SMILES toolkit

The compact textual coding requires no graphical input and additionally permits a fast transmission. These are important advantages of using SMILES in chemical applications via the Internet and in online services. SMILES is also used for the input of structures in the Daylight Toolkit [22]. 

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. 

To obtain a unique SMILES notation, computer programs such as the Toolkit include the CANGEN algorithm [1] which performs CANonicalization, resulting in unique enumeration of atoms, and then GENerates the unique SMILES notation for the canonical structure. In the case of pyridine, this is notation (III). Any molecular structure entered in the Toolkit is converted automatically into its unique representation. 

Numerous toolkits SMILES, Depict, SMARTS, Fingerprint, Monomer, Thor, Merlin, X-Widgets, Program objects. Remote Access, and Reaction Toolkits (see Glossary)... 

The CHORD6 chemical cartridge is a commercial product from gNova, Inc. It is written using C functions and the OEChem toolkit from OpenEye. It provides the core functions discussed in this book, such as cansmiles, matches, count matches, list matches, smiles to molfile, molfile to smiles, and xform. CHORD makes it possible to efficiently process RDBMS tables containing many millions of chemical structures. 

A second eccentricity is that atom labels are drawn smaller when in rings. Additionally, whereas it is customary to omit the C atom label for carbon atoms, DEPICT provides them everywhere except in aromatic rings. Aromatic atoms, in turn, are written in lowercase, betraying a kinship to SMILES notation. These peculiarities detract somewhat from the diagram s aesthetic appearance however, they probably reflect the defaults used to visualize SMILES. Reportedly, the defaults can be replaced by adjustable parameters within the Daylight Toolkit. 

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