On May 8, 2014, at 5:02 PM, Craig James wrote:
>> Is there any way I can ask Open Babel to generate a query which only
>> considers the atom element number, and not the aromaticity? Better yet, if
>> it considers the atom element number, and if the query charge != 0 then also
>> considers the charge?
>
> Replace every occurance of "c" or "C" with "[#6]". Inside brackets, same
> deal, e.g. replace [C@H] with [#6@H]. It's a little trickier with aromatic
> nitrogen, e.g. if you replace [nH] with [#7H], it won't match as a
> substructure if there's a non-H substituent, so you have to erase the H too.
If I understand correctly, you're suggesting that I turn the SMILES into a
SMARTS query.
That's something I can surely do, though it's not a solution for the faint at
heart.
My thought was that the ob.CompileMoleculeQuery /
ob.OBIsomorphismMapper.GetInstance was to make this sort of matching easier.
Andrew
da...@dalkescientific.com
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