Greg and Brian,

Thank you for your useful hints. All the compounds that I want to align are
supposed to belong to the same analogue series so they should shave a
common substructure with substantial size.

What I want to emulate is the "core restrained docking" with glide, where
you specify the common core of the query and the reference ligand using a
SMARTS pattern and then glide docks the query compound to the binding
pocket but takes care to overlay the core atoms of the query to the core
atoms of the reference compound. Since RDKit does not do docking, I just
generate 30 conformers of each query compound and select the best one by
measuring the RMSD between the core of the query and the core of the
reference after the alignment. Of course the conformations of the core
atoms between the query and the reference are never identical hence the bad
alignment. Is there any smarter way to emulate the "core restrained
docking" with RDKit?

I will provide you with more info soon (example sdf, results, etc.).

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