Tuesday, February 15, 2011

An acronym in cheminformatics: SQC for square bracket code

SQC stands for square bracket code; precisely, for square bracket atomic code. AN SQC is a special type of an atomic node code (ANC).

In a SMILES and CurlySMILES notation an SQC encodes a node of the hydrogen-supressed molecular graph. SQC is mandatory for any non-hydrogen atom that does not belong to the organic subset and that has a hydrogen count which differs from the implicit hydrogen attachment assuming that hydrogen atoms make up the remainder of an atom's lowest normal valence, consistent with explicit bond specification: 3, 4, 3, 2, 1 for B, C, N, O, and the halogen atoms, respectively, 3 or 5 for phosphorus and 2, 4, or 6 for aliphatic sulfur atoms. Isotopically labelled atoms and nodes with formal charge specification always have to be SQC-endoded. In CurlySMILES, atomic-wildcard nodes and atoms with an incident quadruple or unspecified bond also have to be SQC-encoded.

[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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