Dear Masgils,
you might look into using
AllChem.ConstrainedEmbed()
and supplying pre-generated 3D coordinates for your 6-membered chair (or
boat) ring conformations; see the example below where I constrain the
piperidine ring in bilastine to have a chair conformation.
You might need
Dear RDKitters,
I want all the nonplanar rings in a group of compounds to have the same
conformation.The goal is to make the rings perfectly aligned.
In RDkit, the boat and chair conformations generated by AllChem.EmbedMolecule()
will have different bond lengths and angles depending on the
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