p.s. nice oneliner for debug….

new MDLV2000Writer(System.out).write(mol);



On 13 May 2014, at 22:06, John May <johnmay@ebi.ac.uk> wrote:

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. 


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>

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