Re: [Cdk-devel] [Cdk-user] Inchi to structure

[Christophe M. <chr...@ma...>]

Thank you very much.
The problem is that in my Inchi code I have something like 2C... for the
molecular formule. A kind of symmetric molecule. So for the moment I'm
requesting chemspider web service for this kind of molecule.
Adding bonds and remove them later won't be a solution for me.


Christophe Marcourt



On Mon, Nov 11, 2013 at 6:04 PM, Egon Willighagen <
ego...@gm...> wrote:

> On Mon, Nov 11, 2013 at 4:42 PM, John May <jo...@eb...> wrote:
> > Yes you need to process the structures separately. It’s not that there
> is a
> > good but more likely there is non-covalent bonding - you can see how
> > toolkits interpret - [Na+].[Cl-].
>
> I have not tried it, but it may be worth trying this:
>
> - add a IBond for salt bridges like this, e.g. with zero electrons,
> and a custom property marking it as a ionic bond
> - do the structure diagram generation
> - remove all bonds marked as ionic bond
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
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>