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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