From: Rajarshi G. <raj...@gm...> - 2009-10-27 12:43:31
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On Tue, Oct 27, 2009 at 8:29 AM, Mark Rijnbeek <ma...@eb...> wrote: > > > > 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 > > > > So if I wrap this in OrChem, the way to use the SQT to match on aromatic > 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. > Correct -- Rajarshi Guha NIH Chemical Genomics Center |