It seems to me that what we are talking about now has (or should have!)
more to do with the interpretation of the terrible old PDB file format than
about any software convention.
It seems to me that software that must read this format should turn the
contents into something generally chemically acceptable (that is, "Cl", not
"CL", in this case) rather than foolishly propagating the error, or
accepting it in other contexts.
As for those who would write that format, fight it! :-)
The above, in my view, represents the voice of reason, and is therefore
unlikely to be generally adopted....
-P.
On Wed, Jan 20, 2016 at 10:42 AM, John M <john.wilkinson...@gmail.com>
wrote:
> Whoops wrong thread this was in regard to the Chlorine molfile question.
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 20 January 2016 at 15:40, John M <john.wilkinson...@gmail.com> 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
>> john.wilkinson...@gmail.com
>>
>> On 20 January 2016 at 13:19, Greg Landrum <greg.land...@gmail.com> 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 <joos.kie...@gmail.com>
>>> 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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