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.
Using SMARTS, flexible and efficient substructure-search specifications can be made in terms that are meaningful to chemists. 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. 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.
Note that atomic primitive H can have two meanings, implying a property or the element itself. H] F O matches if chirality is as specified or is not specified 4. A missing bond symbol is interpreted as "single or aromatic". The logical operators are listed in order of decreasing precedence high precedence operators are evaluated first.
Examples: [CH2] aliphatic carbon with two hydrogens methylene carbon [! R0] same as above "! These expressions can be used in same manner as other atomic primitives also, they can be nested. SMARTS The semantics of the "zero-level" parentheses are that all of the atom and bond expressions within a set of zero-level parentheses must match within a single component of the target.
C CCCC. CCCC yes, the query does match carbons in two different components C. CCCC yes, the first two carbons match different components, the third matches a carbon anywhere These component-level grouping operators were added specifically for reaction processing.
