Hi Asad,

You are generating a generic SMILES, you probably want an isomeric SMILES. Both and non-canonical and intended for storage, canonical equivalence are unique and absolite. 

http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/smiles/SmilesGenerator.html

J

On 13 May 2014, at 17:05, Syed Asad Rahman <asad@ebi.ac.uk> wrote:

Hi,

What is the best way to preserve the stereo chemistry in the CDK while converting an AtomContainer to SMILES and back (round trip)?

IAtomContainer=>SMILES=> IAtomContainer (leads to loss of stereo information)

Thanks,

Asad

PS: Attached is a molecule (L-Alanine) with Stereo centre.

<Mol_Stereo.mol>