Hi Vincent 

> > Finally, I will have to display 3D molecules too. Currently, It
> > appears the CDK alone can't do that, to I guess I've to check JMol,
> 
> (lower case 'm', if you mean Jmol at jmol.org; JMol is a smaller but
> existing viewer too)

That's correct. Jmol is a nice tool for that, and it can collect 
MOLfile data from JChemPaint; if you need help, just ask. It will 
also display the 2D data (no too useful as they are flat but can be 
rotated around in 3D).
Unless you can make use of Bioclipse as Egon suggests.

And BTW, the distinction in name is important but JMol is no longer 
around --at least I've been completely unable to locate it on the web-
-.



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