#509 "show smiles" may hang the app

v12
closed
Algorithms (14)
5
2011-08-30
2011-08-30
No

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)

Discussion

  • Bob Hanson

    Bob Hanson - 2011-08-30

    The imine caused a fault. That is fixed.

     
  • Bob Hanson

    Bob Hanson - 2011-08-30

    The imine caused a fault. That is fixed.

     
  • Bob Hanson

    Bob Hanson - 2011-08-30
    • status: open --> closed
     

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