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 <[email protected]> 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>
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