Let me know when it’s available.
Cheers,
Steve.
From: Greg Landrum [mailto:[email protected]]
Sent: 02 May 2014 15:00
To: Stephen O'hagan
Cc: [email protected]
Subject: Re: [Rdkit-discuss] 3D-Pharmacophore fingerprints ?
On Fri, May 2, 2014 at 3:52 PM, Stephen O'hagan
<[email protected]<mailto:[email protected]>> wrote:
Hi Greg,
Should that be :
dm = Chem.GetDistanceMatrix(mol)
nope, that's the 2D (topological) distance matrix that is generated by default.
I can find no Get3DDistanceMatrix defined?
It is, unfortunately, a new feature. It's in the github version of the rdkit
and will be in the next release (available next week).
For a list of molecules, do we recalculate the dm for each one, or do we use
one molecule’s dm as a ‘reference’?
You would calculate it for each one.
Without trawling through the source code, I’m not clear what’s actually being
done here as the documentation is a bit Spartan.
Is there any reference to a journal article?
Not really.
The best that's available is this:
https://github.com/rdkit/rdkit/blob/master/Docs/Code/Chem/Pharm2D.signatures.jpg
which shows how the bits are determined based on a set of feature definitions
and distance bins.
-greg
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