[Jmol-developers] [ jmol-Bugs-3400976 ] "show smiles" may hang the app

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Bugs item #3400976, was opened at 2011-08-30 21:11
Message generated for change (Tracker Item Submitted) made by aherraez
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Category: Algorithms
Group: v12
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Angel Herraez (aherraez)
Assigned to: Bob Hanson (hansonr)
Summary: "show  smiles" may hang the app

Initial Comment:
Entering "show smiles" in the scrip console hangs the app depending on what or how the model was loaded:
(12.2.RC5)

[ModelKit mode]; show smiles; # OK
load $caffeine; show smiles; # OK
load ==glc; show smiles; # OK
load ==2TY; show smiles; # app hangs

I understand that calculating the smiles is hard for some molecules, but the error should be avoided. Maybe just display "This is too complex to obtain the SMILES string" 

The java console says:
2-HYDROXY-5-{[(1E)-2-PHENYLETHYLIDENE]AMINO}-L-TYROSINE
Exception in thread "QueueThread0" java.lang.NullPointerException
	at javax.vecmath.Tuple3f.sub(Tuple3f.java:253)
	at org.jmol.smiles.SmilesSearch.isDiaxial(Unknown Source)
	at org.jmol.smiles.SmilesGenerator.setBondDirections(Unknown Source)
	at org.jmol.smiles.SmilesGenerator.getSmilesComponent(Unknown Source)
	at org.jmol.smiles.SmilesGenerator.getSmiles(Unknown Source)
	at org.jmol.smiles.SmilesMatcher.getSmiles(Unknown Source)
	at org.jmol.viewer.Viewer.getSmiles(Unknown Source)
	at org.jmol.script.ScriptEvaluator.show(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)


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