I have been struggling with passing the 2D molecule in JME to 3D in Jsmol.
In Jmol the conversion and EM can be done reasonably quick, but JSmol is
slow. I tried to circumvent the problem by the internal function of pass
the SMILES string to nci.cactus, but it is not exactly what I want.
So I am thinking since Jmol can do the job, is it possible to pull the part
of the code out to build a separate server to do the job which should be
quick. But I don't know if it is violating the GPL conditions.
Or if there is any other solutions in your mind?
School of Chemistry and Molecular Biosciences
The University of Queensland
Hello Wenhan Chen
Maybe this helps you:
That's using JSME, the non-Java alternative to JME
JME to Jmol (both Java applets):
When you say it is slow, what size of molecule are you speaking
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
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
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