Enumeration method for chemical compounds containing benzene rings

Abstract

We extend the enumeration algorithm in our previous study for acyclic chemical structures, and propose an algorithm for enumerating chemical structures with benzene rings. These algorithms use a tree to represent a chemical structure, where nodes and edges represent atoms and bonds of the chemical structure, respectively. We include benzene rings in the enumeration by treating a benzene ring as a special kind of atom. To enumerate the structure, firstly, the extended algorithm gets chemical formula as the input, and calculates the number of benzene rings that the input chemical formula can have. Then, we generate non-redundant trees from the chemical formula using the algorithm in the previous study. Because we still do not know if nodes adjacent to a benzene ring have bonds with which carbon of that benzene ring, we generate a rule to assign each node to the carbon atom of a benzene ring. To test the performance of the proposed algorithm, we compared the computational time with that of MOLGEN, a well-known enumeration tool. The result shows that our algorithm is much faster than MOLGEN.