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Simplified Molecular Input Line Entry Specification which stems from traditional string notation of graphs and trees, e.g. the Newick notation. The acronym introduced by David Weininger to represent chemical valence model by a string (e.g. CC=O). It can also be used as an exchange format for chemical data. The algorithm was published in 1988 and is described in detail at the WWW site of Daylight Chemical Information Systems, Inc. http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html . Another description can also be found here: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification The SMILES notation allows one to represent a 2D chemical drawing as a string, (e.g. "C1CCCCC1" for cyclohexane ). The SMARTS notation is an extension of SMILES that allows one to specify chemical patterns with wildcards for atoms or bonds, e.g. "[C,N,O]?" . SMARTSSMARTS is an extension of the SMILES notation to include wildcards. This chemical patterns can be used in chemical queries and is described here: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html The primitives supported in ICM include the following (note that the atom primitives in general are in brackets, e.g. [Cl] for a chlorine atom):
Aromatic vs aliphatic
Note that uppercase atoms in SMARTS will only match aliphatic (not aromatic) atoms.
For example "C" will not match any atom in "c1ccccc1" (or "C1=CC=CC=C1") ring.
If you want to match both cases you should use [#
Recursive SMARTS
This SMARTS feature allows you to define "atomic enviroment" when matching. "Enviroment" atoms
will not be included into result match.
For example [C&!$(C=O)&!$(C#N)] will match any aliphatic carbon not double bonded to an oxygen and
not triple bonded to a nitrogen.
Example:
R-groups, attachment points, and chemical searches.
In reactions, Markush structures and building blocks two additional wildcards
are used:
See also:
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