[Cdk-devel] [ cdk-Bugs-780545 ] Unable to render a single atom molecule in 2D

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Bugs item #780545, was opened at 2003-07-30 22:04
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You can respond by visiting: 
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Category: org.openscience.cdk.renderer
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Stephen Tomkinson (stomkinson)
Assigned to: Nobody/Anonymous (nobody)
Summary: Unable to render a single atom molecule in 2D

Initial Comment:
If I create a single atomed molecule, e.g.:
<molecule>
  <atomArray>
    <atom id="a1" elementType="c" />
  </atomArray>
</molecule>

I am unable to pass this to the 2D Renderer with the 
option of the renderer generating the co-ordinates. I 
haven't tried generating the co-ordinates myself.

I get the following exception:
java.lang.ArrayIndexOutOfBoundsException: -1
        at org.openscience.cdk.AtomContainer.getAtomAt
(AtomContainer.java:162)
        at 
org.openscience.cdk.layout.AtomPlacer.getInitialLongestC
hain(AtomPlac
er.java:357)
        at 
org.openscience.cdk.layout.StructureDiagramGenerator.g
enerateCoordina
tes(StructureDiagramGenerator.java:193)
        at 
org.openscience.cdk.layout.StructureDiagramGenerator.g
enerateCoordina
tes(StructureDiagramGenerator.java:227)
        at MainWindow.jButtonParseActionPerformed
(Unknown Source)
        at MainWindow.access$100(Unknown Source)
        at MainWindow$2.actionPerformed(Unknown 
Source)
        at javax.swing.AbstractButton.fireActionPerformed
(Unknown Source)
        at 
javax.swing.AbstractButton$ForwardActionEvents.actionP
erformed(Unknow
n Source)
        at 
javax.swing.DefaultButtonModel.fireActionPerformed
(Unknown Source)
        at javax.swing.DefaultButtonModel.setPressed
(Unknown Source)
        at javax.swing.AbstractButton.doClick(Unknown 
Source)
        at 
javax.swing.plaf.basic.BasicRootPaneUI$DefaultAction.act
ionPerformed(
Unknown Source)
        at javax.swing.SwingUtilities.notifyAction(Unknown 
Source)
        at javax.swing.JComponent.processKeyBinding
(Unknown Source)
        at javax.swing.KeyboardManager.fireBinding
(Unknown Source)
        at 
javax.swing.KeyboardManager.fireKeyboardAction
(Unknown Source)
        at 
javax.swing.JComponent.processKeyBindingsForAllCompon
ents(Unknown Sou
rce)
        at javax.swing.JComponent.processKeyBindings
(Unknown Source)
        at javax.swing.JComponent.processKeyEvent
(Unknown Source)
        at java.awt.Component.processEvent(Unknown 
Source)
        at java.awt.Container.processEvent(Unknown 
Source)
        at java.awt.Component.dispatchEventImpl
(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown 
Source)
        at java.awt.Component.dispatchEvent(Unknown 
Source)
        at 
java.awt.KeyboardFocusManager.redispatchEvent
(Unknown Source)
        at 
java.awt.DefaultKeyboardFocusManager.dispatchKeyEven
t(Unknown Source)

        at 
java.awt.DefaultKeyboardFocusManager.preDispatchKeyE
vent(Unknown Sour
ce)
        at 
java.awt.DefaultKeyboardFocusManager.typeAheadAssert
ions(Unknown Sour
ce)
        at 
java.awt.DefaultKeyboardFocusManager.dispatchEvent
(Unknown Source)
        at java.awt.Component.dispatchEventImpl
(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown 
Source)
        at java.awt.Window.dispatchEventImpl(Unknown 
Source)
        at java.awt.Component.dispatchEvent(Unknown 
Source)
        at java.awt.EventQueue.dispatchEvent(Unknown 
Source)
        at 
java.awt.EventDispatchThread.pumpOneEventForHierarch
y(Unknown Source)

        at 
java.awt.EventDispatchThread.pumpEventsForHierarchy
(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents
(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents
(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown 
Source)

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