SMARTS...
...means SMiles ARbitrary Target Specification
...is a language used for describing molecular patterns and properties
...rules are straightforward extensions of SMILES
- All SMILES symbols and properties are legal in SMARTS.
- SMARTS includes logical operators and additional molecular descriptors
...can describe structural patterns with varying degrees of specificity and generality:
- SMILES for methane: C or [CH4]
- High specificity SMARTS describing a pattern consistent with methane: [CH4]
Only matches aliphatic carbon atoms that have 4 hydrogens.
Won't match ethane, ethene, or cyclopentane.
- Low specificity SMARTS describing a pattern consistent with methane: C
Matches aliphatic carbon atoms that have any number of hydrogens.
Will match ethane, ethene, and cyclopentane.
 

Introduction

Substructure searching, the process of finding a particular pattern (subgraph) in a molecule (graph), is one of the most important tasks for computers in chemistry. It is used in virtually every application that employs a digital representation of a molecule, including depiction (to highlight a particular functional group), drug design (searching a database for similar structures and activity), analytical chemistry (looking for previously-characterized structures and comparing their data to that of an unknown), and a host of other problems.

SMARTS is a language that allows you to specify substructures using rules that are straightforward extensions of SMILES. For example, to search a database for phenol-containing structures, one would use the SMARTS string "[OH]c1ccccc1", which should be familiar to those aquainted with SMILES. In fact, almost all SMILES specifications are valid SMARTS targets (see "SMARTS Exceptions," below). Using SMARTS, flexible and efficient substructure-search specifications can be made in terms that are meaningful to chemists.

In the SMILES language, there are two fundamental types of symbols: atoms and bonds. Using these SMILES symbols, once can specify a molecule's graph (its "nodes" and "edges") and assign "labels" to the components of the graph (that is, say what type of atom each node represents, and what type of bond each edge represents).

The same is true in SMARTS: One uses atomic and bond symbols to specify a graph. However, in SMARTS the labels for the graph's nodes and edges (its "atoms" and "bonds") are extended to include "logical operators" and special atomic and bond symbols; these allow SMARTS atoms and bonds to be more general. For example, the SMARTS atomic symbol [C,N] is an atom that can be aliphatic C or aliphatic N; the SMARTS bond symbol "~" (tilde) matches any bond.

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