cis/trans isomers unexpectedly showing in SMILES

The monomer for Kel-F is 1-chloro,1,2,2-trifluoroethene.

I would expect the SMILES to read FC(F)=C(F)Cl, but I get either F\C(F)=C(/F)Cl or F\C(F)=C(\F)Cl out of MBeans/MSketch depending on what order I attached the halogen atoms.

Do I need to get my tuition back or is there something wrong with the SMILES generator in MBeans?

If my students use the MSketch GUI on the client-side and MBeans spits out F\C(F)=C(/F)Cl or F\C(F)=C(\F)Cl on the server-side, but I'm grading against FC(F)=C(F)Cl, then they'll get it wrong.

I'm using a_bas and u on export.

Is this a known bug? Is there a fix for it?

Thanks.

Hi,

It shouldn't work like that.

If you just export to plain smiles the local Cis Trans information will be exported, but in case of unique smiles export (with 'smiles:u') the 'q' option is automatically turned on.

See : http://www.chemaxon.com/marvin/help/formats/smiles-doc.html#options

So you should get: FC(F)=C(F)Cl

Are you sure that you export to unique smiles format?

Andras

I'll cross-check with our Java programmers what exactly they are exporting, but the point is that there is no cis/trans-isomerism in this molecule, so why is the system implying there is?

It has some historical aspect and speed consideration, but thank you for warning us we may change the default behaviour in the next major release.