Yep you are right. Looking a bit deeper I found that it was to do with checking if there were any atoms in an unsaturated ring of a certain size. The second one finds there is an unsaturated ring of size 6 (Bit 181) where as the first one does not. 


On 14 Dec 2012, at 06:55, Egon Willighagen <> wrote:

On Thu, Dec 13, 2012 at 7:52 PM, John May <> wrote:
Say for example we query the structures for the following fragment

BTW, these two fragments are both present in both structures...


Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (

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