error

ChemAxon 60ee1f1328

09-02-2006 11:01:26

Can you please explain the error message below?


I think it must be caused by a call to JC_EQUALS using a previously jcman.standardised SMILES string?


"CNC(=O)c1c2CCCCc2sc1NC(=O)c3cccs3"





BEGIN


*


ERROR at line 1:


ORA-29902: error in executing ODCIIndexStart() routine


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


java.lang.Exception: The following exception has been thrown by the servlet:


Exception: cannot import chime format


ORA-06512: at "JCHEM3.SUPPLIERMOLECULESV2TRG", line 1


ORA-04088: error during execution of trigger 'JCHEM3.SUPPLIERMOLECULESV2TRG'


ORA-06512: at "JCHEM3.MIGRATEJCTABLEPCK", line 467


ORA-06512: at line 2

ChemAxon aa7c50abf8

09-02-2006 12:04:05

I could not reproduce the problem using the following query:


Code:
select count(*) from jc_nci_1k where jc_equals(cd_smiles, 'CNC(=O)c1c2CCCCc2sc1NC(=O)c3cccs3') = 1;






Is "CNC(=O)c1c2CCCCc2sc1NC(=O)c3cccs3" the standardized form? If is not, could you specify, please, the standardizer configuration you are using?





Also, could you specify, please, the version of JChem which produces this error?





Also, could you, please, post the Java stack trace found in <tomcat-home>/logs/catalina.out?

ChemAxon 60ee1f1328

09-02-2006 12:25:09

Hi Peter,





This is how I am using jc_equals:





v_sql := 'SELECT molecule_id FROM ' || pJCTableName || ' WHERE jc_equals (cd_smiles,:a) = 1';





EXECUTE IMMEDIATE v_sql INTO RetVal USING pSmiles;





The input pSMILES used was previously generated in an Oracle table using 3.0.12 jcman vanilla standardiser configuration - I'm not sure if an xml file exist for this?





Good luck!





Daniel.

ChemAxon 60ee1f1328

09-02-2006 12:26:42

attachment?

ChemAxon aa7c50abf8

09-02-2006 12:34:39

Yes, please, create an attachement!

ChemAxon 60ee1f1328

09-02-2006 12:42:20

message

ChemAxon aa7c50abf8

09-02-2006 12:54:27

The problem occurs to during the import of the query structure. Bugs with similar symptoms has been fixed in JChem version 3.1.1 and 3.1.5. Would it not be possible to run the same queries with JChem version 3.1.5 to see if the problem persists?

ChemAxon 60ee1f1328

09-02-2006 13:01:39

Hi Peter,





I will assume to upgrade to these versions asap, before continuing.


If I witness the same behaviour with 3.1.5 then I will certianly get back to you on this thread, but in the meantime assume the cup is half full!





Cheers,


Daniel.

ChemAxon 60ee1f1328

09-02-2006 15:08:36

When I try and run jcman for 3.1.5 I get this error:





Unrecognized option: -client


Could not create the Java virtual machine.





If I run jcman for 3.0.12 (my old version), the gui kicks off and I see that I only have JVM 1.3...trouble is I thought I was on 1.4 i.e. my JAVA_HOME references a JRE that is C:\Program Files\Java\j2re1.4.2_10!?





Please help, I am properly confused now!





Daniel.

ChemAxon 9c0afc9aaf

09-02-2006 15:23:51

Hi,





It seems that you are trying to run jcman with an incompatible JRE.





If you type





Code:
java -version






this should confirm this.





Actually it is the PATH environment variable that determines which java will be found and executed.


If you want it to point to JAVA_HOME, then you should mention it in your PATH. Example for Windows:





%JAVA_HOME%\bin





Please note that the PATH is order sensitive, so it's best to put this at the front to make sure it's found first.





Do not forget to start a new console after changing environment variables.


You can check the current setting by typing:


Code:
echo %PATH%









Best regards,





Szilard

ChemAxon 60ee1f1328

09-02-2006 15:55:49

Great Thanks Szilard, that really helped - I'm now back in business using 3.1.5. Now to check that the original error does not occur again...


Thanks again,


Daniel.

ChemAxon 60ee1f1328

13-02-2006 10:55:28

Hi Peter,





SQL> drop index MoleculesV2fJCIdx;


drop index MoleculesV2fJCIdx


*


ERROR at line 1:


ORA-29856: error occurred in the execution of ODCIINDEXDROP routine


ORA-04063: stored procedure "JCHEM3.JC_IDXTYPE_IM" has errors





Do you think this means my cartridge install did not complete correctly?


I want to replace the index but as you can see I cannot?


(I cannot find the procedure above is it pacakged)





Cheers,


Daniel.

ChemAxon aa7c50abf8

13-02-2006 11:03:41

Hi Daniel,





Did you drop the jc_idxtype indexes before upgrading JChem Cartridge?





Cheers,


Peter

ChemAxon 60ee1f1328

13-02-2006 11:05:46

Hi Peter,





Alas I did not, I shall go and do so and re-install the cartridge...and then try again...





Thanks,


Daniel.

ChemAxon aa7c50abf8

13-02-2006 11:13:16

Hi Daniel,





Reinstall the old one, drop the indexes with the old one, then install the new one and re-create the indexes





Recent JChem versions have a more straightforward/simpler upgrade procedure, but this procedure is supported only for JChem version 3.1.1 or later.





Cheers,


Peter

ChemAxon 60ee1f1328

13-02-2006 11:15:22

Loud and clear Peter...thanks for the advice...


Daniel.

ChemAxon 60ee1f1328

13-02-2006 16:36:21

I have now upgraded to 3.1.5 and similarly


the same problem has occured?





Could this problem be related to how I have attempted to implement jc_equals i.e. with a bind variable?





v_sql := 'SELECT molecule_id FROM ' || pJCTableName || ' WHERE jc_equals (cd_smiles,:a) = 1';





EXECUTE IMMEDIATE v_sql INTO RetVal USING pSmiles;





ERROR at line 1:


ORA-29902: error in executing ODCIIndexStart() routine


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


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: cannot import chime format


ORA-06512: at "JCHEM3.SUPPLIERMOLECULESV2TRG", line 1


ORA-04088: error during execution of trigger 'JCHEM3.SUPPLIERMOLECULESV2TRG'


ORA-06512: at "JCHEM3.MIGRATEJCTABLEPCK", line 473


ORA-06512: at line 2





Smiles was previously registered and regenerated to 3.1.5:


"[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F"





The select statement below runs OK but returns no result (which is fine too):


select * from moleculesv2f where jc_equals (cd_smiles,'[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F') = 1





Tries to attach catalina.out!?





Cheers,


Daniel.

ChemAxon 60ee1f1328

13-02-2006 17:11:01

It appears that jc_equals does not work at all now with SMILES that I expect to return results for. The target table has been regenerated...but there are other tables that exist currently which have not yet been regenerated. 3.0.12 did uninstall corretly before install of 3.1.5, test.bat works ok however the jc_idxtype index did create very quickly...

ChemAxon aa7c50abf8

13-02-2006 17:35:27

If your structure tables have been created with JChemManager, the creation of a jc_idxtype index is instantanious.





Please, could you check to see what the jcsearch command line tool returns for the same molecules. The command would be something like:


Code:
jcsearch -q '[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F' DB:moleculesv2f



The connection properties to the DB are taken from the .jchem file in the ~/.chemaxon (on Unix/Linux) or %USERPROFILE%\chemaxon directory. This file is written by JChemManager. Before running jcsearch, connect using JChemManager to the appropriate database with the appropriate user login and JChemProperties table, then exit JChemManager.





Cheers,


Peter

ChemAxon 60ee1f1328

13-02-2006 18:10:46

I'll confess to being confused.


Previously I have had to administed the jc_index separately - I have not noticed jcman creating this index type before.


The jcsearch does not appear to work for structures that do not (a) or do (b) exist in my Moleculesv2f table





(a) C:\JChem3.1.5\jchem\bin>jcsearch -q '[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F' jchem3/autechre@inhibox:moleculesv2f


Error in '[O-][N+]( at molecule 1.file format not recognized





(b) C:\JChem3.1.5\jchem\bin>jcsearch -q 'BrC1=CC(=O)Oc2ccccc12' jchem3/autechre@inhibox:moleculesv2f


error: query file 'BrC1 is not available





I notice that "Exact" search in the JSP application no longer works for SMILES directly copied into the query (like it used to), rather "Exact fragment" appears now to do the same job? Could this be related to my apparently not seeing jc_equals working at all?





Another example where the SMILES certainly exists in the 3.1.5 re-generated table:





Smiles copied directly out of Oracle table "OC(=O)CSCCc1ccccn1"





select * from moleculesv2f where jc_equals (cd_smiles,'OC(=O)CSCCc1ccccn1') = 1


returns no rows





C:\JChem3.1.5\jchem\bin>jcsearch -q 'OC(=O)CSCCc1ccccn1' jchem3/autechre@inhibox


:moleculesv2f


Error in 'OC( at molecule 1.


file format not recognized





JSP "Exact" search - no results.





JSP "Exact fragment" returns the desired results.





I don't really want to rollback to previous version 3.0.12 as I will need to regenerate the tables in the reverse direction and of course my initial problem will still exist.





Best wishes,


Daniel.

ChemAxon 9c0afc9aaf

13-02-2006 18:32:15

Hi,





Just some quick comments on jcsearch usage:





1. Although both single and double quotation works in a Linux command prompt, you should only use double quotation in a Windows terminal.





2. You should not substitute database connection parameters instead of "DB", this should be written literally, it indicates that it is a table name you have specified, not a file name.


jcsearch uses the stored connection parameters that were specified for jcman.





So your command should look exactly like this:


Code:



jcsearch -q "[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F" DB:moleculesv2f






We will get back to you soon with the other issues.





Kind regards,





Szilard

ChemAxon 60ee1f1328

13-02-2006 19:53:57

Doh, Thanks Szilard, another t-shirt on it's way...will try again tomorrow...


Best wishes,


Daniel.

ChemAxon 60ee1f1328

14-02-2006 09:38:03

That's fine - returns results OK.





C:\JChem3.1.5\jchem\bin>jcsearch -q "OC(=O)CSCCc1ccccn1" DB:moleculesv2f


OC(=O)CSCCc1ccccn1


CC(SCCc1ccccn1)C(O)=O

ChemAxon 60ee1f1328

14-02-2006 09:52:25

A jc_equals search on another table seems to work OK and for the same table the JSP exact search returns results...this table is considerably smaller than moleculesv2f...

ChemAxon 60ee1f1328

14-02-2006 09:59:19

The creation of the jc_idxtype index that I create for moleculesv2f completes very fast for >2.5 million records and then of course jc_equals does not appear to work but to confirm other tables do work as noted above...

ChemAxon aa7c50abf8

14-02-2006 10:15:11

So the "cannot import chime format" error message appears to have gone away with the upgrade?





Please, check <tomcat-home>/logs/catalina.out again. Do you see warnings about moleculesv2f not fitting into the structure cache?

ChemAxon 60ee1f1328

14-02-2006 10:30:24

Hi Peter,





I am still having difficulty getting jc_equals to work for one of my larger tables which has been re-generated to 3.1.5...it appears to work for one which had not been through the regeneration process...I am now regenerating the table to 3.1.5 to see if it still works...





Daniel.

ChemAxon aa7c50abf8

14-02-2006 10:40:32

Please, could you check the catalina.out to see if there are any warnings about moleculesv2f not fitting into the structure cache? You can do this even with an on-going regeneration.





Thanks


Peter

ChemAxon 60ee1f1328

14-02-2006 13:22:54

I'm afraid this is happening now...





ORA-29902: error in executing ODCIIndexStart() routine


ORA-29532: Java call terminated by uncaught Java exception: java.lang.RuntimeException: The following exception has been thrown by the servlet:


Exception: ORA-01017: invalid username/password; logon denied


ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM3.JC_IDXTYPE_IM", line 183


ORA-06512: at line 1

ChemAxon 60ee1f1328

14-02-2006 13:51:16

One re-generated table aminesv2f gives me the expected results with an "exact" JSP search (single hit), the other table moleculesv2f gives me the expected results (single hit) with the "exact fragment" search, both search use exactly the same smiles string "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3"





All the queries below result in the warning "No query specified" followed


by lots of return results





jcsearch -t:e "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3" DB:aminesv2f


jcsearch -t:e "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3" DB:moleculesv2f


jcsearch -t:ef "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3" DB:aminesv2f


jcsearch -t:ef "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3" DB:moleculesv2f





Daniel.

ChemAxon aa7c50abf8

14-02-2006 13:57:49

You forgot the -q switch to indicate the query argument. Properly:





Code:
jcsearch -t:e -q "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3" DB:aminesv2f

ChemAxon 60ee1f1328

14-02-2006 14:06:52

Thanks Peter, now I am seeing more expected results.





C:\JChem3.1.5\jchem\bin>jcsearch -t:e -q "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3


" DB:aminesv2f


FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3


C:\JChem3.1.5\jchem\bin>jcsearch -t:e -q "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3


" DB:moleculesv2f


C:\JChem3.1.5\jchem\bin>jcsearch -t:ef -q "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC


3" DB:aminesv2f


FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3


C:\JChem3.1.5\jchem\bin>jcsearch -t:ef -q "FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC


3" DB:moleculesv2f


FC(F)(F)COc1nc(nc(n1)N2CCNCC2)N3CCCCC3





Can you help with my other problem above?


(I cannot use jc_equals at all now due to an apparent connection issue).





java.sql.SQLException: ORA-01017: invalid username/password; logon denied





at oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java)


at oracle.jdbc.ttc7.TTIoer.processError(TTIoer.java)


at oracle.jdbc.ttc7.O3log.receive2nd(O3log.java)


at oracle.jdbc.ttc7.TTC7Protocol.logon(TTC7Protocol.java)


at oracle.jdbc.driver.OracleConnection.<init>(OracleConnection.java)


at oracle.jdbc.driver.OracleDriver.getConnectionInstance(OracleDriver.java)


at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java)


at java.sql.DriverManager.getConnection(DriverManager.java:512)


at java.sql.DriverManager.getConnection(DriverManager.java:140)


at oracle.jdbc.pool.OracleDataSource.getConnection(OracleDataSource.java)


at oracle.jdbc.pool.OracleConnectionPoolDataSource.getPhysicalConnection(OracleConnectionPoolDataSource.java)


at oracle.jdbc.pool.OracleConnectionPoolDataSource.getPooledConnection(OracleConnectionPoolDataSource.java)


at oracle.jdbc.pool.OracleConnectionPoolDataSource.getPooledConnection(OracleConnectionPoolDataSource.java)


at oracle.jdbc.pool.OracleConnectionCacheImpl.getNewPoolOrXAConnection(OracleConnectionCacheImpl.java)


at oracle.jdbc.pool.OracleConnectionCacheImpl.getPooledConnection(OracleConnectionCacheImpl.java)


at oracle.jdbc.pool.OracleConnectionCacheImpl.getConnection(OracleConnectionCacheImpl.java)


at oracle.jdbc.pool.OracleConnectionCacheImpl.getConnection(OracleConnectionCacheImpl.java)


at chemaxon.jchem.cartridge.servlets.JChemCached.getConnection(JChemCached.java:692)


at chemaxon.jchem.cartridge.servlets.JChemCached.getConnectionHandler(JChemCached.java:666)


at chemaxon.jchem.cartridge.servlets.JChemCached.doSearch(JChemCached.java:798)


at chemaxon.jchem.cartridge.servlets.JChemCached.doPerform(JChemCached.java:610)


at chemaxon.jchem.cartridge.servlets.JChemCached.process(JChemCached.java:137)


at chemaxon.jchem.cartridge.servlets.JChemServletBase.doPost(JChemServletBase.java:232)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

ChemAxon aa7c50abf8

14-02-2006 14:19:08

Daniel,





Please, do the following:


1.) point your WEB browser to the JChemStreams URL (the JChem Cartridge administration GUI)


2.) follow the "Configure JChem Cartridge for Oracle..." link


3.) check the entries "Connection properties" cell


4.) click on the "Test connection" button to test the connection


5.) if the connection test was successful, click on the "Update/save configuration" button to save the configuration.





Cheers,


Peter

ChemAxon aa7c50abf8

14-02-2006 14:20:28

And if the connection test was successful, click on the "Update/save configuration" button to save the configuration.

ChemAxon 60ee1f1328

14-02-2006 14:43:19

HI,





2.) follow the "Configure JChem Cartridge for Oracle..." link





Should the above be a URL hyperlink to another page?





Configure JChem Cartridge for Oracle...


Administrator password: [ text box ] ,<login button>





I enter the correct password for my jchem schema and get an incorrect password message.





I do not see any of:





3.) check the entries "Connection properties" cell


4.) click on the "Test connection" button to test the connection


5.) if the connection test was successful, click on the "Update/save configuration" button to save the configuration





Once again help!


Daniel.

ChemAxon 60ee1f1328

14-02-2006 14:48:28

What is the equivalent search to "Exact fragment" in the cartridge now would be the next question?





Thanks for your time Peter!


Daniel.

ChemAxon aa7c50abf8

14-02-2006 14:49:52

Quote:
2.) follow the "Configure JChem Cartridge for Oracle..." link





Should the above be a URL hyperlink to another page?
This link leads you to another HTML page (edit.jsp). For me its: http://morgo:8090/jchemstreams315/edit.jsp

ChemAxon aa7c50abf8

14-02-2006 14:53:07

Quote:
What is the equivalent search to "Exact fragment" in the cartridge
Code:
jc_compare(<structure-column>, <query-structure>, 't:ef')

ChemAxon 60ee1f1328

14-02-2006 15:04:39

Thanks for your suggested detour, alas even that way a password is required...where is it going to check the password? I am providing with the same password as for the user where I created the cartridge objects!?

ChemAxon aa7c50abf8

14-02-2006 15:34:48

Quote:
I am providing with the same password as for the user where I created the cartridge objects!?
This is one of the two available options.





The other option is to set the login and password to garbage in Tomcat and call the jchem_core_pkg.use_password('mypassword') stored procedure at the beginning of each session.





Please, read the pertaining documentation at http://www.chemaxon.com/jchem/doc/admin/cartridge.html#server_jdbc and the section "User credentials and privileges for the JDBC connection" in particular. See also: http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#archi_usercredentials.





Do not hesitate to ask questions that might help clarify the docs.





Cheers,


Peter

ChemAxon 60ee1f1328

15-02-2006 11:06:20

Now on version 3.1.5.





Back to my original problem, the SMILES I am attempting to process is:


'[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F'





I am trying to insert into a non jchem table.


I am running a jc_compare query.


Where can this problem be occuring?





BEGIN


*


ERROR at line 1:


ORA-29902: error in executing ODCIIndexStart() routine


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


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: cannot import chime format


ORA-06512: at "JCHEM3.SUPPLIERMOLECULESV2TRG", line 1


ORA-04088: error during execution of trigger 'JCHEM3.SUPPLIERMOLECULESV2TRG'


ORA-06512: at "JCHEM3.MIGRATEJCTABLEPCK", line 490


ORA-06512: at line 2

ChemAxon 60ee1f1328

15-02-2006 11:13:12

If jc_compare is the possible cause of this error then would like to point out that both calls below generate the same error IN PL/SQL.


(pJCTableName = Moleculesv2f)





v_sql := 'SELECT molecule_id FROM ' || pJCTableName || ' WHERE jc_compare (cd_smiles,:a,:b) = 1';





EXECUTE IMMEDIATE v_sql INTO RetVal USING pSmiles,pOption;





v_sql := 'SELECT molecule_id FROM ' || pJCTableName || ' WHERE jc_compare (cd_smiles,''' || pSmiles || ''',''' || pOption || ''') = 1';





EXECUTE IMMEDIATE v_sql INTO RetVal;





The query below completes with no errors:





SELECT molecule_id


FROM moleculesv2f


WHERE jc_compare (cd_smiles,'[O-][N+](=O)c1ccc(cc1)S(=O)(=O)Oc2c(F)c(F)c(F)c(F)c2F','t:ef') = 1

ChemAxon 60ee1f1328

15-02-2006 11:18:28

Same error occurs using:





CURSOR curs (cpSMILE Moleculesv2f.cd_smiles%type) IS


SELECT molecule_id


FROM moleculesv2f


where jc_compare (cd_smiles,cpSmile,'t:ef') = 1;





BEGIN





FOR recs in curs (pSmiles)


LOOP


EXIT WHEN curs%notfound;


retval := recs.molecule_id;


END LOOP;

ChemAxon 60ee1f1328

15-02-2006 11:33:11

So the code below works:


The only difference is the actual smiles used and it's source table.





CURSOR curs IS


select cd_smiles from moleculesv2f


where rownum < 1000;


BEGIN


for recs in curs


loop


exit when curs%notfound;


v_sql := 'select count (*) from moleculesv2f where jc_compare (cd_smiles,:a,''t:ef'') = 1';


EXECUTE IMMEDIATE v_sql INTO vout USING recs.cd_smiles;





So I guess I need to know why am I getting the chime error when using a SMILES from one 3.1.5 table to query against another 3.1.5 table using jc_compare?

ChemAxon aa7c50abf8

15-02-2006 11:50:03

Execute the following statement in your sqlplus session and look in the session traces in $ORACLE_BASE/admin/<db-name>/udump to see what value gets bound to the query:





Code:
alter session set events '10046 trace name context forever, level 12'

ChemAxon 60ee1f1328

15-02-2006 12:10:12

hopefully trace file attached

ChemAxon 60ee1f1328

15-02-2006 12:37:20

This query (which previously worked this morning) now throws the below error message:





select 1


from moleculesv2f


where jc_compare (cd_smiles,'BrC1=CC(=O)Oc2ccccc12','t:ef') = 1





ORA-29902: error in executing ODCIIndexStart() routine


ORA-29532: Java call terminated by uncaught Java exception: java.lang.RuntimeException: The following exception has been thrown by the servlet:


Exception: null


ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM3.JC_IDXTYPE_IM", line 323


ORA-06512: at line 1





Can you interpret this behaviour?





Daniel.

ChemAxon aa7c50abf8

15-02-2006 12:45:49

The value that gets bound to the query parameter is: "vSmiles". (The enclosing double quotes are my additions.)





This is apparently not a valid a molecular structure. Please, make sure that a valid molecular structure is passed to jc_compare as the second argument. For the list of valid formats please see http://www.chemaxon.com/jchem/marvin/doc/dev/formats.html .





Thank you!





Peter

ChemAxon aa7c50abf8

15-02-2006 12:48:24

Quote:
This query (which previously worked this morning) now throws the below error message:
Please, could you attach the catalina.out file.

ChemAxon 60ee1f1328

15-02-2006 12:59:19

Hi Peter,





I have rebooted tomcat and the problem has disappeared.





Thank you very much for your help over the last couple of days in helping me to work through my issues - your support is outstanding.





Cheers,


Daniel.

ChemAxon 60ee1f1328

20-02-2006 15:04:41

Hi Peter,





OK, a few iterations ago in this thread, the "chime" error message was generated through my own stupidity, once this was resolved, I encountered it again and a re-boot of tomcat server seemed to sort it, however, I'm not so sure this time...I am now seeing this error message again for the following smiles:





'Fc1ccc(NC(=O)COc2ccccc2)c(F)c1F'





This query does complete correctly in SQL+:


select * from moleculesv2f where jc_compare (cd_smiles,'Fc1ccc(NC(=O)COc2ccccc2)c(F)c1F','t:ef') = 1





My trace file is attached.





Alas nothing appears to be obviously wrong (like vSmiles!) however the error does occur for some reason - I am currently choosing to ignore the error in the code and so this is not a show stopper but I am thus not registering a fair number of potentially interesting molecules. I would also like to know if this is a genuine bug or another silly mistake on my part!


Do you see any evidence in the trace file?





Cheers Peter,


Daniel.

ChemAxon 60ee1f1328

20-02-2006 15:23:46

Actually only 10% of structures registered in my last attempt and so this is an issue...hopefully it might be somthing trivial...

ChemAxon 60ee1f1328

20-02-2006 15:33:23

"no oacdef for this bind" is quite possibly the issue - although I'm still trying to pin point what this means.

ChemAxon 60ee1f1328

20-02-2006 15:57:11

do you think that this issue could be caused by using "normal" oracle update/delete statements against jchem table followed by operations like jc_compare?

ChemAxon aa7c50abf8

20-02-2006 16:04:34

At line #26130 in the trace file there should be a value as line #11573,#25934:





Code:
bind 0: dty=1 mxl=32(31) mal=00 scl=00 pre=00 oacflg=03 oacfl2=1 size=64 offset=0


   bfp=40658b40 bln=32 avl=31 flg=05


   value="Fc1ccc(NC(=O)COc2ccccc2)c(F)c1F"






But I do not see any. The same pattern appears in the traces if I bind an empty string to the query (and the statement aborts with the same error message as in your case):


Code:
declare


  v_sql varchar2(3000) := 'select count(*) from jc_nci_1k where jc_compare (cd_smiles, :a,:b) = 1';


  qry varchar(3000) := '';


  opt varchar(100) := 't:e';


begin


  execute immediate v_sql using qry, opt;


end;


/


show errors



Is it not possible that you are trying to use an empty string as a query?

ChemAxon aa7c50abf8

20-02-2006 16:08:21

Quote:
do you think that this issue could be caused by using "normal" oracle update/delete statements against jchem table followed by operations like jc_compare?
I do not think so -- as long as you manipulate only "user defined columns" with those statements.

ChemAxon 60ee1f1328

20-02-2006 16:18:06

Hi Peter,





I have located the offending syntax and you are absolutely correct the jc_compare was being incorrectly called with a null SMILES string.





This issue is now tucked up in bed and sleeping soundly thanks to the master!





Cheers,


Daniel.

ChemAxon 60ee1f1328

22-02-2006 10:58:09

Hey there Peter,





This may or may not warrant a new topic but for now I just thought I would ping it on the end of this thread.





How can I specify an exact "stereo search" using JC_COMPARE, similar to placing a square on a double bond in Marvin (embedded in JSP). I have noticed that in some cases using JC_COMPARE t:ef or t:e can bring back a mix of cis/trans and so is there an additional option I can specify in order to do the same "stereo search" as mentioned above?





Hopefully, last question for the month!





Cheers,


Daniel.

ChemAxon aa7c50abf8

22-02-2006 12:33:58

Hi Daniel,





The jc_compare option for the behavior you mention is:


Code:
doubleBondStereo:a
.





The entire option string would then look something like:


Code:
't:e doubleBondStereo:a'






Cheers,


Peter

ChemAxon a3d59b832c

22-02-2006 12:48:20

Dan,





You can also use the M (Marked) option value instead of A (All). In this case query stereo bonds must be marked by square (mol and mrv formats) or the directional single bonds: "/" "\" (smiles or smarts). The default is M. Please check the documentation below.





http://www.chemaxon.com/jchem/doc/user/Query.html#cisTrans





http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_compare





Szabolcs