SMILES Representation

User 9852713200

26-08-2009 20:06:38

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!

ChemAxon 25dcd765a3

29-08-2009 11:11:33

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

User 9852713200

16-09-2009 21:17:14

OK.  Can we generate canonical/unique cxsmiles?


Thanks!

ChemAxon 25dcd765a3

18-09-2009 09:06:14










neogenesis wrote:

OK.  Can we generate canonical/unique cxsmiles?



Sure!


That will keep the wiggly bond information.


 


Andras

User 9852713200

18-09-2009 14:24:38

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


Thanks!

ChemAxon 25dcd765a3

18-09-2009 16:30:18

Yes


"cxsmiles:u"


Andras