unable to convert to smiles format

I downloaded and installed the latest MarvinBeans and replaced the MarvinBeans.jar in my application. However, when I now try to generate smiles against the same set of compounds which used to work before,it writes somewhere in the middle (actually close to the beginning of the set ):





"Some features of *COCOCO* cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format." It used to work perfectly well with the old version.


Is there any way to avoid it?





I looked up in the forum - found something where it says that these messages would go away in version 4.0.I guess I downloaded the one which is marvinbeans-4.0.1-win_vm.exe.

It seems your molecule contains some features that are not supported in smiles.


I suggest to use the cxsmiles format that stores non-smiles features after the smiles string.





If the structures have query features (not legal either in smiles or cxsmiles), you can also try the smarts or cxsmarts format.





If none of these work for you please send a few examples.