Hi Mikhail,
Sorry for the slow response! Yes, I was passing the molecule(s) in in MOL(SDF) format. Your suggested process of 'dearomatize', then 'aromatize' works - thanks. However, after doing this, I am having some problems with the Substructure Matcher node when I choose to align to query:
ERROR Substructure Matcher Execute failed: array: reserve(): no memory
2011-10-13 10:54:46,278 ERROR KNIME-Worker-2 Substructure Matcher : Execute failed: array: reserve(): no memory
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 Substructure Matcher : Execute failed: array: reserve(): no memory
com.ggasoftware.indigo.IndigoException: array: reserve(): no memory
at com.ggasoftware.indigo.Indigo.checkResult(Indigo.java:49)
at com.ggasoftware.indigo.IndigoObject.clone(IndigoObject.java:63)
at com.ggasoftware.indigo.knime.submatcher.IndigoSubstructureMatcherNodeModel.execute(IndigoSubstructureMatcherNodeModel.java:127)
at org.knime.core.node.NodeModel.execute(NodeModel.java:668)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:524)
at org.knime.core.node.Node.execute(Node.java:873)
at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:840)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:166)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:124)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:239)
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 WorkflowManager : Substructure Matcher 0:0:4 doBeforePostExecution
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 NodeContainer : Substructure Matcher 0:0:4 has new state: POSTEXECUTE
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 KnimeResourceNavigator : Node message changed: ERROR: Error in sub flow.
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 NodeContainer : Align_structures_to_scaffold (v3) 0:0 has new state: EXECUTING
2011-10-13 10:54:46,278 DEBUG KNIME-Worker-2 WorkflowManager : Substructure Matcher 0:0:4 doAfterExecute - failure
I am working with an input of ~10,000 molecules (Win7 64-bit; 32-bit KNIME 2.4.2; latest Indigo nodes)
Kind regards
James