On Tue, Nov 10, 2009 at 9:32 AM, Loren Lenzen <[email protected]> wrote:
>
> > > 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).
>
Actually I had found the problem, at least for [H] as a SMARTS query (I had
replied privately to Mark). Basically the match() method of HydrogenAtom
does not catch the case of a single H, with no charge.
It catches a proton, a H bonded to something else (even another H) a
deuterium (so [H] will match a [2H]) and so on, but fails to ctach neutral
atomic H.
It's an easy fix, but I'm wondering whether this is a bug or whether there
was a reason not to match this case
--
Rajarshi Guha
NIH Chemical Genomics Center
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