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Friday, September 28, 2007

SMILES to become an Open Standard

Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.

Illustrative is my confusion about the sp2 hybridized atoms, which use lower case element symbols in SMILES. Very often this is seen as indicating aromaticity. I have written up the arguments supporting both views in the CDK wiki. I held the position that lower case elements indicated sp2 hybridization, and the CDK SMILES parser was converted accordingly some years ago. A recent discussion, however, stirred up the discussion once more (which led to the aforementioned wiki page).

You can imagine my excitement when I looked up the meaning in the new draft. It states: The formal meaning of a lowercase "aromatic" element in a SMILES string is that the atom is in the sp2 electronic state. When generating a normalized SMILES, all sp2 atoms are written using a lowercase first character of the atomic symbol. When parsing a SMILES, a parser must note the sp2 designation of each atom on input, then when the parsing is complete, the SMILES software must verify that electrons can be assigned without violating the valence rules, consistent with the sp2 markings, the specified or implied hydrogens, external bonds, and charges on the atoms..