Extended Smiles and Relative stereochemistry

Hi,





We have noticed that if you draw a simple amino acid (with only one chiral centre) and try to get its extended Smiles, we obtain

Quote:

C[C@H](N)C(O)=O |r|

Is there a way that the stereochemistry can be automatically converted to 'Absolute' in that case?





Thanks


Catherine

Dear Catherine,





You can use the "-e" option during the export to cxsmiles.


See more information in extended smiles documentation:


http://www.chemaxon.com/marvin/help/formats/cxsmiles-doc.html#options





Eg:

Code:

molconvert cxsmiles:-e -s "C[C@H](N)C(O)=O |r|" C[C@H](N)C(O)=O

of no "|r|" appears in the cxsmiles then the molecules has absolute stereoconfiguration.





All the best


Andras