Assuming I'm understanding correctly what you're asking for, the RDKit
actually has code for doing exactly this. That's the good news. The bad
news is that there's pretty much no documentation for it.

Since it's kind of interesting code (at least I think so) and it came up in
an earlier conversation I had this week, I put together a little example:
https://gist.github.com/greglandrum/e6e6b011648af0484ff91bdfafaa704f

This is using the RDKit's FeatMap functionality. This is described as part
of the Feature Map Vector paper and in some of the references therein:
https://link.springer.com/article/10.1007/s10822-006-9085-8

The general idea is to create a feature map from the features on one
molecule and then score the features from the other molecule against that.
The scores are normalized by the number of features in the smaller feature
map (there's likely a smarter way to do this).

I hope this doesn't create more questions than it answers; I will try to do
a somewhat longer writeup, but I wanted to at least get something minimal
out there quickly.

-greg




On Fri, Oct 20, 2017 at 4:58 PM, Andy Jennings <andy.j.jenni...@gmail.com>
wrote:

> Hi,
>
> 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,
> Andy
>
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