SMILES generation

Hi,

I'm using Marvin 5.2.2.

Attached are two different structures.  The one on the top is "cis-", and the bottom one is "trans-".  So they should have different smiles strings, but Marvin always generates same smiles CO[C@]1(CCC(CC1)C1=NC=CC=C1)C(O)=O

 

ChemDraw (v11) generates two different smiles as follows:

<top one>        OC([C@]1(OC)CC[C@H](C2=CC=CC=C2)CC1)=O
<bottom one>  OC([C@@]1(OC)CC[C@H](C2=CC=CC=C2)CC1)=O

Is this a bug?  Can this be fixed?

Thanks,

Hi!

Marvin interprets only the narrow end of the wedge as stereocenter.

In the attached image only the atom marked  with numbre 1 can be a stereocenter.

The atom at the wider end (2) will never mark stereocenter.

If you change the wedge orientation marvin will generate correct SMILES.

 

PS: at API level it is possible to change wedge interpretation to accept both side of the wedge.

Andras