On Tue, Oct 27, 2009 at 8:29 AM, Mark Rijnbeek <email@example.com>
>So if I wrap this in OrChem, the way to use the SQT to match on aromatic
> Actually, I think this makes sense. The SQT does not know that the query
> is an actual molecule (i.e., completely defined SMILES). As a result,
> initialization of the query does not include aromaticity perception
> (which for SMARTS patterns in general, wouldn't be appropriate (?)).
> As a result, the query refers to an aliphatic C connected by a double
> bond to an aliphatic N - which is not the case in the target structure,
> after aromaticity has been perceived.
> Hence the failure to match
compounds would be to instruct users to set aromaticity explicitly in
their query structure, like with c1ccncn1. If a user relies on
aromaticity detection (like you can with SMILES), things may not work.