On Thu, May 8, 2014 at 5:34 AM, Andrew Dalke <da...@dalkescientific.com>wrote:
> I want to evaluate the effectiveness of Open Babel's substructure screen
> fingerprint.
>
[...]
> I want to use the molecule as a query, and find all matches, then generate
> the fingerprint for the query and the targets and do a substructure screen.
> Then I can compare the screen count to the actual count.
>
[...]
> The problem is, this doesn't report any matches. I think that's because
> the "CC" in the query doesn't exactly match the "c-C" in the target - the
> ring carbon aromaticity gets in the way.
>
> 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.
Craig
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