In working with RDKit I've been able to align 2D structures based upon a
common core of MCS using
AllChem.GenerateDepictionMatching2DStructure(m,p)
The next step for me is to generate 3D structures and align them based upon
that same common core. Obviously this leads to multiple steps, not the
least of which is generating conformations that are consistent across the
common core for the various molecules. I seem to recall the ability to
generate a conformation and minimize it (either UFF or MMFF) and apply
constraints based upon an input substructure, but I cannot find the details.
Any tips to accomplish this one?
-Kirk
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