Hi Martin,
On 27 June 2013 13:27, Martin Guetlein <martin.guetl...@googlemail.com>wrote:
> Anyone?
>
> Maybe theres a workaround for this? But AFAIK there is no kekulize
> option in CDK, right?
>
Actually there is - check org.openscience.cdk.smiles.FixBondOrdersTool
Regards,
Nina
>
>
> 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/
> >> 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
>
>
>
> --
> 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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