On Wed, Jun 22, 2011 at 4:28 PM, Nina Jeliazkova
<jeliazkova.n...@gmail.com>wrote:
> Hello Martin,
>
> On 22 June 2011 17:19, Noel O'Boyle <baoille...@gmail.com> wrote:
>
>> On 22 June 2011 13:35, Martin Guetlein <martin.guetl...@googlemail.com>
>> wrote:
>> >
>> > On Mon, Jun 20, 2011 at 2:28 PM, Martin Guetlein
>> > <martin.guetl...@googlemail.com> wrote:
>> >>
>> >> Hello all,
>> >>
>> >> when converting a aromatic smiles to sdf, it does only contain single
>> and
>> >> double bonds (kekule notation).
>> >>
>> >> how can I have aromatic bonds in my sdf?
>> >>
>> >> (I tried openbabel-2.3.0, via command line and c++ api)
>> >>
>> >> Best regards,
>> >> Martin
>> >
>> > Anybody?
>> > Isn't possible to avoid the kekulization when printing the SDF?
>>
>> Looks like you're right.
>>
>>
> Citing the SDF spec :
>
> http://www.symyx.com/downloads/public/ctfile/ctfile.jsp
> ctfile.pdf , page 16
> Bond type
> Integer:
> 1 = single
> 2 = double
> 3 = triple
> 4 = aromatic
> 5 = single or double
> 6 = single or aromatic
> 7 = double or aromatic
> 8 = any
> Types 4 through 8 are for queries only.
>
I dont really understand this limitation, why should 4=aromatic be only used
for queries, its not ambigious like the others? (maybe its a typo, and it
should be '5 though 8' ;-) ).
Still, I am using a software that can handle aromatic bonds in SDF. Is there
a way to achieve this with OpenBabel?
Best regards,
Martin
>
> Regards,
> Nina Jeliazkova
>
>
>> > Please help,
>> > Martin
>> >
>> >
>> >>
>> >> --
>> >> Dipl-Inf. Martin Gütlein
>> >> Phone:
>> >> +49 (0)761 203 7633 (office)
>> >> +49 (0)177 623 9499 (mobile)
>> >> Email:
>> >> guetl...@informatik.uni-freiburg.de
>> >
>> >
>> >
>> > --
>> > Dipl-Inf. Martin Gütlein
>> > Phone:
>> > +49 (0)761 203 7633 (office)
>> > +49 (0)177 623 9499 (mobile)
>> > Email:
>> > guetl...@informatik.uni-freiburg.de
>> >
>> >
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>>
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>
>
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@informatik.uni-freiburg.de
------------------------------------------------------------------------------
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
Nope - It's vRanger. Get your free trial download today.
http://p.sf.net/sfu/quest-sfdev2dev
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