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.


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...

Christophe Marcourt
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