorithm for structural homomorphism, isomorphism, and maximal common substructure match and its applications

Structural homomorphism, isomorphism, and maximal common substructure match (MCSS) have been studied for many years. Traditionally, these problems are processed separately and considered as the factorial computing complexity relying on the number of atoms. This paper will show the following: (1) All these problems can be processed in one generic match algorithm (GMA) without raising computing complexity. (2) The computing complexity can rely on the adjacent degrees of atoms instead of simply the number of atoms. (3) Many sophisticated structural perception algorithms can be solved and simplified by using GMA in efficient ways. GMA is based upon the partial ordering set theory. The distinctive concept of GMA is that it considers a query structure as a ''program'', which will be run on the queried structure (or superstructure). Also, the paper reports its implementation in SSSR and other ring perception algorithms, absolute stereochemical configuration detection, and related problems.