SMILES Representation

Hello,

Both structures in the attachment have the same SMILES string "CC12CCCN[C@@]1(C)CC(=O)CC2".  Are they supposed to have the same smiles string?  If so, if one pastes in this smiles into the marvinsketch, which structure should be generated?

Thanks!

Hi,

SMILES language is not capable of storing wiggly bonds so the two structures have the same SMILES representation. If one pastes this smiles into the marvinsketch then the one without wiggly bond (the one on the left side in your attached document) will be generated.

If you want to keep the wiggly bond information please use cxsmiles instead of smiles.

Andras

OK.  Can we generate canonical/unique cxsmiles?

Thanks!

neogenesis wrote:

OK.  Can we generate canonical/unique cxsmiles?

Sure!

That will keep the wiggly bond information.

 

Andras

OK.  What is the format?  Is "cxsmiles:u" right?

Thanks!

Yes

"cxsmiles:u"

Andras