Hi Joos,
As long as you are sure to be consistent, it is certainly ok to generate
fingerprints for molecules with Hs still attached, but it's very easy to
make a mistake.
The default behavior of the RDKit is to remove Hs. This is what I would
recommend before doing things like generating fingerprints or descriptors.
-greg
On Wed, Jan 20, 2016 at 7:06 AM, Joos Kiener <[email protected]> wrote:
> Hi all,
>
> I've been looking at different Fingerprints within the RDKit when I
> realized, that it matters for many of them whether Hydrogens are
> explicitly present or not. This probably was obvious and clear for many of
> you but I wasn't aware of that.
>
> To visualize what I mean please see below notebook:
>
>
> http://nbviewer.jupyter.org/github/kienerj/notebooks/blob/master/Fingerprint%20Similarity%20-%20with%20and%20without%20hydrogens.ipynb
>
> Now my questions are:
>
> Should I always add hydrogens before generating fingerprints or should I
> remove them?
>
> How is this handled in KNIME nodes? Do I need to perform the according
> action (add/remove H) before generating the fingerprint? Or is this done
> correctly already internally of the node?
>
> Thank you for your help.
>
> Best Regards,
>
> Joos
>
>
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