Hi Noel,
Thanks for looking into this ... I'm on vacation right now but I'll try to
get back to it when I return after the 18th. I looked through the tautomer
code briefly, but nothing jumped out at me. The tautomer code requires a
bit of study and doesn't yield to a quick look.
Craig
On Fri, Jun 8, 2012 at 4:03 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> I'm not going to spend any more time on this now, but as a brief
> update, tautomer test will pass if the molecules are copied before
> writing out as "can". I can only assume that this is because of
> reperception of some property which invalidates some assumption in the
> tautomer code. This code uses a functor, or what I would call a
> callback, so that the call to "can" occurs right in the middle of
> tautomer processing.
>
> Anyway, changing
>
> conv.SetOutFormat("can");
> tautomers.push_back(conv.WriteString(mol));
>
> to
>
> conv.SetOutFormat("can");
> OBMol mol2 = *mol;
> tautomers.push_back(conv.WriteString(&mol));
>
> in the functor allows the test to pass (along with a similar change
> elsewhere in the test). The underlying problem should be identified
> and fixed though.
>
> - Noel
>
> On 8 June 2012 10:15, Noel O'Boyle <baoille...@gmail.com> wrote:
> > I've edited the SMILES writer so that it doesn't add hydrogens to
> > chiral centers (and fixed the resulting problems)...but tautomer test
> > is still failing.
> >
> > - Noel
> >
> > On 30 May 2012 16:29, Craig James <cja...@emolecules.com> wrote:
> >> Hi Tim,
> >>
> >> When I reverted the SMILES canonicalizer (that is,
> >> SMIBaseFormat::WriteMolecule()) back so that it doesn't copy the
> molecule, I
> >> solved the performance problem, but it causes the Tautomer Test to fail.
> >> I've looked through your tautomer code briefly, but before I spend a
> great
> >> deal of time figuring it all out, I wonder if you can spot the problem
> >> quickly since you wrote the tautomer code.
> >>
> >> My guess is that the SMILES canonicalizer screws up your tautomer code
> >> because it adds explicit hydrogens to chiral centers (mostly for
> convenience
> >> so that there would always be four bonds to every tetrahedral center),
> which
> >> understandably would alter the nature of what the tautomer generator is
> >> doing.
> >>
> >> So the first question: Does the SMILES canonicalizer still need to add
> >> explicit hydrogens to the chiral atoms? You rewrote all of the stereo
> code,
> >> and I wonder if the extra hydrogens are even necessary. I looked
> through
> >> the graphsym.cpp can canon.cpp files and couldn't see any need for the
> >> explicit hydrogens. I might try disabling the add-explicit-hydrogens
> >> feature and see if the tests still pass, but I prefer a more analytical
> >> approach.
> >>
> >> Second question: Is there some reason why the tautomer code gets
> screwed up
> >> by the added explicit hydrogens? Is it something that could be fixed
> >> easily?
> >>
> >> I'm going to dig around an older version of smilesformat.cpp and
> canon.cpp
> >> to refresh my memory about where the explicit hydrogens were needed.
> >>
> >> Thanks,
> >> Craig
> >>
> >>
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