Hi Greg,
thanks for your prompt reply.
What added to my confusion was the comparing of AtomPair fingerprints in 2D
and 3D eg:
http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Atom%20Pair%20Fingerprints.ipynb
So if I understand you correctly here you need the Hs in 2D because you
have them present in 3D?
And if you use AtomPair FP in 2D only, you do not need hydrogens?
Best Regards,
Joos
2016-01-20 14:19 GMT+01:00 Greg Landrum <[email protected]>:
> 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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