Generation of molecular graphs based on flexible utilization of the available structural information

Abstract

Classical theory of chemical structure has remained the basis for a comprehensive understanding of organic chemistry. Graph theory provides an extremely useful mathematical language for the description of both chemical structure and its properties. In many practical computer applications such as structure elucidation, synthesis planning and molecular design the generation of sets of candidate-structures (molecular graphs) is required. It is essential, that the generation process is constrained by the input structural information derived from any spectral, physical, chemical, etc., data. On the other hand, in most of the cases this information is incomplete, overlapping and ambiguous, which calls for approaches reflecting these features. Several problems, such as the isomorphism problem, and the combinatorial explosion complicate additionally the generation process. They should find their solutions under these constraints. Hence, the application of any general method for graph generation does not produce satisfactory results. All this calls for the development of specific graphgeneration schemes flexibly constrained by the input structural information. Some procedures treating special classes colored graphs (describing the real chemical structure), and employing sets of subgraphs (molecular fragments), etc., are introduced within the generation scheme. Furthermore, the generation method must reflect the fuzzy character of the information usually available to the chemist and to provide a straightforward pathway to the correct solution in the process of automated reasoning. In the present paper a wide variety of problems emerging from the generation of molecular graphs in the case of computer-aided structure elucidation are addressed and their possible solutions discussed.