Automatic structure identification algorithm

Automatic computer identification of alkanes was reported in 1989 by Davidson. His FORTRAN program has implemented, although with many restrictions and limitations, the Recommendations A-1 through A-4 for nomenclature of acyclic hydrocarbons. The program identified all the alkane chains in a structure and was able to select a master chain. Any introduction of functionalities containing heteroatoms or any, even the simplest, cyclic characteristics led to rejection by the algorithm... 

We are developing an expert system to automate the first step of this process, the interpretation of molecular spectra and identification of substructures present in the molecule. The automatic interpretation of spectra would by itself provide a useful tool for an organic chemist who may not be an expert spectroscopist. Also, reported algorithms for the assembly of candidate structures from known substructures, such as the GENOA program. (3-6) rely on the input of accurate and specific substructures in order to function correctly and efficiently. Identification of substructures is thus a logical starting point. 

This review discusses several approaches for the automatic identification of common structural features or structural similarity of organic molecules. The organization of the chapter is as follows. Section 2 gives an overview of the methods for structural feature analysis. Identification of common structural features is discussed in Sect. 3 with a few applications in structure-activity studies, which is subsequently followed by the identification of structural similarity in Sect. 4. The quantification of structural similarity is discussed in Sect. 5. The basic algorithms of these approaches and the relative software systems are also referred to with some illustrative examples. 

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