Actually if I transfer the structure from a mol file to JSmol and then try to optimize the structure, the charity cannot be preserved as well ...



_________________________________
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland




2013/10/30 陈文瀚 <chenwh795@gmail.com>
Basically, molecules with more than 30 atoms sent in JME format(not including H) will cause a halt for the browser as the js try to hold the browser.
But you are right, it was quick using Jmol with JRE. I think JSmol try to do EM using MMFF which takes the most time.
When the molecule in MOL format passes onto JSmol, it works fine with no EM. 

Even so I still am trying to address the problem using mol format, as the charge information (the number of H atoms) in the mol file is not presented right in JSmol.

Herein is an example :

           C+
          /   \
        C -- -C
The mol file for the above mol is :

  CWRITER31030r]09392D                              
Created with ChemWriter - http://chemwriter.com
  3  3  0  0  0  0  0  0  0  0999 V2000

    4.3530   -4.7830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3530   -4.7830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8530   -3.9169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0
  2  3  1  0  0  0
  3  1  1  0  0  0
M  CHG  1   3   1
M  END

JSmol cannot add an H atom to the C+ atom.




_________________________________
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland




2013/10/30 Angel Herráez <angel.herraez@uah.es>
Thanks for the feedback, Pino

Then maybe the 3D minimization is much slower in the Javascript
version that in the Java version.

I've now added an option to the JSME page to check if it is the
transfer (unlikely), adding the hydrogens or the 3D minimization
which gives the delay
That is only useful for MOL transfer.
JME transfer must necessarily go to 3D conversion, that may be the
bottleneck.

It seems indeed that it is the JmeReader routine that takes its time



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