Hello,
I cannot execute the “99_Community/04_Vernalis/03_Simple_MMP_Example” worflow available in KNIME examples server.
It fails on the MMP Molecule Fragment (RDKit) node, giving the following eror message:
INFO MMP Molecule Fragment (RDKit) 2:2 Fragmentation SMIRKS: [#6+0;!$(*=,#[!#6]):1]!@!=!#[*:2]>>[*:1]-[*].[*:2]-[*] (Upto 1 cuts)
INFO MMP Molecule Fragment (RDKit) 2:2 Using 6 threads and 120 queue items to parallel process...
INFO MMP Molecule Fragment (RDKit) 2:2 Starting fragmentation at Wed Jun 12 11:30:04 CEST 2019
ERROR MMP Molecule Fragment (RDKit) 2:2 Execute failed: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
2019-06-12 11:40:47,247 : DEBUG : KNIME-Worker-34 : Node : MMP Molecule Fragment (RDKit) : 2:2 : Execute failed: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
java.util.concurrent.ExecutionException: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at com.vernalis.knime.mmp.nodes.fragutil.fragment.abstrct.AbstractMMPFragmentNodeModel$5.processFinished(AbstractMMPFragmentNodeModel.java:677)
at org.knime.core.util.MultiThreadWorker.callProcessFinished(MultiThreadWorker.java:316)
at org.knime.core.util.MultiThreadWorker.access$1(MultiThreadWorker.java:297)
at org.knime.core.util.MultiThreadWorker$ComputationTask.done(MultiThreadWorker.java:462)
at java.util.concurrent.FutureTask.finishCompletion(FutureTask.java:384)
at java.util.concurrent.FutureTask.set(FutureTask.java:233)
at java.util.concurrent.FutureTask.run(FutureTask.java:274)
at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328)
at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:657)
at java.util.ArrayList.get(ArrayList.java:433)
at com.vernalis.knime.mmp.fragmentors.RWMolFragmentationFactory.applyDirectionalBond(RWMolFragmentationFactory.java:449)
at com.vernalis.knime.mmp.fragmentors.RWMolFragmentationFactory.assignCreatedDblBondGeometry(RWMolFragmentationFactory.java:1315)
at com.vernalis.knime.mmp.fragmentors.RWMolFragmentationFactory.assignCreatedDblBondGeometry(RWMolFragmentationFactory.java:1)
at com.vernalis.knime.mmp.fragmentors.AbstractFragmentationFactory.rawFragmentMoleculeAlongBond(AbstractFragmentationFactory.java:729)
at com.vernalis.knime.mmp.fragmentors.AbstractFragmentationFactory.breakMoleculeAlongMatchingBonds(AbstractFragmentationFactory.java:401)
at com.vernalis.knime.mmp.nodes.fragutil.fragment.abstrct.AbstractMMPFragmentNodeModel.runFragmentationsOnRow(AbstractMMPFragmentNodeModel.java:967)
at com.vernalis.knime.mmp.nodes.fragutil.fragment.abstrct.AbstractMMPFragmentNodeModel$5.compute(AbstractMMPFragmentNodeModel.java:643)
at com.vernalis.knime.mmp.nodes.fragutil.fragment.abstrct.AbstractMMPFragmentNodeModel$5.compute(AbstractMMPFragmentNodeModel.java:1)
at org.knime.core.util.MultiThreadWorker$ComputationTask$1.call(MultiThreadWorker.java:442)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
... 6 more
KNIME 3.7.2 on Windows 7 x64
Vernalis plugin 1.20.1
RDKit plugin 3.6.1