Tuesday, February 15, 2011

An acronym in cheminformatics: ANC for atomic node code

An atomic node code (ANC) is part of a SMILES or CurlySMILES notation. The latter are linear notations that encode a molecular structure based on the associated hydrogen-suppressed molecular graph. Such a linear notation is a sequence of ANCs and may additionally contain special symbols to represent bonds and indicate branching as well as ring formation. Notations are further enhanced via CurlySMILES by inserting annotations after particular ANCs to add detailed molecular information or to modify it.

A typical ANC represents a non-hydrogen atom along with the attached hydrogen atoms and can include an isotopical label and/or a formal charge. For example, the notation [13CH4] consists of a single ANC encoding methane-13C.

The CurlySMILES notation SCC{R}(N)C(=O)O for the amino acid (R)-2-amino-3-sulfanylpropanoic acid (L-Cysteine) consists of seven ANCs. The third ANC, representing the asymmetric C-atom of the molecule, is followed by a stereodescriptor annotation to specify the particular enantiomer.

[1] Axel Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. Journal of Cheminformatics 2011, 3:1.
DOI: 10.1186/1758-2946-3-1.
[2] Axel Drefahl: The CurlySMILES Project [www.axeleratio.com/csm/proj/main.htm].

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