IllegalArgumentException: MolSearch: Unknown search type: 3

 

Hi All,

I am performing a SIMILARITY search for a MOL file along with a SUBFORMULA search on a molecular formula but in return getting the following exception:

SEVERE: Error during ABAS in table "ChemistryStructureMolecule" for cd_id: 4776

chemaxon.sss.search.SearchException: An error occured during search:java.lang.IllegalArgumentException: MolSearch: Unknown search type: 3

Query:c1ccc2ccccc2c1

Target:c1ccc2ccccc2c1

Caused by:

MolSearch: Unknown search type: 3

at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:656)

at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:646)

at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:4744)

at chemaxon.jchem.db.JChemSearch.access$1500(JChemSearch.java:121)

at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:554)

........

 

The code I am using is:

 

        ConnectionHandler connectionHandler = null;

        try {

            connectionHandler = connectionHandlerFactory.createReadOnly();

         

            final byte[] queryMolFile = "SOME VALID MOL FILE";

            final Molecule queryMolecule = moleculeFactory.create(queryMolFile);

            final String molecularFormula = "SOME MOL FORMULA";

 

            float similarityThreshold = SOME THRESHOLD VALUE IN FLOAT;

 

            JChemSearchOptions searchOptions = new JChemSearchOptions(JChemSearchOptions.SIMILARITY);

            searchOptions.setDissimilarityThreshold(1 - similarityThreshold);

 

            if (molecularFormula != null) {

                searchOptions.setFormulaSearchQuery(molecularFormula);

                searchOptions.setFormulaSearchType(FormulaSearch.SUBFORMULA);

            }

 

            final String filterQuery = "SOME SQL QUERY";

            searchOptions.setFilterQuery(filterQuery);

 

            final String structureTable = structureTableLookup.lookup("ChemistryStructureMolecule");

 

            final JChemSearch searcher = jChemSearchFactory.create();

            searcher.setQueryStructure(queryMolecule);

            searcher.setConnectionHandler(connectionHandler);

            searcher.setStructureTable(structureTable);

            searcher.setRunMode(JChemSearch.RUN_MODE_SYNCH_COMPLETE);

            searcher.setSearchOptions(searchOptions);

            searcher.run();

 

        } catch (Exception e) {

            throw new RuntimeException(e);

        } finally {

            if (connectionHandler != null) {

                try {

                    connectionHandler.close();

                } catch (SQLException e) 

            }

        }

Can somebody please look into this and let me know if I am missing something?

Many thanks,

Isha

 

I moved this to the JChem forum as its more releavnt to that forum.
You should get an answer soon. 

Tim

Hi,

Just a quick answer, the experts may provide more detail.

You can only run one type of search at a time, so you have to choose between similarity or formula.

When using formula search, just set the search type to DEFAULT, and it should wotk fine.

 

Best regards,

 

Szilard

But as part of a separate code I do run SUBFORMULA search with SUBSTUCTURE search for the MOL file. And they two seem to work?

 

Is the combination of SIMILARITY(MOL file) and SUBFORMULA not valid?? The online documentation doesn't mention anything like that?? 

Hi,

 

I think I spoke too soon, and formula search is indeed supposed to be used together with other search types.

So it is probably a bug that we are trying to invoke the graph search even with similarity search.

Please let us know your exact JChem version.

The experts will respond soon.

Best regards,

Szilard

Thanks Szilard,

The version we are using is 1.0

  <dependency>

            <groupId>chemaxon.jchem</groupId>

            <artifactId>jchem</artifactId>

            <version>1.0</version>

</dependency>

Also just to bring into your notice that I think that seems to work on one of the web sites:

http://www.chemaxon.com/ajax/

Maybe the version I have with me is not the correct one?

Thanks,

Isha

 

 

Hi,

 

You can obtain the JChem version by printing the value of the following constant:

 

chemaxon.jchem.VersionInfo.JCHEM_VERSION

Szilard

It prints:

5.5.1.0

Dear Isha,

 

I am sorry for the late answer.

We will look into this issue in more detail soon.

 

Best regards,

Szabolcs

Thanks Szabolcs....

Dear Isha,

We have investigated the issue and we could reproduce it even with the latest JChem versions. (I do not understand why it seemed to work in the AJAX example site.) Currently, formula search filtering is only supported for the following search types: SUBSTRUCTURE, FULL, FULL_FRAGMENT, SUPERSTRUCTURE, and NO_SCREEN.

It is not clear now which release could fix this issue, but until then you can apply a quite simple workaround as follows. Instead of executing one JChemSearch process with all the required filters, you can first execute a simple formula search (without a query molecule) and then execute a similarity search using the results of the first search as a filter ID list. Here is an example code (using your variable names):

    final JChemSearch searcher = jChemSearchFactory.create();
    searcher.setConnectionHandler(connectionHandler);
    searcher.setStructureTable(structureTable);
    searcher.setRunMode(JChemSearch.RUN_MODE_SYNCH_COMPLETE);

    int[] formulaResults = null;
    if (molecularFormula != null) {
        JChemSearchOptions formulaSearchOpts =
                new JChemSearchOptions(JChemSearchOptions.SUBSTRUCTURE);
        formulaSearchOpts.setFormulaSearchQuery(molecularFormula);
        formulaSearchOpts.setFormulaSearchType(FormulaSearch.SUBFORMULA);
        searcher.setSearchOptions(formulaSearchOpts);
        searcher.run();
        formulaResults = searcher.getResults();
    }

    JChemSearchOptions simSearchOpts =
            new JChemSearchOptions(JChemSearchOptions.SIMILARITY);
    simSearchOpts.setDissimilarityThreshold(1 - similarityThreshold);
    simSearchOpts.setFilterQuery(filterQuery);
    searcher.setSearchOptions(simSearchOpts);
    searcher.setQueryStructure(queryMolecule);
    if (molecularFormula != null) {
        searcher.setFilterIDList(formulaResults);
    }

    searcher.run();

For efficiency reasons, you can apply your filter query to the first search, as well (by invoking simSearchOpts.setFilterQuery(filterQuery) before the first call of searcher.run()).

I hope this helps!

Best regards,
Peter

Thanks Peter for looking into this... 

I tried your suggested approach but I get the following error:

Caused by: java.lang.ArrayIndexOutOfBoundsException: 24 >= 0

at chemaxon.util.FloatVector.elementAt(FloatVector.java:280)

at chemaxon.jchem.db.JChemSearch.filterScreened(JChemSearch.java:5195)

at chemaxon.jchem.db.JChemSearch.getScreened(JChemSearch.java:3946)

at chemaxon.jchem.db.JChemSearch.searchCore(JChemSearch.java:2218)

at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2081)

at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:1879)

at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:1722)

at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:1745)

Dear Isha,

I checked the exception you reported, but I could not reproduce this issue neither with JChem 5.5.1 (the version you have) nor with the recent releases. However, we made some changes and a bug fix releated to the handling of filter ID lists in case of similarity search since the release of JChem 5.5.1. Could you please try upgrading your JChem installation to a recent release? (The latest one is JChem 5.10.1) Maybe, it would solve your problem, otherwise your experiments would help us in the further investigation of this issue.

Best regards,
Peter

Dear Isha,

I would like to refine my previous comment: finally I could reproduce similar exceptions (even with the latest JChem version), but only in case if JChemSearchOptions.setReturnsNonHits() is called with true value, i.e. JChemSearch is required to return the non-hits instead of hits (in case of similarity search, it means that dissimilar targets are returned instead of similar ones).

So this is obviously a bug in our code, we will fix it soon. However, it seems to be related to the non-hits option. Could you check the value of this option in your use case? For example, by calling

System.out.println(searcher.getSearchOptions().isReturnsNonHits());

before searcher.run(). Thank you in advance.

Regards,
Peter

Hi Peter,

This prints 'false'.

Thanks,

Isha

 

Hi Isha,

It is strange, we could only reproduce such problems if this non-hits option is set to true. Could you please update your JChem installation to see whether a recent version also produces such an exception?

Thanks,
Peter

Hi Peter,

I have tried it with the latest version (5.10.1) as well but still get the same error:

Caused by: java.lang.ArrayIndexOutOfBoundsException: 10 >= 0

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.common.util.FloatVector.elementAt(FloatVector.java:297)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.filterScreened(JChemSearch.java:5801)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.getCandidates(JChemSearch.java:4455)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.searchCore(JChemSearch.java:2634)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2494)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2274)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:1994)

[12:45:20.207][warn][talledLocalContainer]      at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2017)

Dear Isha,

Thank you. This stack trace is useful for us to localize and fix this issue. We will inform you about any progress.

Regards,
Peter

Dear Isha,

The upcoming major release, JChem 5.11 will be released in September 2012. It will contain several bug fixes related to filtering and ordering issues, including problems like the one you encountered. We hope that this release will fix your problem, although we could not reproduce the error exactly the same way.

Regards,
Peter

Thanks, I will try upgrading my version to the latest one as soon as its out and see if it works?

Regards,

Isha