I'm curious if anyone has figured out a way to compare two molecules based
upon their pharmacophore similarities. Specifically, I want to compare 2
molecules in their _absolute_ locations, and not simply see if they have 2
pharmacophores that match well via a translation/rotation. From what I can
see in the RDKit code the current implementation, whilst excellent, is
limited to distance matrices and not absolute coordinates.

My use-case is where I have aligned 2 molecules in some fashion and then
want to compare how similar their electrostatic surfaces/pharmacophores are
in that specific relative orientation. Think 'R0CS' color for RDKit, if
that helps. I appreciate that thinking about bringing more 3D functionality
to a cheminformatics toolkit may be heresy, but I'll run that risk.

My current nasty hack is to locate all pharmacophores in query/reference
molecules, assign coordinates and orientation to them, and loop over any
pharmacophoric patterns that both molecules contain.

Thanks in advance,
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