NullPointerException running FlexX from Biosolveit

Hi,

i just started using KNIME in combination with FlexX Docking software from Biosolveit. Testing the FlexX installation worked fine but everytime I try to execute the FlexX Node I get a NullPointerException. Maybe somebody can help me with this problem ( find Debug output below ). It looks like a problem occuring not in the FlexX part itself.

Philipp

DEBUG NodeContainerEditPart OpenBabel 0:0:1 (EXECUTED) DEBUG NodeContainerEditPart SDF Reader 0:0:2 (EXECUTED) DEBUG ExecuteAllAction Starting execution of all nodes DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: MARKEDFOREXEC DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: QUEUED DEBUG KnimeResourceNavigator state changed to EXECUTING DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG NodeContainer Workflow Manager 0 has new state: EXECUTING DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforePreExecution DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: PREEXECUTE DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforeExecution DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: EXECUTING DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG LocalNodeExecutionJob Compute FlexX Docking 0:0:3 Start execute DEBUG Compute FlexX Docking reset DEBUG Compute FlexX Docking clean output ports. ERROR Compute FlexX Docking Execute failed: ("NullPointerException"): null DEBUG Compute FlexX Docking Execute failed: ("NullPointerException"): null java.lang.NullPointerException at biosolveit.toolkit.Toolkit.readMoleculeToBufferedDataTable(Unknown Source) at biosolveit.flexx.docking.FlexXNodeModel.execute(Unknown Source) at org.knime.core.node.NodeModel.execute(NodeModel.java:582) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:438) at org.knime.core.node.Node.execute(Node.java:704) at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:785) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:143) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238) DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforePostExecution DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: POSTEXECUTE DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doAfterExecute - failure DEBUG Compute FlexX Docking reset DEBUG Compute FlexX Docking clean output ports. DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: IDLE DEBUG Compute FlexX Docking Configure succeeded. (Compute FlexX Docking) DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: CONFIGURED DEBUG KnimeResourceNavigator state changed to CONFIGURED DEBUG NodeContainer KNIME_project 0:0 has new state: CONFIGURED DEBUG NodeContainer KNIME_project 0:0 has new state: CONFIGURED DEBUG NodeContainer Workflow Manager 0 has new state: IDLE DEBUG NodeContainerEditPart SDF Reader 0:0:2 (EXECUTED) DEBUG NodeContainerEditPart Compute FlexX Docking 0:0:3 (CONFIGURED) DEBUG WorkflowRootEditPart WorkflowRoot: command stack changed DEBUG NodeContainerEditPart ExtraInfo changed, updating bounds and visuals...

This is obviously a problem in the FlexX node so you should ask the author/vendor of this node.

Hi Philipp,

which version of the BioSolveIT interface nodes do you use?
We had this type of problem in a former version, if no project
file was configured for the FlexX Docking node.
However, we thought to have fixed this problem already.
The latests version is 1.2.0 which can be found at
http://www.biosolveit.de/KNIME/

Holger

Hi Holger,

thanks for your reply. I’m using Biosolveit version 1.2.0.000042 and KNIME version 2.1.1.
Furthermore I’m using LeadIT as binary. But the test in preferences worked fine. I tried
different project files and different ligands with the same result in each case.

Philipp

Hi Philipp,
in the configure dialog for FlexX Docking there is at the very end a checkbox called “Keep debug files an show after run”.

Could you please ckeck this box and rerun the test.
In this case a log message should pop up after running
the docking. Could you please send us the content of the file.
Maybe as text file attachment directly to support@biosolveit.de

Thanks

Holger

Hi Holger,
i’ve enabled the checkbox you mentioned but there is no pop up after the run failed. I can zip the temporary biosolveit project directory created by KNIME and send it to you. From these files I can see that the FlexX run itself worked fine. Would these files help you (including FlexX_Debug.txt) ?
Philipp

Hi Philipp,

this is really strange. Yes it would help very much, if you could send the whole project. Best would if if you would also include all the data, i.e. disable "Exclude data from export.

Thanks,
Holger

Hi Holger,
sent all the data to support@bios…
Philipp

Hi Philipp,

I actually figured out, what causes the problem.

Here is a quick fix for this problem, that you can
add yourself.
We will of course fix the problem in the next version.

Here is the workaround (for version 1.2.0):
In the configure dialog of the FlexX Docking node
goto the tab “Script Settings” and add the extension
.mol2 to @posesfile.

So, exchange these lines

  LIGAND
    WRITE "@posesfile" y y 1-@nof_poses
  END

by the following ones

  LIGAND
    WRITE "@posesfile.mol2" y y 1-@nof_poses
  END

Now the results are written in mol2 format instead of SD format.
This circumvents the actual problem that we currently have with
poses written in SD format in this case.

Holger

Hi,

I just want to add that we now fixed this problem in our
latest version is 1.2.1 which can be found at
http://www.biosolveit.de/KNIME/

Holger