Re: [Rdkit-discuss] Highlighting Gobbi Pharmacophore Elements

[Greg L. <gre...@gm...>]

Hi Andy,

Great question.
The functionality to get the atoms involved in a bit from a 2D
pharmacophore fingerprint is missing from the currently released version of
the RDKit. Fortunately it was easy to add.

Here's how the new code works using the example from the documentation:

In [7]: m = Chem.MolFromSmiles('OCC=CC(=O)O')

In [8]: bi = {}

In [9]: fp = Generate.Gen2DFingerprint(m,Gobbi_Pharm2D.factory,bitInfo=bi)

In [10]: list(fp.GetOnBits())
Out[10]: [23, 30, 150, 154, 157, 185, 28878, 30184]

In [11]: Gobbi_Pharm2D.factory.GetBitDescription(30184)
Out[11]: 'HA HD HD |0 3 0|3 0 3|0 3 0|'

In [12]: bi[30184]
Out[12]: [[(5,), (0,), (6,)]]


If you have than one match, the list contains one element for each:

In [13]: Gobbi_Pharm2D.factory.GetBitDescription(157)
Out[13]: 'HA HD |0 3|3 0|'

In [14]: bi[157]
Out[14]: [[(0,), (6,)], [(5,), (0,)]]



This is now in github and will be part of the next release.

-greg


On Mon, Jun 29, 2015 at 5:39 PM, <fa...@mo...> wrote:

> I'm a few weeks into the most in-depth exploration of rdkit features I've
> had so far. I've started using the ipython console integration, including
> the highlighting of substructure search matches. But now I've come to the
> topological pharmacophore fingerprints. Using the pre-defined Gobbi
> fingerprints, I've been able to generate fingerprints and query the
> definition of individual bits, but I can't seem to find a way to highlight
> the matching bits of individual molecules that have a given fingerprint bit
> set. Is there a good way to do this, or should I just resign myself to
> manual comparison?
>
> Thanks,
> Andy
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>
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