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SMILES Depiction Generator
GNU Lesser General Public License v2.1
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Aromatic display #81

Open JonasSchaub opened 4 months ago

JonasSchaub commented 4 months ago

Dear all, is aromatic display (like DepictionGenerator.withAromaticDisplay()) available in the CDK Depict web app? By default, it seems to be turned off (see below) and I could not find a setting to turn it on.

image

johnmay commented 4 months ago

Yes it is not an option because IUPAC does not recommend it in general. The main issue is around fusion bonds, i.e. you end up with what could be a triple bond (three lines drawn):

image

Also you can not do it on larger rings, like porphyrin - the ring in red is aromatic and can alternate:

image

Note it will turn on the delocalised if there is a kekulisation failure.

https://iupac.qmul.ac.uk/drawing/drawing.html

It is generally not acceptable to use curves in two adjacent fused rings, since such diagrams are at best ambiguous in terms of the character of the shared fusion bond between the two rings. If it is known that there is delocalization over only one ring in a fused ring system, a curve should be used for that ring only.

JonasSchaub commented 4 months ago

Thank you very much for the explanation and pointing out the IUPAC recommendations.