Computer-encodable structure representation

Computer-Aided Property Estimation Computer-aided structure estimation requires the structure of the chemical compounds to be encoded in a computer-readable language. Computers most efficiently process linear strings of data, and hence linear notation systems were developed for chemical structure representation. Several such systems have been described in the literature. SMILES, the Simplified Molecular Input Line Entry System, by Weininger and collaborators [2-4], has found wide acceptance and is being used in the Toolkit. Here, only a brief summary of SMILES rules is given. A more detailed description, together with a tutorial and examples, is given in Appendix A. 

Any representation of chemical structure is thus a complex cipher, allowing our model of structure such brevity as to mask the distinction between the model and the reality of chemical structure. The foregoing evolution of such representations is a testament to both our evolving understanding of structure and the human capacity for encoding any information. In this latter sense, however, chemical structure representation is quite naturally suited to the computer age. 

For many computer tasks and for the transfer of structiural information from one computer program to another, a linear representation of the chemical structure may be more suitable. " A popular linear representation is the SMILES notation. Part of its appeal is that for acyclic structures the SMILES is similar to the traditional linear diagram. For example, ethane is denoted by CC and ethylene C=C. Examples of additional SMILES are given in Figure 4. SMILES is the basis of a chemical information system, and this notation provides a convenient framework for more sophisticated computer coding of chemistry described below. For some internal computer functions, structures encoded in a linear notation may be converted to connection tables. 

This parametric approach to spectral simulation was developed and utilized by Grant and Paul and Lindeman and Adams in their studies of linear and branched alkanes. These initial studies involved the calculation of simple topological parameters to be used as descriptions of the local structural environments of carbon atoms. This approach has been implemented more extensively and effectively with an interactive computer system that handles the calculation and manipulation of large numbers of structural descriptors. Topological, geometric, and electronic representations of local atomic environments can be encoded as descriptors. This computational methodology has been successfully applied to several structural classes of compounds cydo-hexanols and decanols, steroids, cyclopentanes and cyclopentanols, nor-bornanols, decalones, and carbohydrates. ... 

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