Hello Wenhan Chen

Maybe this helps you:
http://biomodel.uah.es/en/DIY/JSME/

That's using JSME, the non-Java alternative to JME

JME to Jmol (both Java applets):
http://biomodel.uah.es/en/DIY/JME/JME.htm

When you say it is slow, what size of molecule are you speaking 
about?

If you pass the molecule as SMILES, I think it needs a server as 
intermediate. But you can pass the molecule as MOL or as JME format, 
then you don't need any servers and J(S)mol will do the 3D 
calculation.

Why do you expect that the server will be quicker? Do you mean 
running it in Java in trhe server?
Regarding the GPL, I'm no expert but Jmol exists as a library to be 
included in other software and also as JmolData.jar which does 
calculations without the rendering as may be suitable to be run in 
the server.



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