Hi Greg, Thanks very much for the link to the documentation and for the explanation - yes I think it makes sense…
I just noticed this because I found other toolkits have the exact opposite behaviour. I can see the point of view from both sides. With other toolkits, we can search for chirally pure molecules; however, in RDKit we cannot (e.g. using @ in a query would return @, OR and AND). Also it seems with RDKit, using a more general query e.g. OR, gives fewer hits than a more restrictive query e.g. ABS. Best wishes, Susan On Wed, Jul 20, 2022 at 1:32 PM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Susan, > > The expected behavior for substructure search with enhanced stereo is > documented here: > > https://www.rdkit.org/docs/RDKit_Book.html#enhanced-stereochemistry-and-substructure-search > > A quick explanation of the logic, assuming a single stereocenter for > simplicity: > - OR contains either the @ or the @@ form > - AND contains both the @ and the @@ form. > > So OR is automatically a substructure of AND, but AND can never be a > substructure of OR. > ABS is clearly a substructure of AND (but not vice versa) > whether or not ABS is a subset of OR isn't obvious; the code currently > says that it is, but one could argue the other way > > Does that make sense? > > -greg > > > On Wed, Jul 20, 2022 at 2:11 PM Susan Leung <susanhle...@gmail.com> wrote: > >> Hi all, >> >> >> >> I am trying to do substructure search, taking into account enhanced >> stereochemistry using the postgres cartridge. >> >> >> >> I am finding : >> >> with an absolute query, it matches AND stereochemistry and OR >> stereochemistry, >> >> With an OR query it matches AND stereochemistry, >> >> With an AND query it matches neither. >> >> >> >> Is this expected? Or please can anyone clarify the expecting behaviour >> with rdkit.do_enhanced_stereo_sss=true? (Or point me to some >> documentation if I've missed it!) >> >> >> Thanks! >> >> >> Susan >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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