Simplified molecular input line entry specification

The simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation

Line notation

Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature.Line notation is a word and symbol description of an electrochemical cell widely used in chemistry.-Chemistry:...

for describing the structure of chemical

Chemistry

Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....

molecule

Molecule

A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

s using short ASCII

ASCII

The American Standard Code for Information Interchange is a character-encoding scheme based on the ordering of the English alphabet. ASCII codes represent text in computers, communications equipment, and other devices that use text...

strings

String (computer science)

In formal languages, which are used in mathematical logic and theoretical computer science, a string is a finite sequence of symbols that are chosen from a set or alphabet....

. SMILES strings can be imported by most molecule editor

Molecule editor

A molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...

s for conversion back into two-dimensional drawings or three-dimensional

Dimension

In physics and mathematics, the dimension of a space or object is informally defined as the minimum number of coordinates needed to specify any point within it. Thus a line has a dimension of one because only one coordinate is needed to specify a point on it...

models of the molecules.

The original SMILES specification was developed by Arthur Weininger and David Weininger

David Weininger

David Weininger is a chemist and entrepreneur. He is a co-founder of Daylight Chemical Information Systems, a company in Santa Fe, New Mexico that does rapid analysis of massive chemical databases. Weininger is the inventor of Simplified Molecular Input Line Entry Specification , a universal...

in the late 1980s. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard

Open standard

An open standard is a standard that is publicly available and has various rights to use associated with it, and may also have various properties of how it was designed . There is no single definition and interpretations vary with usage....

called "OpenSMILES" was developed by the Blue Obelisk

Blue Obelisk

Blue Obelisk is an informal group of chemists who promote Open Data, Open Source, and Open Standards; it was initiated by Peter Murray-Rust and others in 2005...

open-source chemistry community. Other 'linear' notations include the Wiswesser Line Notation

Wiswesser Line Notation

Wiswesser Line Notation, also referred to as WLN, invented by William J. Wiswesser in 1949, was the first line notation capable of precisely describing complex molecules. It was the basis of ICI Ltd's CROSSBOW database system developed in the late 1960's...

(WLN), ROSDAL and SLN

SYBYL Line Notation

The SYBYL line notation or SLN is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings....

(Tripos Inc).

In July 2006, the IUPAC

International Union of Pure and Applied Chemistry

The International Union of Pure and Applied Chemistry is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science . The international headquarters of IUPAC is located in Zürich,...

introduced the InChI

International Chemical Identifier

The IUPAC International Chemical Identifier is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web...

as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical (e.g., graph theory

Graph theory

In mathematics and computer science, graph theory is the study of graphs, mathematical structures used to model pairwise relations between objects from a certain collection. A "graph" in this context refers to a collection of vertices or 'nodes' and a collection of edges that connect pairs of...

) backing.

Terminology

The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. The terms Canonical and Isomeric can lead to some confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive.

Typically, a number of equally valid SMILES can be written for a molecule. For example, CCO, OCC and C(O)C all specify the structure of ethanol

Ethanol

Ethanol, also called ethyl alcohol, pure alcohol, grain alcohol, or drinking alcohol, is a volatile, flammable, colorless liquid. It is a psychoactive drug and one of the oldest recreational drugs. Best known as the type of alcohol found in alcoholic beverages, it is also used in thermometers, as a...

. Algorithms have been developed to ensure the same SMILES is generated for a molecule regardless of the order of atoms in the structure. This SMILES is unique for each structure, although dependent on the canonicalisation algorithm used to generate it, and is termed the Canonical SMILES. These algorithms first convert the SMILES to an internal representation of the molecular structure and do not simply manipulate strings as is sometimes thought. Various algorithms for generating Canonical SMILES have been developed, including those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, and the Chemistry Development Kit

Chemistry Development Kit

The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...

. A common application of Canonical SMILES is indexing and ensuring uniqueness of molecules in a database

Chemical database

A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.- Chemical structures :...

.

SMILES notation allows the specification of configuration at tetrahedral centers

Molecular configuration

The configuration of a molecule is the permanent geometry that results from the spatial arrangement of its bonds. The ability of the same set of atoms to form two or more molecules with different configurations is stereoisomerism...

, and double bond geometry. These are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed Isomeric SMILES. A notable feature of these rules is that they allow rigorous partial specification of chirality. The term Isomeric SMILES is also applied to SMILES in which isotope

Isotope

Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation...

s are specified.

Graph-based definition

In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first

Depth-first search

Depth-first search is an algorithm for traversing or searching a tree, tree structure, or graph. One starts at the root and explores as far as possible along each branch before backtracking....

tree traversal

Tree traversal

In computer science, tree-traversal refers to the process of visiting each node in a tree data structure, exactly once, in a systematic way. Such traversals are classified by the order in which the nodes are visited...

of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree

Spanning tree (mathematics)

In the mathematical field of graph theory, a spanning tree T of a connected, undirected graph G is a tree composed of all the vertices and some of the edges of G. Informally, a spanning tree of G is a selection of edges of G that form a tree spanning every vertex...

. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree.

Atoms

Atom

The atom is a basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons...

s are represented by the standard abbreviation of the chemical element

Chemical element

A chemical element is a pure chemical substance consisting of one type of atom distinguished by its atomic number, which is the number of protons in its nucleus. Familiar examples of elements include carbon, oxygen, aluminum, iron, copper, gold, mercury, and lead.As of November 2011, 118 elements...

s, in square brackets, such as [Au] for gold

Gold

Gold is a chemical element with the symbol Au and an atomic number of 79. Gold is a dense, soft, shiny, malleable and ductile metal. Pure gold has a bright yellow color and luster traditionally considered attractive, which it maintains without oxidizing in air or water. Chemically, gold is a...

. Brackets can be omitted for the "organic subset" of B, C, N, O, P, S, F, Cl, Br, and I. All other elements must be enclosed in brackets. If the brackets are omitted, the proper number of implicit hydrogen atoms is assumed; for instance the SMILES for water

Water

Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...

is simply O.

An atom holding one or more electrical charge(s) is enclosed in brackets (whichever is), followed by the symbol H if it is bonded to one or more atoms of hydrogen (these ones are followed by their number so, except if there is one only: NH4 for ammonium

Ammonium

The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...

), then by the sign '+' for a positive charge or by '-' for an negative charge. Number of charges is specified after the sign (except if there is one only); however, it is also possible write the sign as many as the ion hold of charges: instead of "Ti+4", one can also write "Ti++++" (Titanium

Titanium

Titanium is a chemical element with the symbol Ti and atomic number 22. It has a low density and is a strong, lustrous, corrosion-resistant transition metal with a silver color....

IV, Ti⁴⁺). Thus, the hydroxide

Hydroxide

Hydroxide is a diatomic anion with chemical formula OH−. It consists of an oxygen and a hydrogen atom held together by a covalent bond, and carrying a negative electric charge. It is an important but usually minor constituent of water. It functions as a base, as a ligand, a nucleophile, and a...

anion is represented by [OH-], the oxonium

Oxonium ion

The oxonium ion in chemistry is any oxygen cation with three bonds. The simplest oxonium ion is the hydronium ion H3O+. Another oxonium ion frequently encountered in organic chemistry is obtained by protonation or alkylation of a carbonyl group e.g...

cation is [OH3+] and the cobalt

Cobalt

Cobalt is a chemical element with symbol Co and atomic number 27. It is found naturally only in chemically combined form. The free element, produced by reductive smelting, is a hard, lustrous, silver-gray metal....

III cation (Co³⁺) is either [Co+3] or [Co+++].

Bonds

Bonds between aliphatic

Aliphatic compound

In organic chemistry, aliphatic compounds are acyclic or cyclic, non-aromatic carbon compounds.Thus, aliphatic compounds are opposite to aromatic compounds.- Structure :...

atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES. For example the SMILES for ethanol

Ethanol

can be written as CCO. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES, which for cyclohexane

Cyclohexane

Cyclohexane is a cycloalkane with the molecular formula C6H12. Cyclohexane is used as a nonpolar solvent for the chemical industry, and also as a raw material for the industrial production of adipic acid and caprolactam, both of which being intermediates used in the production of nylon...

and dioxane can be written as C1CCCCC1 and O1CCOCC1 respectively. For a second ring, the label will be 2 (naphthalene

Naphthalene

Naphthalene is an organic compound with formula . It is a white crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromatic hydrocarbon, naphthalene's structure consists of a fused pair of benzene rings...

: c1cccc2c1cccc2), and so on. After 9, the label must be preceded by a '%', in order to differentiate it from two different labels bonded to the same atom (~C12~ will mean the atom of carbon hold the ring closure labels 1 and 2, whereas ~C%12~ will indicate one label only, the 12). Double, triple, and quadruple bonds

Chemical bond

A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...

are represented by the symbols '=', '#', and '$' respectively as illustrated by the SMILES O=C=O (carbon dioxide

Carbon dioxide

Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...

,) C#N (hydrogen cyanide,) and [Ga-]$[As+] (gallium arsenide).

Aromaticity

Aromatic

Aromaticity

In organic chemistry, Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. The earliest use of the term was in an article by August...

C, O, S and N atoms are shown in their lower case 'c', 'o', 's' and 'n' respectively. Benzene

Benzene

Benzene is an organic chemical compound. It is composed of 6 carbon atoms in a ring, with 1 hydrogen atom attached to each carbon atom, with the molecular formula C6H6....

, pyridine

Pyridine

Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It is structurally related to benzene, with one C-H group replaced by a nitrogen atom...

and furan

Furan

Furan is a heterocyclic organic compound, consisting of a five-membered aromatic ring with four carbon atoms and one oxygen. The class of compounds containing such rings are also referred to as furans....

can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1. Bonds between aromatic atoms are, by default, aromatic although these can be specified explicitly using the ':' symbol. Aromatic atoms can be singly bonded to each other and biphenyl

Biphenyl

Biphenyl is an organic compound that forms colorless crystals. It has a distinctively pleasant smell. Biphenyl is an aromatic hydrocarbon with a molecular formula 2...

can be represented by c1ccccc1-c2ccccc2. Aromatic nitrogen bonded to hydrogen, as found in pyrrole

Pyrrole

Pyrrole is a heterocyclic aromatic organic compound, a five-membered ring with the formula C4H4NH. It is a colourless volatile liquid that darkens readily upon exposure to air. Substituted derivatives are also called pyrroles, e.g., N-methylpyrrole, C4H4NCH3...

must be represented as [nH] and imidazole

Imidazole

Imidazole is an organic compound with the formula C3H4N2. This aromatic heterocyclic is a diazole and is classified as an alkaloid. Imidazole refers to the parent compound, whereas imidazoles are a class of heterocycles with similar ring structure, but varying substituents...

is written in SMILES notation as n1c[nH]cc1.

The Daylight and OpenEye algorithms for generating canonical SMILES differ in their treatment of aromaticity.

Branching

Branches are described with parentheses, as in CCC(=O)O for propionic acid

Propionic acid

Propanoic acid is a naturally occurring carboxylic acid with chemical formula CH3CH2COOH. It is a clear liquid with a pungent odor...

and C(F)(F)F for fluoroform

Fluoroform

Fluoroform is the chemical compound with the formula CHF3. It is one of the "haloforms", a class of compounds with the formula CHX3 . Fluoroform is used in diverse niche applications and is produced as a by-product of the manufacture of Teflon...

. Substituted rings can be written with the branching point in the ring as illustrated by the SMILES COc(c1)cccc1C#N (see depiction) and COc(cc1)ccc1C#N (see depiction) which encode the 3 and 4-cyanoanisole isomers. Writing SMILES for substituted rings in this way can make them more human-readable.

Stereochemistry

Configuration around double bonds is specified using the characters "/" and "\". For example, F/C=C/F (see depiction) is one representation of trans-difluoroethene, in which the fluorine atoms are on opposite sides of the double bond, whereas F/C=C\F (see depiction) is one possible representation of cis-difluoroethene, in which the Fs are on the same side of the double bond, as shown in the figure.

Configuration at tetrahedral carbon is specified by @ or @@. L-Alanine, the more common enantiomer

Enantiomer

In chemistry, an enantiomer is one of two stereoisomers that are mirror images of each other that are non-superposable , much as one's left and right hands are the same except for opposite orientation. It can be clearly understood if you try to place your hands one over the other without...

of the amino acid

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

alanine

Alanine

Alanine is an α-amino acid with the chemical formula CH3CHCOOH. The L-isomer is one of the 20 amino acids encoded by the genetic code. Its codons are GCU, GCC, GCA, and GCG. It is classified as a nonpolar amino acid...

can be written as N[C@@H](C)C(=O)O (see depiction). The @@ specifier indicates that, when viewed from nitrogen along the bond to the chiral center, the sequence of substituents hydrogen (H), methyl (C) and carboxylate (C(=O)O) appear clockwise. D-Alanine can be written as N[C@H](C)C(=O)O (see depiction). The order of the substituents in the SMILES string is very important and D-alanine can also be encoded as N[C@@H](C(=O)O)C (see depiction).

Isotopes

Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene

Benzene

Benzene is an organic chemical compound. It is composed of 6 carbon atoms in a ring, with 1 hydrogen atom attached to each carbon atom, with the molecular formula C6H6....

in which one atom is carbon-14

Carbon-14

Carbon-14, 14C, or radiocarbon, is a radioactive isotope of carbon with a nucleus containing 6 protons and 8 neutrons. Its presence in organic materials is the basis of the radiocarbon dating method pioneered by Willard Libby and colleagues , to date archaeological, geological, and hydrogeological...

is written as [14c]1ccccc1 and deuterochloroform is [2H]C(Cl)(Cl)Cl.

Application on some molecules

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate Methyl isocyanate Methyl isocyanate is an organic compound with the molecular formula CH3NCO. Synonyms are isocyanatomethane, methyl carbylamine, and MIC. Methyl isocyanate is an intermediate chemical in the production of carbamate pesticides . It has also been used in the production of rubbers and adhesives... (MIC)	CH₃–N=C=O	CN=C=O
Copper(II) sulfate	Cu²⁺ SO4^2-	[Cu+2].[O-]S(=O)(=O)[O-]
Œnanthotoxin Oenanthotoxin Oenanthotoxin is a toxin extracted from hemlock water dropwort and other plants of the genus Oenanthe. It is a central nervous system poison, and acts as a noncompetitive gamma-aminobutyric acid antagonist. This toxin played some role in euthanasia in ancient Sardinia, for inducing risus... (C₁₇H₂₂O₂)		CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
Pyrethrin Pyrethrin The pyrethrins are a pair of natural organic compounds that have potent insecticidal activity. Pyrethrins are neurotoxins that attack the nervous systems of all insects. When present in amounts not fatal to insects, they still appear to have an insect repellent effect. Pyrethrins are gradually... 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 Aflatoxin Aflatoxins are naturally occurring mycotoxins that are produced by many species of Aspergillus, a fungus, the most notable ones being Aspergillus flavus and Aspergillus parasiticus. Aflatoxins are toxic and among the most carcinogenic substances known... B1 (C₁₇H₁₂O₆)		O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5
Glucose Glucose Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate... (glucopyranose) (C₆H₁₂O₆)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1
Bergenin Bergenin Bergenin alias Cuscutin is trihydroxybenzoic acid glycoside. It is the C-glycoside of 4-O-methyl gallic acid. It possesses an O-demethylated derivative called norbergenin. These are chemical compounds and drugs of Ayurveda, commonly known as Paashaanbhed... (cuscutin) (a resin Resin Resin in the most specific use of the term is a hydrocarbon secretion of many plants, particularly coniferous trees. Resins are valued for their chemical properties and associated uses, such as the production of varnishes, adhesives, and food glazing agents; as an important source of raw materials... ) (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 Pheromone A pheromone is a secreted or excreted chemical factor that triggers a social response in members of the same species. Pheromones are chemicals capable of acting outside the body of the secreting individual to impact the behavior of the receiving individual... of the Californian scale insect Scale insect The scale insects are small insects of the order Hemiptera, generally classified as the superfamily Coccoidea. There are about 8,000 species of scale insects.-Ecology:...		CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C
2S,5R-Chalcogran: a pheromone Pheromone A pheromone is a secreted or excreted chemical factor that triggers a social response in members of the same species. Pheromones are chemicals capable of acting outside the body of the secreting individual to impact the behavior of the receiving individual... of the bark beetle Pityogenes chalcographus		CC[C@H](O1)CC[C@@]12CCCO2
Vanillin Vanillin Vanillin is a phenolic aldehyde, an organic compound with the molecular formula C8H8O3. Its functional groups include aldehyde, ether, and phenol. It is the primary component of the extract of the vanilla bean. It is also found in Leptotes bicolor, roasted coffee and the Chinese red pine...		O=Cc1ccc(O)c(OC)c1
Melatonin Melatonin Melatonin , also known chemically as N-acetyl-5-methoxytryptamine, is a naturally occurring compound found in animals, plants, and microbes... (C₁₃H₁₆N₂O₂)		CC(=O)NCCC1=CNc2c1cc(OC)cc2
Flavopereirin (C₁₇H₁₅N₂)		CCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4
Nicotine Nicotine Nicotine is an alkaloid found in the nightshade family of plants that constitutes approximately 0.6–3.0% of the dry weight of tobacco, with biosynthesis taking place in the roots and accumulation occurring in the leaves... (C₁₀H₁₄N₂)		CN1CCC[C@H]1c2cccnc2
Alpha-thujone Thujone Thujone is a ketone and a monoterpene that occurs naturally in two diastereomeric forms: -α-thujone and -β-thujone. It has a menthol odor. Even though it is best known as a chemical compound in the spirit absinthe, recent tests show absinthe contains only small quantities of thujone, and may or may... (C₁₀H₁₆O)		CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2
Thiamin (C₁₂H₁₇N₄OS⁺) (vitamin B1)		OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2

Illustration with a molecule with more of 9 rings, the Cephalostatin-1 (a steroidic trisdecacyclic pyrazine

Pyrazine

Pyrazine is a heterocyclic aromatic organic compound with the chemical formula C4H4N2.Pyrazine is a symmetrical molecule with point group D2h. Derivatives like phenazine are well known for their antitumor, antibiotic and diuretic activity. Pyrazine is less basic in nature than pyridine, pyridazine...

with the empirical formula

Empirical formula

In chemistry, the empirical formula of a chemical compound is the simplest positive integer ratio of atoms of each element present in a compound. An empirical formula makes no reference to isomerism, structure, or absolute number of atoms. The empirical formula is used as standard for most ionic...

C₅₄H₇₄N₂O₁₀ isolated from the Indian Ocean

Indian Ocean

The Indian Ocean is the third largest of the world's oceanic divisions, covering approximately 20% of the water on the Earth's surface. It is bounded on the north by the Indian Subcontinent and Arabian Peninsula ; on the west by eastern Africa; on the east by Indochina, the Sunda Islands, and...

hemichordate Cephalodiscus gilchristi):
Will give, starting by the left-most methyl group on the figure:

C[C@@](C)(O1)C[C@@H](O)[C@@]1(O2)[C@@H](C)[C@@H]3CC=C4[C@]3(C2)C(=O)C[C@H]5[C@H]4CC[C@@H](C6)[C@]5(C)Cc(n7)c6nc(C[C@@]89(C))c7C[C@@H]8CC[C@@H]%10[C@@H]9C[C@@H](O)[C@@]%11(C)C%10=C[C@H](O%12)[C@]%11(O)[C@H](C)[C@]%12(O%13)[C@H](O)C[C@@]%13(C)CO

(Notice the '%' in front of the index of the ring closure labels upper to 9, see the section "Bonds", higher).

Other examples of SMILES

The SMILES notation is described extensively in the SMILES theory manual provided by Daylight Chemical Information Systems and a number of illustrative examples are presented. Daylight's depict utility provides users with the means to check their own examples of SMILES and is a valuable educational tool.

Extensions

SMARTS

Smiles arbitrary target specification

SMiles ARbitrary Target Specification is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing....

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

Wildcard character

-Telecommunication:In telecommunications, a wildcard character is a character that may be substituted for any of a defined subset of all possible characters....

atoms and bonds, which can be used to define substructural queries for chemical database

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 subgraph isomorphism

Isomorphism

In abstract algebra, an isomorphism is a mapping between objects that shows a relationship between two properties or operations. If there exists an isomorphism between two structures, the two structures are said to be isomorphic. In a certain sense, isomorphic structures are...

. SMIRKS is a line notation for specifying reaction transforms.

Conversion

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

Terminology

Graph-based definition

Atoms

Bonds

Aromaticity

Branching

Stereochemistry

Isotopes

Application on some molecules

Other examples of SMILES

Extensions

Conversion

See also

Specifications

SMILES related software utilities