About CDK in MolView (http://molview.org)
Sorry for the late response, I was not subscribed to the CDK devel mailing list so I haven't recievee your replies (until I found them on sourceforge)
MolView is built on top of GLmol, ChemDoodle Web and JSmol.
GLmol is used as primary render engine (fast), ChemDoodle is used for crystals (CIF is not yet implemented in GLmol) and JSmol is used as Canvas2D fallback and for advanced actions like force field minization, dipole calculation and measurements.
I've looked at the CDK source but there are a lot of dependencies (eg. other packages in the DiagramGenerator)
Can CDK also generate 3D coordinates? (without force field minimization but using templates etc.) Because that would be a great alternative to the Chemical Identifier Resolver (http://cactus.nci.nih.gov/chemical/structure
Maybe I should use J2S after all...
I'm also thinking about a larger server-side part in MolView (but I'll need some crowdfunding) Then I could put CDK on a Tomcat server or something like that.
Btw, MolView will be made open-source in the future!