Thanks Greg!
I found an alternative solution which is also no so straightforward.
I set an isotope label to aromatic atoms, generate isomeric SMILES and
make regex replacement.
But your suggestion to set remove hydrogens is important, since this
can cause other ambiguity.
import re
Hi Pavel,
It is, unfortunately, not that easy.
The canonicalization algorithm does not use atomic aromaticity when
determining atom ordering, so as far as it is concerned there is no
difference between atoms 0 and 2 in either of your examples. What does get
used is the number of hydrogens, so you
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