Simplified molecular input line entry specification
||The English used in this article may not be easy for everybody to understand. (September 2011)|
The simplified molecular input line entry specification or SMILES is a line notation for the chemical structure of molecules. It uses a short series ASCII characters to represent structures. Most molecule editor computer programs can draw a two-dimensional diagram or a three-dimensional model of a molecule based on its SMILES code.
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".
In July 2006, the IUPAC introduced the InChI as a standard line notation for representing chemical structures. People think that it is easier for humans to understand SMILES than InChI. Some chemists argue that SMILES is better than InChI because many different software programs support it. SMILES also has theoretical (for example, graph theory) backing.
Conversion[change | change source]
SMILES can be converted back to 2-dimensional representations using Structure Diagram Generation algorithms. This conversion can sometimes be ambiguous. Because SMILES just says which atoms are connected without any information about the angles between chemical bonds, computer programs use energy minimization to convert SMILES to 3-dimensional representations. There are many downloadable and web-based conversion utilities.
Examples[change | change source]
Here are some examples of the SMILES for molecules:
|Methyl isocyanate (MIC)||CH3–N=C=O||CN=C=O|
|Copper(II) sulfate||Cu2+ SO42-||[Cu+2].[O-]S(=O)(=O)[O-]|
|Pyrethrin II (C22H28O5)||COC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=C|
|Aflatoxin B1 (C17H12O6)||O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5|
|Glucose (glucopyranose) (C6H12O6)||OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1|
|Bergenin (cuscutin) (a resin) (C14H16O9)||OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2|
|A pheromone of the Californian scale insect||CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C|
|2S,5R-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographus||CC[C@H](O1)CC[C@@]12CCCO2|
References[change | change source]
- Helson, H.E. (1999). "Structure Diagram Generation". In Lipkowitz, K. B. and Boyd, D. B.. Rev. Comput. Chem.. 13. New York: Wiley-VCH. pp. 313–398. .
- Isolation of Pheromone Synergists of Bark Bettle, Pityogenes chalcographus, From Complex Insect-Plant Odors by Fractionation and Subtractive-Combination Bioassay
- 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.
- 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.
- 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.
- Helson, H.E. (1999). "Structure Diagram Generation". In Lipkowitz, K. B. and Boyd, D. B.. Rev. Comput. Chem.. 13. New York: Wiley-VCH. pp. 313–398.
Other websites[change | change source]
Specifications[change | change source]
- "SMILES - A Simplified Chemical Language"
- The OpenSMILES home page
- "SMARTS - SMILES Extension"
- Daylight SMILES tutorial
- Parsing SMILES
[change | change source]
- NCI/CADD Chemical Identifier Resolver – resolves or generates SMILES from chemical names, CAS Registry Numbers, InChI/InChIKey and many other chemical structure file formats
- NCI/CADD Online SMILES Translator and Structure File Generator – Java online molecule editor
- PubChem server side structure editor – online molecule editor
- smi23d – 3D Coordinate Generation
- Daylight Depict – Translate a SMILES formula into graphics
- GIF/PNG-Creator for 2D Plots of Chemical Structures
- JME molecule editor
- Marvin by ChemAxon – online chemical editor/viewer and SMILES generator/converter
- Instant JChem by ChemAxon – desktop application for storing/generating/converting/visualizing/searching SMILES structures, particularly batch processing; personal edition free
- JChem for Excel by ChemAxon – MS Excel add-in for storing/generating/converting/visualizing/searching SMILES structures
- Smormo-Ed – a molecule editor for Linux which can read and write SMILES
- InChI.info – an unofficial InChI website featuring on-line converter from InChI and SMILES to molecular drawings
- Balloon – A free program for 3D coordinate generation and conformational analysis.
- Indigo – an open-source cross-platform cheminformatics library with a plugin for IUPAC-compliant molecule and reaction 2D structural formula rendering.
- Open Babel – an open-source chemical toolbox allowing anyone to search, convert, analyze, or store biochemical data.
- Bioclipse – a free and open source workbench for the life sciences
- MolEngine – A .NET cheminformatics toolkit to read/write SMILES, generate 2D coordinate from SMILES, and convert SMILES from/into other Chemical file formats.