On Fri, May 2, 2014 at 3:52 PM, Stephen O'hagan <soha...@manchester.ac.uk>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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