Whoops wrong thread this was in regard to the Chlorine molfile question.
Regards,
John W May
[email protected]
On 20 January 2016 at 15:40, John M <[email protected]> wrote:
> The joys of the molfile - was curious whether it was accepted/correctly
> interpreted:
>
> ISIS Draw 2.5 Yes (arguably the arbitrator of the format)
> ChemDraw 15 Yes
> ChemDoodle No (accepted but only as a text label 'CL' no conversion)
> MarvinSketch Yes
> CDK Yes
> OEChem Yes
> Open Babel Yes
> Indigo Yes
>
> J
>
> Regards,
> John W May
> [email protected]
>
> On 20 January 2016 at 13:19, Greg Landrum <[email protected]> wrote:
>
>> 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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