Hi All,
I’m trying to use the 3D Alignment Node. I’ve used it in the past without issue. But with my current workflow I constantly get an error:
ERROR RDKit Open 3D Alignment Execute failed: (“GenericRDKitException”): null
Memory usage is fine. Should not be an out of memory issue. I’m generating conformers, optimize them and then select by RMSD with RDKit nodes. I then want to align them on each other. But for some reason I always get this error. See below for log file.
EDIT:
Another issue I have is that I get no alignments at all:
WARN RDKit Open 3D Alignment Alignment of query molecule failed: org.RDKit.GenericRDKitException [All rows]
This happens with the same molecule but different conformers. If I do the align in RDKit-Python with the exact same molecules it works as expected.
Log file:
2014-03-04 14:42:34,231 ERROR KNIME-Worker-16 RDKit Open 3D Alignment : Execute failed: (“GenericRDKitException”): null
2014-03-04 14:42:34,232 DEBUG KNIME-Worker-16 RDKit Open 3D Alignment : Execute failed: (“GenericRDKitException”): null
org.RDKit.GenericRDKitException
at org.RDKit.RDKFuncsJNI.ForceField_MMFFHasAllMoleculeParams(Native Method)
at org.RDKit.ForceField.MMFFHasAllMoleculeParams(ForceField.java:224)
at org.rdkit.knime.nodes.open3dalignment.RDKitOpen3DAlignmentNodeModel.preProcessing(RDKitOpen3DAlignmentNodeModel.java:512)
at org.rdkit.knime.nodes.AbstractRDKitNodeModel.execute(AbstractRDKitNodeModel.java:773)
at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
at org.knime.core.node.Node.execute(Node.java:924)
at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)