superstructure search error - ChemAxon Forum Archive

User da00f5c453

09-04-2010 20:28:10

Hi all,

I am trying to create a database of query structures to be queried with regular structures to see what chemical structures contain the query structures in the database. All queries are encoded as SMARTS and imported into a query table in IJC, however for some particular query/target examples the search fails with an exception:

java.lang.NullPointerException

	at chemaxon.sss.search.StructureSearch.initQueryProperties(StructureSearch.java:3183)

	at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1455)

	at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6109)

	at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:6693)

	at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:6685)

	at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:703)

Caused: chemaxon.sss.search.SearchException: An error occured during search:java.lang.NullPointerException

  Query:c1cnnc1

  Target:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5"

          elementType="C C N N C"

          mrvQueryProps="a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])]"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="A" />

        <bond atomRefs2="a2 a3" order="A" />

        <bond atomRefs2="a3 a4" order="A" />

        <bond atomRefs2="a4 a5" order="A" />

        <bond atomRefs2="a1 a5" order="A" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>





Caused by:

java.lang.NullPointerException

	at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:729)

	at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:719)

	at chemaxon.jchem.db.JChemSearch.isMatching(JChemSearch.java:4117)

	at chemaxon.jchem.db.JChemSearch.access$1300(JChemSearch.java:120)

	at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:471)

Caused: org.springframework.dao.InvalidDataAccessResourceUsageException: Exception occurred when executing JChem search; nested exception is chemaxon.sss.search.SearchException: An error occured during search:java.lang.NullPointerException

  Query:c1cnnc1

  Target:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5"

          elementType="C C N N C"

          mrvQueryProps="a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])] a1;str:[x2!$(*=[!R])]"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="A" />

        <bond atomRefs2="a2 a3" order="A" />

        <bond atomRefs2="a3 a4" order="A" />

        <bond atomRefs2="a4 a5" order="A" />

        <bond atomRefs2="a1 a5" order="A" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>





Caused by:

java.lang.NullPointerException

	at com.im.ijcs.impl.query.JChemExecutor.executeJChemSearch(JChemExecutor.java:268)

	at com.im.ijcs.impl.query.JChemExecutor.execute(JChemExecutor.java:156)

	at com.im.ijcs.impl.query.JChemExecutor.run(JChemExecutor.java:359)

	at com.im.ijcs.impl.query.Executor.visitStructureQuery(Executor.java:152)

	at com.im.ijcs.impl.query.Executor.visitSqlQuery(Executor.java:185)

	at com.im.ijcs.impl.query.Executor.execute(Executor.java:143)

	at com.im.df.server.local.LocalQueryExecutor.access$001(LocalQueryExecutor.java:14)

	at com.im.df.server.local.LocalQueryExecutor$1.doInTransactionWithoutResult(LocalQueryExecutor.java:48)

	at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:33)

	at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:128)

	at com.im.df.server.local.LocalQueryExecutor.execute(LocalQueryExecutor.java:46)

	at com.im.ijcs.impl.query.DefaultQueryService.findIDs(DefaultQueryService.java:44)

	at com.im.df.impl.db.DBSchemaDataProviderImpl.queryForIdsImpl(DBSchemaDataProviderImpl.java:439)

	at com.im.df.impl.db.DBEntityDataProviderImpl.queryForIds(DBEntityDataProviderImpl.java:156)

	at com.im.df.impl.db.ResultSetImpl.applyQueryInternal(ResultSetImpl.java:195)

	at com.im.df.impl.db.ResultSetImpl.applyWorkingQuery(ResultSetImpl.java:148)

	at com.im.ijc.core.query.exec.ExecutableQueryPanel$2.phase1InRequestProcessor(ExecutableQueryPanel.java:232)

	at com.im.commons.progress.BackgroundRunner.processTheTask(BackgroundRunner.java:126)

	at com.im.commons.progress.BackgroundRunner$1.run(BackgroundRunner.java:90)

	at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:577)

[catch] at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1030)

I can reproduce the error with a simple Java program:

	Molecule query = MolImporter.importMol("c1cnnc1", "smiles");


		Molecule target = MolImporter.importMol("[c;x2!$(*=[!R])]:1:[c;x2!$(*=[!R])]:[n;x2!$(*=[!R])]:[n;x2!$(*=[!R])]:[c;x2!$(*=[!R])]:1", "smarts:d");


		StandardizedMolSearch ms = new StandardizedMolSearch();


		ms.setSearchType(SearchConstants.SUPERSTRUCTURE);


		ms.setTarget(target);


		ms.setQuery(query);


		System.out.println(ms.isMatching());

wich raises the same exception. Am I doing something wrong? Are the SMARTS used in my application not supported?

IJC 5.3.1 and JChem 5.3.1 with Java 1.6 on Mac OSX 10.6

Oleg.

ChemAxon a3d59b832c

12-04-2010 20:51:26

Hi Oleg,

The SMARTS is OK, the problem is in our code.

It seems that the "x" (ring bond) query property in a SMARTS logical expression is causing the problem.

Until we fix it, a workaround is to give it as an "rb" query property in mrv:

<?xml version="1.0" ?>
<cml>
<MDocument>
  <MChemicalStruct>
    <molecule molID="m1">
      <atomArray
          atomID="a1 a2 a3 a4 a5"
          elementType="C C N N C"
          mrvQueryProps="a1;rb2;str:[!$(*=[!R])] a1;rb2;str:[!$(*=[!R])] a1;rb2;str:[!$(*=[!R])] a1;rb2;str:[!$(*=[!R])] a1;rb2;str:[!$(*=[!R])]"
          x2="2.3057002501002226 1.8298140787628048 0.2898140787628045 -0.18607209257461532 1.0598140787628036"
          y2="1.1748129563317335 -0.2898140787628034 -0.2898140787628045 1.174812956331732 2.0800022448621416"
          />
      <bondArray>
        <bond atomRefs2="a1 a2" order="A" />
        <bond atomRefs2="a2 a3" order="A" />
        <bond atomRefs2="a3 a4" order="A" />
        <bond atomRefs2="a4 a5" order="A" />
        <bond atomRefs2="a1 a5" order="A" />
      </bondArray>
    </molecule>
  </MChemicalStruct>
</MDocument>
</cml>

Best regards,

Szabolcs

User da00f5c453

30-06-2010 04:51:49

Hi Szabolcs,

I think this also could be in the same line as the error I found earlier

code:

Molecule mol1 = MolImporter.importMol("[#6,#16&X2H0,X3H1,X4H2,X5H3,X6H4&!$(S=*),#35,#53;R0;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5]~*(~[#6,#16&X2H0,X3H1,X4H2,X5H3,X6H4&!$(S=*),#35,#53;R0;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5])~[#6,#16&X2H0,X3H1,X4H2,X5H3,X6H4&!$(S=*),#35,#53;R0;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5]", "smarts");
Molecule mol2 = MolImporter.importMol("C(C)(C)C", "smiles");
MolSearch ms = new MolSearch();
ms.setQuery(mol1);
ms.setTarget(mol2);
System.out.println(ms.isMatching());

throws the following exception:

Exception in thread "main" chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: -1
  Query:[R0;#6,#16X2H0,X3H1,X4H2,X5H3,X6H4!$(S=*),#35,#53;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5]~*(~[R0;#6,#16X2H0,X3H1,X4H2,X5H3,X6H4!$(S=*),#35,#53;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5])~[R0;#6,#16X2H0,X3H1,X4H2,X5H3,X6H4!$(S=*),#35,#53;!$(*~[!#1;!#6;!$([#16;X2H0,X3H1,X4H2,X5H3,X6H4])]);X1H0,X2H1,X3H2,X4H3,X5H4,X6H5]
  Target:CC(C)C

Caused by:
-1
    at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:729)
    at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:719)
    at edu.unm.health.biocomp.molfp.Test1.main(Test1.java:24)
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
    at chemaxon.util.BondClassifier.isRingAtom(Unknown Source)
    at chemaxon.sss.search.StructureSearch.compareAtomQueryProperties(StructureSearch.java:4265)
    at chemaxon.sss.search.StructureSearch.compareAtoms(StructureSearch.java:4459)
    at chemaxon.sss.search.StructureSearch.initMaps(StructureSearch.java:3481)
    at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6138)
    at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:6693)
    at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:6685)
    at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:703)
    ... 1 more

I tested the SMARTS expresion and match at

http://www.daylight.com/daycgi_tutorials/depictmatch.cgi

and it parses the SMARTS and gives 1 unique match, I also tested it with OEChem toolkit and it passes with 1 unique match. This indicates that the SMARTS expression should be ok. I hope this also helps in debuging the previous error. Note that the SMARTS expression in this example doesn't contain "x" (ring bonds) atom primitive.

Oleg.