Output a CDKCell

Community Extensions CDK
#1

Hi all,

I am writing a node that outputs a column of CDKCell which stores IAtomContainer object. I already imported the available knime-cdk.jar library (file attached) but my node fails with a  null returned when I tried to create a column:

DataColumnSpec[] allColSpecs = new DataColumnSpec[1];

allColSpecs[0] =
 new DataColumnSpecCreator("Molecules Properties", CDKCell.TYPE).createSpec();

I appreciate any help.

#2

Can you please post the NodeModel class, from the code above I don't see any problem where null might be returned. Thanks.

#3

Hi Gabriel,

I attached my NodeModel java file. I appreciate any help. Thanks.

#4

Hi,

are you sure that the execute fails at line 77 rather than at line 85? You create a CDKCell with a null pointer, which will give you a NullPointerException.

We are currently changing that behaviour to improve the API.

If you declare org.openscience.cdk.knime as dependency in your plugin.xml, you won't have to import the actual knime-cdk.jar file.

Cheers,

Stephan

#5

Hi Stephan,

Yes, the execute fails at line 77 when I debug the program.

I tried adding org.openscience.cdk.knime as dependency in my plugin.xml and there was not matched plug-in to add. Is there any way to deal with that apart from importing the knime-cdk.jar file?

I appreciate any help. Thanks.

Caroline


        


        

        

           
           
           
         


         

            
            
          


      

      

        

          

            
              

                
              

          

          

          


          
              
              
          #6
          
        

        

          
Hi Caroline,


when you install the CDK plugin via the community update site, you should be able to find org.openscience.cdk.knime in the plugin dependencies tab. That should do it. Have you installed the plugin before attempting to add it as dependency?


If it is still not working, please post your plugin.xml (either here or to beisken@ebi.ac.uk), and I can take a look at your settings.


Cheers,


Stephan