Inconsistency with import/export feature

Hello everyone,

I have a trange problem in MarvinJS. I have two editors on my website. The purpose of the first is to draw a skeleton of a molecule. Then I export this molecule (cxsmiles format with lonepair calculation disabled) and import it to the second editor.

When I try to do this with SO₃ : I draw the molecule on the left (I have valence errors turned off, but marvinjs shows that there is a valence error) in the attachment and after import I get the molecule on the right (with the monovalent radical o sulfur atom). Same thing happens with NH₄ molecule, which also appear with a radical after import. 

This happens also, when I change the export/import format to "smiles" only.

The strange thing is that with molecules such as SeO₃ , which is "similar" to the SO₃ and PH₄ (similar to NH₄) this is not happenning.

The question is: Why there is suddenly a monovalent radical after import in certain molecules?

I would appreciate any advice/help

Thank you

Martin

Hi Martin,

The phenomenon caused by SMILES representation:
"Since radicals are not stored in SMILES format, they are calculated during SMILES import for atoms that tend to have radicals. It is done in the case when no implicit Hydrogens can be added because of the SMILES definition and the valence of the atom has to be corrected." 

You can read more details about SMILES representation in our documentation here:
https://docs.chemaxon.com/display/docs/SMILES

Cxsmiles format however exports radical information, which would prevent the automatically calculated radical appearance, but if you disable the lonepair calculation, and add no radicals, all atoms will get zero lone pairs and radicals, this way simple SMILES format will be exported.

If you need to have the lone pair calculation disabled, I would recommend considering the usage of another file format, for example mrv or mol, which contains explicit radical information and not requires auto calculation.

If you need more information or help, please let us know.

Best regards,
Eszter 

Dear Eszter,

thank you for your answer. I've used another file format (mrv works great).

Martin

Dear Martin,

It is great to hear that the problem is solved. :)

Please let us know, if any further question arises.

Eszter