Simplified Molecular Input Line Entry System: Difference between revisions

Revision as of 02:00, 21 May 2023

Revision as of 01:25, 16 June 2023

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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&gt;AGENT&gt;PRODUCT</code> (without spaces), where any of the fields can either be left blank or filled with multiple molecules deliminateddelineated 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/ | publisher = Daylight Chemical Information Systems, Inc. |access-date=29 October 2018}}</ref> for example in .<ref>{{cite web |title=Reaction SMILES and SMIRKS |url=http://www.daylight.com/meetings/summerschool01/course/basics/smirks.html |access-date = 29 October 2018 | publisher = Daylight Chemical Information Systems, Inc. }}</ref>

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>