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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