Dear RDKiters,
I would like to be able to generate all Kekule forms or resonance isomers of a
species.
Eg. starting with
I would like to generate both of these
Is this possible with RDKit? How would you do it?
For systems like this I can think of a hacky work-around to post-process the
result of a Kekulize call (swap all the single and double bonds around the
aromatic ring), but for fused rings it would be a little harder.
Secondly (and this may be a separate issue, and is of less urgency) it would be
nice if I could represent these with distinct SMILES-like strings. I say
“SMILES-like" because the strict Daylight SMILES spec may insist that they are
all the same SMILES. But I would like to be able to represent those three forms
of 2-Hydroxy-1-methylbenzene as Cc1ccccc1O, CC1C=CC=CC=1O and CC1=CC=CC=C1O
respectively.
Any ideas?
Thanks,
Richard
--
Richard H. West, Ph.D.
Assistant Professor, Department of Chemical Engineering,
Northeastern University, 360 Huntington Ave, Boston, MA 02115
http://neu.edu/comocheng Phone: 617-373-5163
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