Constraints for generating graphs with imposed and forbidden patterns: an application to molecular graphs

Although graphs are widely used to encode and solve various computational problems, little research exists on constrained graph construction. The current research was carried out to shed light on the problem of generating graphs, where the construction process is guided by various structural restrictions, like vertex degrees, proximity among vertices, and imposed and forbidden patterns. The main contribution of this paper is an encoding of the constrained graph generation problem in terms of a constraint satisfaction problem (CSP). This approach is motivated by the flurry of efficient solution algorithms available within the constraint programming (CP) framework. The obtained encoding has given rise to the CP-MolGen program, a new open source program dedicated to the generation of molecular graphs with imposed and forbidden fragments. Experimental results on several real-world molecular graph generation instances have shown the effectiveness and efficiency of the proposed program, especially the benefits of forbidding cyclic patterns as induced subgraphs.