Using Reactor with IJC

Good morning

I am trying to use Reactor within IJC, and addding our own reactions.

I choose 'Select Reaction' > Select tab user Library

There already appears to be some place holders for reactiosn there.

So I chose 'Edit' and sketched my reaction (attached)

Entered a name and choose 'Save'

The following stack trace appears

java.lang.ArrayIndexOutOfBoundsException: -1
 at java.util.Vector.setElementAt(Unknown Source)
 at com.im.ijc.reactor.editor.ReactionInputPanel$ReactionFilterListModel.setElementAt(ReactionInputPanel.java:151)
 at com.im.ijc.reactor.editor.ReactionInputPanel$7.actionPerformed(ReactionInputPanel.java:428)
 at org.netbeans.core.windows.services.NbPresenter$ButtonListener.actionPerformed(NbPresenter.java:1276)
 at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
 at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
 at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
 at java.awt.Component.processMouseEvent(Unknown Source)
 at javax.swing.JComponent.processMouseEvent(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.LightweightDispatcher.retargetMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
 at java.awt.Container.dispatchEventImpl(Unknown Source)
 at java.awt.Window.dispatchEventImpl(Unknown Source)
[catch] at java.awt.Component.dispatchEvent(Unknown Source)
 at java.awt.EventQueue.dispatchEvent(Unknown Source)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:104)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
 at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
 at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
 at java.awt.Dialog$1.run(Unknown Source)
 at java.awt.Dialog$3.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.awt.Dialog.show(Unknown Source)
 at org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:985)
 at org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:1019)
 at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:1007)
 at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:115)
 at org.openide.util.Mutex.doEventAccess(Mutex.java:1355)
 at org.openide.util.Mutex.readAccess(Mutex.java:268)
 at org.netbeans.core.windows.services.NbPresenter.show(NbPresenter.java:992)
 at java.awt.Component.show(Unknown Source)
 at java.awt.Component.setVisible(Unknown Source)
 at java.awt.Window.setVisible(Unknown Source)
 at java.awt.Dialog.setVisible(Unknown Source)
 at com.im.ijc.reactor.editor.ReactionInputPanel$3.actionPerformed(ReactionInputPanel.java:272)
 at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
 at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
 at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
 at java.awt.Component.processMouseEvent(Unknown Source)
 at javax.swing.JComponent.processMouseEvent(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.LightweightDispatcher.retargetMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.dispatchEvent(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 org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:104)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
 at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
 at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
 at java.awt.Dialog$1.run(Unknown Source)
 at java.awt.Dialog$3.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.awt.Dialog.show(Unknown Source)
 at org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:985)
 at org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:1019)
 at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:1007)
 at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:115)
 at org.openide.util.Mutex.doEventAccess(Mutex.java:1355)
 at org.openide.util.Mutex.readAccess(Mutex.java:268)
 at org.netbeans.core.windows.services.NbPresenter.show(NbPresenter.java:992)
 at java.awt.Component.show(Unknown Source)
 at java.awt.Component.setVisible(Unknown Source)
 at java.awt.Window.setVisible(Unknown Source)
 at java.awt.Dialog.setVisible(Unknown Source)
 at com.im.ijc.reactor.editor.ReactorEditorPanel.selectReactionButtonActionPerformed(ReactorEditorPanel.java:687)
 at com.im.ijc.reactor.editor.ReactorEditorPanel.access$200(ReactorEditorPanel.java:71)
 at com.im.ijc.reactor.editor.ReactorEditorPanel$2.actionPerformed(ReactorEditorPanel.java:165)
 at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
 at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
 at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
 at java.awt.Component.processMouseEvent(Unknown Source)
 at javax.swing.JComponent.processMouseEvent(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.LightweightDispatcher.retargetMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
 at java.awt.LightweightDispatcher.dispatchEvent(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 org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:104)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
 at java.awt.EventDispatchThread.pumpEventsForFilter(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)

I have also tried to choose 'Add', sketch the reaction, add a name, but the list of reactions stays blank as if nothing as happened.

When I choose a reaction from the list, it works fine and I can select inputs and enumerate compounds.

Can you let us know what the correct procedure is to add new reactions ?

Thanks

Catherine

Dear Catherine,

Thank you for reporting this issue, we will fix the problem as soon as possible.

Until then, you have to copy your library file (or an empty file) to the .chemaxon folder in your home directory. (Note that the first character is dot) If you are using an existing library file, it must be in mrv format.

Your home directory is usually C:\Documents and Settings\loginname in most Windows systems, C:\Users\loginname in Windows7 systems, and /home/username in linux systems.

The name of the file must be "user_reaction_library.mrv" (without the quotes, fully lowercase).

When the file is present, the user library can be edited properly.

Sorry for the inconvenience.

Best regards,

Istvan Rabel

Thanks for your help

I have now noticed that after restarting IJC, my reaction is there now.

Catherine

This problem should be fixed since IJC 5.3.6.

Tim

I have just tried it and it works perfectly now.

Thanks

Catherine