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From: SourceForge.net <no...@so...> - 2003-07-30 22:04:28
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Bugs item #780545, was opened at 2003-07-30 22:04 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=780545&group_id=20024 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) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=780545&group_id=20024 |