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Simplified molecular input line entry specification

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Revision as of 14:44, 20 September 2011 by Racepacket (talk | changes) (simplify language)

The simplified molecular input line entry specification or SMILES is a line notation for the structure of chemical molecules. It uses short ASCII strings to represent structures. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

Arthur Weininger and David Weininger wrote the original SMILES specification in the late 1980s. It has since been modified and extended by others, including by Daylight Chemical Information Systems Inc. In 2007, the Blue Obelisk open-source chemistry community developed an open standard called "OpenSMILES". Other 'linear' notations include the Wiswesser Line Notation (WLN), ROSDAL and SLN (Tripos Inc).

In July 2006, the IUPAC introduced the InChI as a standard for representing chemical structures. People think that SMILES is slightly more human-readable than InChI. SMILES also has a wide base of software support with extensive theoretical (for example, graph theory) backing.

Conversion

SMILES can be converted back to 2-dimensional representations using Structure Diagram Generation algorithms (Helson, 1999). This conversion is not always unambiguous. Computer programs use energy minimization to convert SMILES to 3-dimensional representations. There are many downloadable and web-based conversion utilities.

References

  • Anderson, E.; Veith, G.D; Weininger, D. (1987). SMILES: A line notation and computerized interpreter for chemical structures. Report No. EPA/600/M-87/021. Duluth, MN 55804: U.S. EPA, Environmental Research Laboratory-Duluth.{{cite book}}: CS1 maint: location (link) CS1 maint: multiple names: authors list (link)
  • Weininger, David (1988). "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules". Journal of Chemical Information and Modeling. 28: 31. doi:10.1021/ci00057a005.
  • Weininger, David; Weininger, Arthur; Weininger, Joseph L. (1989). "SMILES. 2. Algorithm for generation of unique SMILES notation". Journal of Chemical Information and Modeling. 29 (2): 97. doi:10.1021/ci00062a008.
  • Helson, H.E. (1999). "Structure Diagram Generation". Rev. Comput. Chem. Vol. 13. New York: Wiley-VCH. pp. 313–398. doi:10.1002/9780470125908.ch6. {{cite book}}: Unknown parameter |editors= ignored (|editor= suggested) (help)

Other websites

Specifications


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