one petition:
for 11111-4444:
Please use for the parsing as much 'single helper classes' as possible, so i can pick them up for JOELib. If you will heavily integrate the parsing into the Jmol plugin, the code fragments must be invented twice.
Eventually the put/get can be based on simple String methods !!!
1111
Understood. So in this case no data goes to the Jmol viewer ... all is processed by the plugin as part of the Jmol application.
2222
3) the cgi-program writes to the output something like "the final energy is xx kJ/mol" and this information is passed to the plugin ; also the final coordinates are passed to the plugin, for example using the coordinates record of the ghemical file format:
!Coord 0 1.122 0.222 2.434 1 0.232 2.434 0.223 etc...
3333
4) the plugin reads the output, parses the energy information from it, and shows the result to the user ; then it also reads in the coordinate information, *and* passes that to Jmol by updating the atom coordinates at Jmol ; now the user gets both the final energy and the final coordinates as well, which is the optimized structure. Now the whole operation is processed remotely, and the user has all the results.
4444
So please remember that it is the task of the plugin to read the output and display it to the user ; it might either display it directly (like showing the value of the calculated energy) or it might let Jmol show it (like by updating the atom coordinates at Jmol and asking Jmol to update the graphics).
Regards, Joerg
-- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:[EMAIL PROTECTED] WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway)
Never mistake action for meaningful action.
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