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==History==
The original SMILES specification was initiated by [[David Weininger]] at the USEPA Mid-Continent Ecology Division Laboratory in [[Duluth, Minnesota|Duluth]] in the 1980s.<ref name="Weininger-1988">{{cite journal| vauthors = Weininger D | title=SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules| journal=Journal of Chemical Information and Computer Sciences| volume=28| issue= 1|pages=31–6|date=February 1988|doi=10.1021/ci00057a005 }}</ref><ref name="Weininger-1989">{{cite journal| vauthors = Weininger D, Weininger A, Weininger JL | title=SMILES. 2. Algorithm for generation of unique SMILES notation| journal=Journal of Chemical Information and Modeling| volume=29| issue=2| pages=97–101|date=May 1989|doi=10.1021/ci00062a008 }}</ref><ref name="Weininger-1990">{{cite journal| vauthors = Weininger D | title=SMILES. 3. DEPICT. Graphical depiction of chemical structures| journal=Journal of Chemical Information and Modeling| volume=30| issue= 3|pages=237–43|date=August 1990|doi=10.1021/ci00067a005 }}</ref><ref name="Swanson-2004">{{cite book | vauthors = Swanson RP | veditors = Rayward WB, Bowden ME |title=The History and Heritage of Scientific and Technological Information Systems: Proceedings of the 2002 Conference of the American Society of Information Science and Technology and the Chemical Heritage Foundation |date=2004 |publisher=[[Information Today]] |___location=Medford, NJ |isbn=
It has since been modified and extended by others, most notably by [[Daylight Chemical Information Systems]]. In 2007, an [[open standard]] called "OpenSMILES" was developed by the [[Blue Obelisk]] open-source chemistry community. Other 'linear' notations include the [[Wiswesser Line Notation]] (WLN), [[ROSDAL]] and [[SYBYL Line Notation|SLN]] (Tripos Inc).
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[[Smiles arbitrary target specification|SMARTS]] is a line notation for specification of substructural patterns in molecules. While it uses many of the same symbols as SMILES, it also allows specification of [[Wildcard character|wildcard]] atoms and bonds, which can be used to define substructural queries for [[chemical database]] searching. One common misconception is that SMARTS-based substructural searching involves matching of SMILES and SMARTS strings. In fact, both SMILES and SMARTS strings are first converted to internal graph representations which are searched for [[Glossary of graph theory#Subgraphs|subgraph]] [[isomorphism]].
{{anchor|SMIRKS}}SMIRKS, a superset of "reaction SMILES" and a subset of "reaction SMARTS", is a line notation for specifying reaction transforms. The general syntax for the reaction extensions is <code>REACTANT>AGENT>PRODUCT</code> (without spaces), where any of the fields can either be left blank or filled with multiple molecules deliminated with a dot (<code>.</code>), and other descriptions dependent on the base language. Atoms can additionally be identified with a number (e.g. <code>[C:1]</code>) for mapping,<ref>{{cite web |title=SMIRKS Tutorial |url=http://daylight.com/dayhtml_tutorials/languages/smirks/ |
SMILES corresponds to discrete molecular structures. However many materials are macromolecules, which are too large (and often stochastic) to conveniently generate SMILES for. BigSMILES is an extension of SMILES that aims to provide an efficient representation system for macromolecules.<ref>{{cite journal | vauthors = Lin TS, Coley CW, Mochigase H, Beech HK, Wang W, Wang Z, Woods E, Craig SL, Johnson JA, Kalow JA, Jensen KF, Olsen BD | display-authors = 6 | title = BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules | journal = ACS Central Science | volume = 5 | issue = 9 | pages = 1523–1531 | date = September 2019 | pmid = 31572779 | pmc = 6764162 | doi = 10.1021/acscentsci.9b00476 }}</ref>
== Conversion ==
SMILES can be converted back to two-dimensional representations using structure diagram generation (SDG) algorithms.<ref name="Helson-1999">{{cite book | vauthors = Helson HE | year = 1999 | chapter = Structure Diagram Generation | title
== See also ==
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