Tuning representation of aromatic cycles

Hi,





I am a bit new with standardizer and I am a bit surprized the way some of my cycles were aromatized...





For example, I have this compound:





[H][N+]([#6])C1=C(CC2=C(C=CO2)C([#8-])=O)C(=O)CCC1 |c:8,t:6|





after standardization with either basic or general style aromatization, I get this:





[#6][N+]=C1CCCC(=O)C1Cc2occc2C([#8-])=O |w:1,0|





I would prefer to have the furan not aromatized. In the same order of idea, I'd prefer pyrroles or thiophenes not to be aromatized.





Is there a way to use standaradizer to do that? I am using jchem 3.2.3





Thanks in advance,


Gilles Marcou

If you do not include aromatize in the standardization configuration, your compounds will not be aromatized at all, so your rings remain in the Kekule form having alternating single/double bonds.





If you need aromatization during the standardization process before a specific transform, you can apply a dearomatize action in the end to convert your compounds to Kekule forms.

I think you are right. We have finaly decided to dearomatize at the end of our standardization process. In fact, some of our cheminformatic tools are sensible to modelization of aromaticity. So we might want to compare dearomatized modelization of our database to aromatized one.





Thanks.