Trying to post my message again as there seems to be a problem with my
first attempt.

Hello all:

I am trying to perform a 2D alignment of molecules by using a pattern for
which I am using Compute2DCoords.

If I use a smarts string matching napthalene the 2D depiction is as one
would expect.
However, if I am switching to a 5,6 aromatic smarts pattern the matched
benzoxazol the 2D structure looks rather unusual.

Is there a way to match the 5,6 with the 6,6 pattern behavior?

Any hint is very much appreciated,


P.S. a work book is attached.

Attachment: 2dDepiction.ipynb
Description: Binary data

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