On Fri, Mar 22, 2013 at 1:25 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> One thing you could try is rather than use SMARTS to write some code
> to check for membership of the LSSR. I've never really looked into
> this, but it may be what you are looking for.
>
Another possibility: it looks trivially easy to change
OBAtom::MemberOfRingSize() to use the LSSR rather than the SSSR, which (as
I mentioned yesterday) should give correct results in all cases. Two
potential problems. FIrst, I'm 99% convinced that my graph-theory analysis
is correct, but not 100% sure (i.e. would changing from SSSR to LSSR really
work?). Second, the LSSR algorithm should in theory be faster than the
SSSR algorithm, but I don't know if in practice that's the case. I'd hate
to add a significant slowdown to SMARTS processing.
Craig
> - Noel
>
> On 21 March 2013 21:45, mbloodforsythe <martin.bloodforsy...@gmail.com>
> wrote:
> > I wasn't familiar with the shortcomings of SSSR identification, but it
> makes
> > complete sense. I know that Daylight determines 'R' membership using
> SSSR
> > (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html), so it
> seems
> > likely that the SMARTS default would be to determine 'r' using SSSR as
> well.
> >
> > Any thoughts on:
> > (a) how to track down if this is the issue?
> > (b) what to do about it other than just move to using OpenEye?
> >
> > Since I devoted quite a bit of time to developing scripts in PyBel for
> > processing these molecules I'd really like to stay within OpenBabel
> SMARTS
> > searching if I can.
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/5-membered-ring-SMARTS-matching-problem-tp4656088p4656090.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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