[Cdk-devel] [ cdk-Bugs-862930 ] Smiles parser loops endlessly on H[O+](H)H

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Bugs item #862930, was opened at 2003-12-19 14:34
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Category: org.openscience.cdk.smiles
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Egon Willighagen (egonw)
Assigned to: Christoph Steinbeck (steinbeck)
Summary: Smiles parser loops endlessly on H[O+](H)H

Initial Comment:
When entering H[O+](H)H in JCP, the SMILES parser 
hangs with this trace: 
 
InsertSMILES: [H][O+]([H])[H] 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
Processing: [ 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
Assembling atom from: H 
org.openscience.cdk.smiles.SmilesParser DEBUG: Parse 
everythings before and including element symbol 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
Parsing char: H 
org.openscience.cdk.smiles.SmilesParser DEBUG: Found 
element symbol: null 
org.openscience.cdk.smiles.SmilesParser ERROR: Could 
not parse atom string: H 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
Exception: null 
org.openscience.cdk.smiles.SmilesParser DEBUG: 
java.lang.NullPointerException 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
org.openscience.cdk.smiles.SmilesParser.assembleAtom(SmilesParser.java:453) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:228) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
org.openscience.jchempaint.InsertFromSmiles$OpenAction.generateModel(InsertFromSmiles.java:95) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
org.openscience.jchempaint.InsertFromSmiles$OpenAction.actionPerformed(InsertFromSmiles.java:87) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1786) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1839) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:245) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Component.processMouseEvent(Component.java:5100) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Component.processEvent(Component.java:4897) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Container.processEvent(Container.java:1569) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Component.dispatchEventImpl(Component.java:3615) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Container.dispatchEventImpl(Container.java:1627) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Component.dispatchEvent(Component.java:3477) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:3483) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3198) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3128) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Container.dispatchEventImpl(Container.java:1613) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Window.dispatchEventImpl(Window.java:1606) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.Component.dispatchEvent(Component.java:3477) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventQueue.dispatchEvent(EventQueue.java:456) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:145) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137) 
org.openscience.cdk.smiles.SmilesParser DEBUG:  at 
java.awt.EventDispatchThread.run(EventDispatchThread.java:100) 
org.openscience.cdk.smiles.SmilesParser DEBUG: null 
o 
 
(last line keeps repeating) 
 

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