Re: [Cdk-user] Stereo Chem

[John M. <jo...@eb...>]

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 <as...@eb...> 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>