java.rmi.RemoteException: error: unknown flag: absolute

Hello again.





Well I seem to get the error below when executing the following in the cartridge:





jc_compare (t2.cd_smiles,t1.arosmiles,'t:e exactChargeMatchingOption:e doubleBondStereo:A HCountMatching:E exactStereoMatching:y absoluteStereo:a stereoSearch:y') = 1





error output:





ORA-29532: Java call terminated by uncaught Java exception:


java.rmi.ServerException: RemoteException occurred in server thread; nested


exception is:


java.rmi.RemoteException: error: unknown flag:


absolutestereo


Use -h for help.


ORA-29532: Java call terminated by uncaught Java exception:


java.rmi.ServerException: RemoteException occurred in server thread; nested


exception is:


java.rmi.RemoteException: error: unknown flag:


absolutestereo


Use -h for help.


BEGIN


*


ERROR at line 1:


ORA-29532: Java call terminated by uncaught Java exception:


java.rmi.ServerException: RemoteException occurred in server thread; nested


exception is:


java.rmi.RemoteException: error: unknown flag: absolutestereo


Use -h for help.


ORA-06512: at "CSPACE.QUICKBUILDPCKV3D", line 609


ORA-06512: at line 2





SEVERE: Error in RMI call


java.lang.IllegalArgumentException: error: unknown flag: absolutestereo


Use -h for help.


at chemaxon.sss.search.SearchOptions.setOption(SearchOptions.java:1248)


at chemaxon.sss.search.MolSearchOptions.setOption(MolSearchOptions.java:419)


at chemaxon.jchem.interop.core.InteropJChemSearch.setOptions(InteropJChemSearch.java:58)


at chemaxon.jchem.interop.core.InteropMolSearch.<init>(InteropMolSearch.java:75)


at chemaxon.jchem.cartridge.rmi.impl.MolSearchImpl.matchCount(MolSearchImpl.java:49)


at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)


at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)


at java.lang.reflect.Method.invoke(Method.java:597)


at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:305)


at sun.rmi.transport.Transport$1.run(Transport.java:159)


at java.security.AccessController.doPrivileged(Native Method)


at sun.rmi.transport.Transport.serviceCall(Transport.java:155)


at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:535)


at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)


at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)


at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)


at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)


at java.lang.Thread.run(Thread.java:619)





Can you please explain how this error might arise, considering all the data is ChemAxon generated and unmodified (I have not explicitly removed any flags prior to the search)...This has worked in the past and so I assume this is an internal data issue of sorts or related to the source file data which is Enamine screening collection part 4)





Cheers,





Daniel.

Hi Daniel,





Which JChem version is it?





Thanks


Peter

Hello Peter,





I think everything is currently at version 5.0.3...





Thanks,





Daniel.

Daniel,





This is a bug in JChem Cartridge which will be fixed in JChem version 5.0.6 or JChem version 5.1 whichever comes first.





Until then, the following workaround may or may not be applicable in your environment:





Force jc_compare to execute in domain index scan mode. The most straightforward way of doing this is to avoid referencing table t1 in the SELECT statement in which jc_compare is called:


1. open a cursor on table t1 returning the desired values from the arosmiles column;


2. in a loop, call jc_compare on table t2 for each value arosmiles returned by the cursor.





In a quasi-pseudo-code:

Code:

declare   cursor c1 is select arosmiles from t1;   qry blob; begin   for t in c1 loop     execute immediate 'select ... from t2 where jc_compare  (t2.cd_smiles,:a,''t:e exactChargeMatchingOption:e doubleBondStereo:A HCountMatching:E exactStereoMatching:y absoluteStereo:a stereoSearch:y'') = 1' using t.arosmiles;   end loop; end;

Thank you for reporting this bug and sorry for the inconvenience.





Peter

Thanks Peter - great turnaround - we will wait until 5.1





Cheers,





Daniel.

Hi Daniel,





JChem 5.0.6 has been released with the fix for this problem.





Thank you for your patience,


Peter