> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such
> way that the bond orders are no longer dependent on the way the molecule was
> entered? For example, the two smiles representations of the indole ring,
> N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12,
First off, I need to point out that your SMILES are hydrogen deficient. Both
nitrogens should have explicit Hs.
But yes, this is a bug in kekulize.cpp. I'll try to take a look later this week
-- I had a range of indole SMILES tests, but not with the explicit
single/double pattern.
-Geoff
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