From: 陈文瀚 <che...@gm...> - 2013-10-30 01:06:52
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Does anyone every go into the code to see what really happening when Jmol/JSmol parsing the JME format, cuz the JME format works incredible well for the limited information containing in the JME format. There should be some sort of internal conversion which really computational expensive for JSmol, but fine with Jmol. Cheers _________________________________ Wenhan Chen School of Chemistry and Molecular Biosciences The University of Queensland 2013/10/30 陈文瀚 <che...@gm...> > 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 <che...@gm...> > >> 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 <ang...@ua...> >> >>> 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 >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Android is increasing in popularity, but the open development platform >>> that >>> developers love is also attractive to malware creators. Download this >>> white >>> paper to learn more about secure code signing practices that can help >>> keep >>> Android apps secure. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> >> > |