Hi Christophe,

The InChI stores coordinates in the AuxInfo and without that the IUPAC binary (called by the CDK) won’t set structure coordinates. To obtain a depiction you need to generate coordinates from scratch. The 2D coordinates are generated using the StructureDiagramGenerator whilst 3D coordinates are generated with ModelBuilder3D. It should be noted that neither method currently respects stereochemistry although that information is present.

Thanks,
John

On 11 Nov 2013, at 12:59, Christophe Marcourt <christophe@marcourt.ch> wrote:

Hello all,

I'm using cdk-inchi packages to turn an Inchi code to a strcuture.
I used the written code from the InChIToStructure javadoc.
It works fine but as the javadoc said "The generated IAtomContainer will have all 2D and 3D coordinates set to 0.0" !
When I used chemspider web services, it returns with a good structure.
So how can one use InChIToStructure to have the real structure ? And not only with 0 in it...
Thanks.

Christophe Marcourt
------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user