Implicit hydrogens on aromatic nitrogen : in jchem too ?

Dear All,





Concerning :





http://www.chemaxon.com/marvin/doc/user/mol-csmol-doc.html#implicith





I have an sdf file containing structure having the MRV_IMPLICIT_H field. When opening them in Msketch and looking at their smiles (edit/souce), the smiles makes as expected the implicit H explicit ([nH]).


But when getting their smiles through the toFormat("smiles") method of jchem (using 3.1.5), the corresponding implicit H are not made explicit.





Is there some options I should use ?





thanks,





Vincent

Hi Vincent,

vincentberenz wrote:

Concerning : http://www.chemaxon.com/marvin/doc/user/mol-csmol-doc.html#implicith I have an sdf file containing structure having the MRV_IMPLICIT_H field. When opening them in Msketch and looking at their smiles (edit/souce), the smiles makes as expected the implicit H explicit ([nH]). But when getting their smiles through the toFormat("smiles") method of jchem (using 3.1.5), the corresponding implicit H are not made explicit. Is there some options I should use ?

No extra option is needed, this should be done automatically. Can you send us an example molfile and the code with which you are reading/writing the molecule?





Is there any operation on the molecule between import from sdf and the toFormat() call?





Best regards,


Szabolcs

Dear Szabolcs,





I updated to jchem 3.1.7 and it works just fine !





thx,





Vincent

I am glad it works now. Thanks for the feedback.





Szabolcs