I'm still unsure on this but I believe it is correct. Consider biphenyl - a
bond between aromatic atoms is not always aromatic. We could perhaps say
then a bond between aromatic atoms that is in a ring is aromatic but then
consider biphenylene?
In your example it is the outer envelope ring that
Actually I misread what you originally quoted. I'm not sure why (if it is)
the listeners that're causing a problem. I still can't figure out whether
it's a genuine Thread collision, or if it's an iterator having an
addition/removal somewhere. The stack trace seems to point to the
listeners
Ok, I'll give in my modified version of the original CDK method I obtained
(forgot how). Be warned though - there're a lot of hacks in this because
basically - AMBIT SMARTS had issues regarding implicit hydrogens, and when
you are dealing with SMARTS atom types I did the minimum necessary to get
Just to put everyone on the same page the issue is when to mark a bond
between two aromatic atoms as aromatic? Consider the following where the
fused bond is always single and not in an aromatic ring (only the outer
ring is 4n+2).
[image: Inline images 1][image: Inline images 2]
[image: Inline
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