p.s. nice oneliner for debug….
> new MDLV2000Writer(System.out).write(mol);
On 13 May 2014, at 22:06, John May 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
> uni
Yes, molfile can only correctly indicate stereochemistry via a depiction. The
structure diagram generator will add in required wedge bonds and adjust
geometric isomers (with the exception of macrocycles).
The best way to do this properly is to store the coordinates in an auxiliary
layer (just
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 smilesPar
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 201
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_
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