> > It doesn't work, but does work if you remove the [H]. The Universal
> > Isomorphism Tester looks to be the culprit, getSubgraphMaps does not
> > give a list back. I was wondering if this is expected behaviour.
>
>
> I think this behavior is also an issue with the SMARTS query tool as
> [H] does not match [H] - which does not invoke the UIT
>
I think the problem with a leading explicit hydrogen is actually a problem
with the CDK AtomContainer. For example, I have found out that
AtomContainerManipulator.removeHydrogens(IAtomContainer)
will not remove a leading explicit Hydrogen (and a few others that I have
not discovered a pattern for yet).
Interestingly, daylight's depictmatch service also won't match the
original poster's query, but I believe that to be for other reasons
(perhaps having to do with the interplay between the leading Hydrogen and
the chiral carbon).
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