The 1.5.x branch is unstable. However there are features which are useful as
they stand. In order to deliver there features in Knime new features which
cause complications were removed.
As far as I know the only thing which has currently been removed was
SINGLE_OR_DOUBLE flag as this impacted so many things it was easier to simple
remove it. It causes more errors being left in then out as the bond order is
left as null and many existing tools would have to be updated to cope with it.
It's the same case as the aromaticity, a lot the existing code base either
ignores it, only looks at bonds, only looks or atoms or re-calculates it. The
aromaticity flag has been around for a while so although there are still issues
(as is evident by your patch) it more or less works - sometimes. Adding an
additional flag like this really does cause too many head aches. Actually flags
in general cause issues...
Stephan says you should ask him @ http://tech.knime.org/forum/cdk - he can
patch it quicker then it would be going into the main codebase the propagating
to Knime.
Thanks,
J
On 23 May 2013, at 13:29, Martin Guetlein <martin.guetl...@googlemail.com>
wrote:
> Hi John,
>
> So the cdk.jar that is part of the CDK-plugin ( i.e. this one:
> plugins/org.openscience.cdk.knime_1.4.2.201301221437/lib/cdk-1.5.1.jar),
> is not the actual cdk-1.5.1.jar that you can download at sourceforge?
> Why? Is there documentation about what has been removed?
> This could actually cause errors in Knime, whenever another Knime-Node
> makes use of CDK and has to add its own cdk.jar instead of using the
> one thats added by the cdk-knime-plugin.
>
> Best regards,
> Martin
>
>
>
>
> On Thu, May 23, 2013 at 1:07 PM, John May <john...@ebi.ac.uk> wrote:
>> Just a note,
>>
>> The knime node isn't the 'official' jar. Some features which don't work
>> (actually loosely relating to aromatic SMILES) have been removed.
>>
>> J
>>
>> On 23 May 2013, at 11:03, Martin Guetlein <martin.guetl...@googlemail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> This bug is still in the generator, I just checked in a fix here:
>>> http://sourceforge.net/p/cdk/bugs/1177/
>>> So far, I have fixed it locally and built my own cdk.jar, but now Im
>>> working on a Knime-Node that relys on the 'official' cdk.jar.
>>> I would be great if you could patch this?
>>>
>>> Thanks and kind regards,
>>> Martin
>>>
>>>
>>>
>>> On Wed, Oct 5, 2011 at 2:00 PM, Egon Willighagen
>>> <egon.willigha...@gmail.com> wrote:
>>>> On Wed, Oct 5, 2011 at 1:49 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
>>>> wrote:
>>>>> Oh, there's a patch for this bug?
>>>>
>>>> Not for this bug in the generator... but I was wondering if it was
>>>> related to the bug in the *parser*... for the latter I uploaded
>>>> patches...
>>>>
>>>> Egon
>>>>
>>>> --
>>>> Dr E.L. Willighagen
>>>> Postdoctoral Researcher
>>>> Institutet för miljömedicin
>>>> Karolinska Institutet (http://ki.se/imm)
>>>> Homepage: http://egonw.github.com/
>>>> LinkedIn: http://se.linkedin.com/in/egonw
>>>> Blog: http://chem-bla-ics.blogspot.com/
>>>> PubList: http://www.citeulike.org/user/egonw/tag/papers
>>>>
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>>>
>>>
>>> --
>>> Dipl-Inf. Martin Gütlein
>>> Phone:
>>> +49 (0)761 203 8442 (office)
>>> +49 (0)177 623 9499 (mobile)
>>> Email:
>>> guetl...@informatik.uni-freiburg.de
>>>
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>>
>
>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 8442 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> guetl...@informatik.uni-freiburg.de
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