Study on chemical graph generation based on reduced graphs

Abstract

Generating virtual chemical structures by combining building blocks is frequently conducted by chemists with the help of computer programs. This simple task usually suffers from generating duplicates, leading to inefficiency of the structure generation. On top of that, diversity-oriented structure generation is required when exhaustive generation is intractable. Here, we have proposed a structure generation algorithm by combining ring systems and atom fragments in a tree-like way without generating duplicates. The algorithm makes use of reduced graphs, which retain the same topology as that of the corresponding ring systems but have less vertices than in the corresponding ring systems. For diversity-oriented structure generation, we have proposed an algorithm that generate a chemical graph per atom-fragment-based framework. One of the biggest advantages of this algorithm is that it takes diversity into account during structure generation instead of sampling diverse structures after structure generation. The features and efficiencies of the proposed two algorithms were demonstrated with simple structure generation case studies.