Just from the slides, it's not clear that Roger had a solution; the slides
seem to just suggest an approach. Am I missing something here?
That is, he defined the invariants that all tautomers of a compound have to
share and expressed it as a SMARTS + constraints; but I didn't see that he
provided a methodology to derive a canonical matching SMILES from a SMARTS
+ constraints. True, if two structures match the SMARTS + constraints, they
are likely tautomers. (I can't think of why they wouldn't be, but maybe
it's not always the case.) So that part provides deduplication of an input
stream, which is good, but no way to derive and store a canonical
representation.
Again, perhaps I'm missing something, but if so, what?
-P.
On Tue, Apr 11, 2017 at 2:43 AM, MARIA BRANDL <m.bra...@btinternet.com>
wrote:
> Dear all,
>
>
> Is there going to be an attempt at coding Roger Sayle's "Alternative
> Approach" to tautomers described in
> RDKit: Six Not-So-Easy Pieces [RDKit UGM 2016]
> <https://de.slideshare.net/NextMoveSoftware/rdkit-six-notsoeasy-pieces-rdkit-ugm-2016>
> into
> RDKit ?
>
>
> I have managed to get reasonable tautomers out of Resonance.cpp using:
>
> suppl =
> rdchem.ResonanceMolSupplier(m,rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION
> | \
>
> rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS
> | \
>
> rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS
> | \
> rdchem.ResonanceFlags.
> UNCONSTRAINED_ANIONS)
>
> with some post-filtering for e.g. carbocations, but feel that it may be
> more efficient to put user defined constraints on each atom during the
> backtracking loops, as Roger suggests.
>
> Looking forward to hearing your thoughts on this.
>
> Best regards,
>
> Maria Brandl
>
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