radicals and SMILES

We recently upgraded to JChem 3.0.13. When we try to convert a MOL file containing a radical (for example, CH₃·) into a SMILES, we get this error message:








Generic error:


java.lang.IllegalArgumentException: Some features of [#6] cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.








This is a brand-new error message which wasn't generated in previous versions of JChem, as far as we can tell. Why is it being generated now? Why can't we convert a radical-containing structure into a SMILES string?





-- Bob

Hi Bob,





Previous versions (like the 2.3.x series) did not throw an exception indeed, but the conversion was not quite correct, the radical was lost.





The 3.0.x versions throw an exception indeed, as proper radical support for SMILES is not implemented yet in these versions.





Correct handling of radicals will be available from JChem 3.1 (and Marvin 4.0).


These releases are expected to come out soon.





You may also test some of the new features before the release by downloading one of our test builds:





http://www.chemaxon.com/download.php?d=/data/download/jchem/test





Best regards,





Szilard

I can confirm that when radicals are now converted into SMILES, the radical information is preserved.





However, when they are converted into SMARTS, the radical information is lost. This behavior seems like a bug, because SMARTS should encompass all SMILES functionality.

Hi Bob,





In case of SMILES the radical information is calculated from the implicit H count and the valence, which is not possible in case of SMARTS.


If you want to use SMARTS with radical support I suggest you to use cxsmarts instead.





All the best


Andras

Radicals don't appear to be supported by cxsmiles or cxsmarts in Marvin 3.5.5, although they are in Marvin 4.0. So in what version of Marvin and JChem were they first supported?

They were introduced in Marvin 4.0.1 and JChem 3.1.





Szabolcs