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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