Joos,
In that workbook, the code that generates 3D conformations (in block [6])
adds Hs to the 2D molecule before doing the conformation generation. This
is essential to generate realistic conformations. The Hs are left on
through the UFF minimization of the structures (also in block [6]), but are
then removed before any fingerprints are generated.
If I'm reading the notebook properly (it's been a while since I generated
it), fingerprints are always generated for molecules without Hs.
-greg
On Thu, Jan 21, 2016 at 2:14 AM, Joos Kiener <[email protected]> wrote:
> 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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