[Jmol-users] State scripts with calculated H bonds

[Brian M. <bm...@iu...>]

There is an apparent bug, or at least over-sensitivity in the way Jmol
reads in a state script for a small molecule which contains calculated
hydrogen bonds. I attach two scripts derived from Bob's sucrose example
("load sucrose.cif {1 1 1}; hbonds calculate;"). The first is as written out
by the signed applet with "Save script with state"; the second is identical
excepte for some white-space changes (most notably the inclusion of a blank
line within the data "connect_atoms" block).

The first loads and renders fine; the second causes the applet to crash
and the Java console shows the following error trace:

Exception in thread "QueueThread0" java.lang.ArrayIndexOutOfBoundsException: 0
	at org.jmol.modelset.ModelSet.connect(Unknown Source)
	at org.jmol.viewer.Viewer.connect(Unknown Source)
	at org.jmol.script.ScriptEvaluator.data(Unknown Source)
	at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
	at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
	at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
	at org.jmol.script.ScriptEvaluator.function(Unknown Source)
	at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
	at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
	at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
	at org.jmol.script.ScriptEvaluator.function(Unknown Source)
	at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
	at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
	at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
	at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
	at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source)
	at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source

Can this be easily fixed? (The IUCr enhanced figure toolkit saves scripts
is a manner that is not guaranteed to preserve whitespace.)

The problem appears to have been present since at least Jmol 12.0.10, but is
still present in 12.1.44.

Thanks
Brian