No IUPAC and smiles calculation: NullPointerException

Im using instant J chem 5.5

If you make a new entry in the database and draw a molecule it used to generate a smiles and a IUPAC name. However after about 100 entries this doesn't work anymore. This is the error message:

 

java.lang.NullPointerException
 at com.im.ijc.core.api.renderers.TextRendererHelper.<init>(TextRendererHelper.java:50)
 at com.im.ijc.renderers.impl.MultiLineTextRenderer.createViewer(MultiLineTextRenderer.java:160)
 at com.im.ijc.renderers.impl.TextRenderer.createViewer(TextRenderer.java:45)
 at com.im.ijc.widgets.table.TableCellViewer.fromRendererViewable(TableCellViewer.java:57)
 at com.im.ijc.widgets.table.WBTableWidget.showViewer(WBTableWidget.java:513)
 at com.im.ijc.core.api.actions.DetailViewSelectedDataAction.performAction(DetailViewSelectedDataAction.java:32)
 at org.openide.util.actions.NodeAction.performAction(NodeAction.java:295)
 at org.openide.util.actions.CallableSystemAction$1.run(CallableSystemAction.java:129)
 at org.openide.util.actions.ActionInvoker$1.run(ActionInvoker.java:95)
 at org.openide.util.actions.ActionInvoker.doPerformAction(ActionInvoker.java:116)
 at org.openide.util.actions.ActionInvoker.invokeAction(ActionInvoker.java:99)
 at org.openide.util.actions.CallableSystemAction.actionPerformed(CallableSystemAction.java:126)
 at org.openide.util.actions.NodeAction.actionPerformed(NodeAction.java:283)
 at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
 at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
 at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
 at javax.swing.AbstractButton.doClick(Unknown Source)
 at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
 at javax.swing.plaf.basic.BasicMenuItemUI$Handler.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.dispatchEventImpl(Unknown Source)
 at java.awt.EventQueue.access$000(Unknown Source)
 at java.awt.EventQueue$1.run(Unknown Source)
 at java.awt.EventQueue$1.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
 at java.awt.EventQueue$2.run(Unknown Source)
 at java.awt.EventQueue$2.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
 at java.awt.EventQueue.dispatchEvent(Unknown Source)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:137)
 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)
[catch] at java.awt.EventDispatchThread.run(Unknown Source)

What should I do?

Greetings

Hello,

looking at the error message this tells us that you've tried to view the value in its viewer (using 'view value' action or its F3 shortcut) but there is a bug when the value is missing and thus the error is displayed. This should be easy to fix and we will deliver the fix on next version.

OTOH the doesn't solve the original problem: IJC not generating smiles and IUPAC name. Can you tell us more details what exactly you have done before?

-Radim Kubacki

Thanks for the reply.

You're right about the 'view value' button and the error message. I don't understand why the calculation of IUPAC and Smiles doesn't work anymore. It did a week ago.

I have made a local database on a local computer. I make new entries by clicking on new field and then I sketch the molecule in the marvin application. I click on 'add' and then the IUPAC and smiles should be calculated. I have entered 110 entries and this has worked. I have arrived now at the 116 entry and it doesn't work anymore.

 

Could you check your license? Possibly missing or expired license can cause that chemical terms fields can stop working.

If licenses are correct, could you tests a few more things, please:

- when you add a new chemical terms field (any calculation) is it computed for all rows?

- when you modify a molecule (which already has IUPAC chemical terms column calculated correctly) is it updated or it remains as it is?

Dear sir/madam,

 

It is still not working. I checked the license: is ok.

 

-If I add a new compound both IUPAC and smiles are not calculated. There are no other calculated fields.

-If I change an already existing compound, it does re-calculate.

 

Thanks in advance for the help.

 

Greetings

Annemiek

We are still unable to reproduce this. Any of the following could help us to resolve it:

• if it's local db, is it possible to zip it and send to us (phamernik at chemaxon dot com) - r-click to schema and use "backup schema to zip". If it's not localdb, is it possible to export the data and send just sdf?


• if you can add some other chemical terms field to that table and see if it's calculated for all rows or just some?


• does any IUPAC and smiles chemical terms fields for you in other schema?

thank you.