UFF.txt is a resource within the Jar file. Specifically it is in:
JmolApplet0_Minimize.jar/org/jmol/minimize/forcefield
JmolAppletSigned0_Minimize.jar/org/jmol/minimize/forcefield
If you use
set debug
you should see its contents listed when the minimizer runs.
Very odd that the system can't find it. This could be an odd threading issue
-- the thread that runs from a click of a button is not the same thread that
runs when you use the Jmol console or menu.
Local files -- sounds like a Java bug. But I could be doing something
slightly wrong there.
Suggestions:
compare application and applet.
2010/6/8 Angel Herráez <[email protected]>
> This is the summary and a test case:
>
> 1. Problem is there only for local files, not from server. Seems to
> be related to Jmol reading text files (either scripts or the UFF.txt
> file embedded somehow inside Jmol) from a folder where the applet
> jars are but the webpage is not.
>
> Main_folder
> |
> -- Pages_folder
> |
> -- mypage.htm
> |
> -- Jmol_folder
> |
> -- *.jar files
> -- Jmol.js
> -- model.mol
> -- test.spt
>
> 2. The problem shows for reading script files (that do no model
> loading, just simple commands) and also for running "minimize"
>
> 3. The same script commands or the minimize command work fine when
> issued from teh script console. It'sonly calling them from a
> jmolButton or an <input type="button" onClick="jmolScript()"> that
> causes the problem.
>
> 4. Same behaviour in 11.6, 11.8.24 and 12.0.RC17
>
> 5. Errors are like:
>
> For loading a script file:
>
> FileManager opening
> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
> 12.0.RC17/halos.spt
> script ERROR: script ERROR:
> io error reading
> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
> 12.0.RC17/halos.spt:
> java.security.AccessControlException:
> access denied (java.io.FilePermission
> F:\webs\_Proyectos\_pruebas\Jmol_local_scripts\Jmol-
> 12.0.RC17\halos.spt read)
>
>
> For running minimize:
>
> Minimizing 17 atoms
> minimize: initializing (steps = 100 criterion =
> 0.0010000000474974513) ...
> minimize: using org.jmol.minimize.forcefield.ForceFieldUFF
> 17 atoms will be minimized.
> minimize: creating bonds...
> minimize: setting atom types...
> Couldn't find file: UFF.txt
> Exception null in getResource UFF.txt
> 0 force field parameters read
>
>
>
I don't think these are related, but they might be both security settings
issues. Pretty much that's what we are seeing changing in browser updates
these days.
> Test case is avalable at
> http://biomodel.uah.es/angel/test/Jmol_local_scripts.zip
> Unzip and run from disk, not from server.
> (Uses monolithic applet for simplicity; I've tested with the split
> applet too)
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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