Sorry Noel - your reply made me realise my original reply was only to
Heather not the whole list, so the text is copied below. Crucially, it
looks like OpenBabel is adding some extra query features during the
conversion. I just had a bit of a dig around and the latest version of
KNIME (3.6.2) is running the following version:
Open Babel 2.3.1 -- May 16 2012 -- 14:59:54
Heather - it may be a good idea to post on the KNIME forums somewhere if
Noel can confirm that this is an old version of openbabel?
Steve
===My original response===
It is a molecule query feature from the Marvin renderer view of the
molecules. Sometimes it is a little over-enthusiastic!
It maybe worth comparing the results with those from the 'Molconvertor'
node, which is one of the free Marvin / JChem nodes - the option '-a'
performs kekulisation, and doesnt show these extras.
The mol files are for the MolConvertor:
Mrv1813 11121817262D
8 6 0 0 0 0 999 V2000
0.8250 0.0000 0.0000 Li 0 3 0 0 0 0 0 0 0 0 0 0
-1.6500 -1.4289 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.2375 -0.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9520 -0.3020 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.5230 -1.1270 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.8250 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2375 0.7145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
3 5 1 0 0 0 0
3 6 1 0 0 0 0
6 7 2 0 0 0 0
6 8 1 0 0 0 0
M CHG 2 1 1 8 -1
M END
And:
OpenBabel11121817262D
8 6 0 0 0 0 0 0 0 0999 V2000
0.8250 0.0000 0.0000 Li 0 3 0 0 0 *15* 0 0 0 0 0 0
-1.6500 -1.4289 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.2375 -0.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9520 -0.3020 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.5230 -1.1270 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.8250 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2375 0.7145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
3 5 1 0 0 0 0
3 6 1 0 0 0 0
6 7 2 0 0 0 0
6 8 1 0 0 0 0
M CHG 2 1 1 8 -1
M END
You can see that OpenBabel adds a query feature on the Li atom, hence the
rendering
If you have Indigo toolkit installed, you can change the column renderer
(you can change manually in an individual table view, or also change the
defaults in File -> Preferences then KNIME -> Preferred Renderers)
Also in Preferences under KNIME -> Marvin -> Marvin Renderer Option, if you
uncheque 'Valence', then that will stop it being shown, but you need to
consider whether it should be there in the mol block or not for your
purposes!
On Wed, 14 Nov 2018 at 21:51, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hi Heather,
>
> I think this is a question for Knime. We don't maintain the Open Babel
> Knime node. I have no idea what version it uses, or what it's doing. If you
> want to kekulize your structures with Open Babel we can help with that, of
> course.
>
> Regards,
> - Noel
>
> On Mon, 12 Nov 2018 at 17:01, Heather Lambert <heath...@fluorochem.co.uk>
> wrote:
>
>> Hello,
>>
>>
>>
>> I am using the OpenBabel Knime node as a way to convert structures from
>> being aromatised to kekulized. This works well by converting from mol- MDL
>> MOL format to sdf- MDL MOL format.
>>
>>
>>
>> However, when I apply this conversion to all structures in my original
>> SDF file (even if they do not need to be kekulized), I get results like
>> this:
>>
>>
>>
>>
>>
>> What does (v0) mean on the structure? And how do I remove it?
>>
>>
>>
>> Thanks
>>
>> Heather
>>
>>
>>
>>
>> Heather Lambert​
>> Technical Sales
>> Fluorochem Ltd
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