[Cdk-user] hand-built molecules and the renderer

[Thorsten M. <Tho...@un...>]

Hi,

When I built up molecules "by hand", i.e. using Java code with addAtom
and addBond, the renderer will afterwards not draw aromatic rings. The
ring is instead composed only of single bonds. I set the bond orders
with bond.setOrder(CDKConstants.BONDORDER_AROMATIC) and a Smiles string
generated from the molecule shows the ring correctly with ":" and small
atom symbols. What else do I have to do, so that the 2D renderer shows
the correct ring structure?

Regards,

Thorsten


-- 
Thorsten Meinl                        room: Z813
ALTANA Chair for Bioinformatics       fax: +49 (0)7531 88-5132
and Information Mining                phone: +49 (0)7531 88-5016
Box M712, 78457 Konstanz, Germany