Hi Martin,
There is a work around but let me double check first. I believe the issue is
the aromatic types is written but not read.
As for the kekulization - FixBondOrdersTool.kekuliseAromaticRings().
J
On 27 Jun 2013, at 11:27, Martin Guetlein <martin.guetl...@googlemail.com>
wrote:
> Anyone?
>
> Maybe theres a workaround for this? But AFAIK there is no kekulize
> option in CDK, right?
>
>
> On Mon, Jun 24, 2013 at 5:41 PM, Martin Guetlein
> <martin.guetl...@googlemail.com> wrote:
>> Hi,
>>
>> this is apparently still not fixed, I just reported a bug:
>> https://sourceforge.net/p/cdk/bugs/1307/
>>
>> Kind regards,
>> Martin
>>
>>
>> On Tue, Aug 16, 2011 at 3:18 PM, Egon Willighagen
>> <egon.willigha...@gmail.com> wrote:
>>> On Tue, Aug 16, 2011 at 2:47 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
>>> wrote:
>>>> If the bond type 4 is misused couldn't the SDF writer just write out
>>>> the kekule version?
>>>
>>> I think it does. But it won't deduce the kekule version
>>> automatically... so, if you happen to start with SMILES...
>>>
>>> One could argue to hook in the DeduceBondOrderTool, but I don't think
>>> it's general enough, neither have I seen any statistics on its
>>> performance, and it would be against our ideas to have separate
>>> building blocks...
>>>
>>> I now see you are using the SDFWriter... that one is currently not
>>> inheriting the IO setting from the MDLV2000Writer... so, that explains
>>> why it is ignored. Please file a bug report.
>>>
>>> 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/
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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
>
>
>
> --
> 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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