Outstanding - thanks! This looks to be as close to what I wanted as I could
have dared hope. I had no idea where to even begin looking.

Fine work. Very fine.


On Fri, Oct 20, 2017 at 5:21 PM, Greg Landrum <>

> 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:
> 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:
> 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 <>
> 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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