Thanks,
I tried this code, the isomeric seems to hold the stereo information but
converting it back to MDL file format, I am loosing the Stereo information in
the bond connection table.
Here is my snippet.
The MDL is loosing the up/down info. in the bond section.
SmilesParser smilesParser = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = smilesParser.parseSmiles("C[C@H](N)C(O)=O");
String sm = SmilesGenerator.isomeric().aromatic().create(mol);
Assert.assertEquals("C[C@H](N)C(O)=O", sm);
try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
try (MDLV2000Writer mdlWriter = new MDLV2000Writer(baos)) {
mdlWriter.write(mol);
mdlWriter.close();
}
System.out.println("ac " + baos.toString());
On 13 May 2014, at 22:06, John May <john...@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.
>
> 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 <a...@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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