Dearomatizing problem (molconvert)

Hi,





Our code uses the chemaxon "molconvert" to dearomatize the aromatic molecules (to kekulize them). The way we do this as the second example on the chemaxon molconvert document page [1],





But when I used this method on the a compound [2],


molconvert smiles:-a -s "[O-]C(=O)C=[c]1-cccc-[c]1=CC(=O)C([O-])=O"


I got the result,


[O-]C(=O)C=[c]1-cccc-[c]1=CC(=O)C([O-])=O





Why this compound still keep aromatic atom types in its SMILES?





[1] http://www.chemaxon.com/marvin/doc/user/molconvert.html


[2] http://umbbd.msi.umn.edu/servlets/ypageservlet?ptype=c&compID=c0998





Thanks!





Jeff

Hi,








In this smiles ‘[O-]C(=O)C=[c]1-cccc-[c]1=CC(=O)C([O-])=O’


the aromatic ring is mixed from aliphatic and aromatic bonds as well. This smiles string is questionable from chemical point of view.





A more straightforward smiles string would be this





‘[O-]C(=O)C=c1ccccc1=CC(=O)C([O-])=O’





Here aromatic ring is built only from aromatic bonds.





I would propose to use this latest smiles string instead of the first one.











Now, I have fixed this problem.





Dearomatization module can handle both smiles strings from now on. This bug fixed release will come soon.








Thanks for reporting this problem!





Jozsi