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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