Exception when performing API MolSearch

Hi,

 

I am getting an error when running the following code in jchem 5.4.0.0 (java 1.5.0_17-b04)

 

        Molecule mol = MolImporter.importMol("OC(C(O)C(O)=O)C(O)=O");

        MolSearch s = new MolSearch();

        MolSearchOptions so = new MolSearchOptions();

        so.setExactFragment(true);

        so.setStereoSearchType(SearchConstants.STEREO_EXACT);

        s.setSearchOptions(so);

        Molecule m = MolImporter.importMol("OC(C(O)C(O)=O)C(O)=O |&1:1,2,w:1.0,2.2|");

        s.setTarget(mol);

        s.setQuery(m);

        int[][] hits = s.findAll();

        if (hits!=null) {

            System.out.println("found");

        }

 

If I comment out this line:

so.setStereoSearchType(SearchConstants.STEREO_EXACT);

then I no longer get an exception.

 

Am I doing something incorrectly?

 

Thanks for any help.

 

The exception is:

 

chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: 64

  Query:OC(C(O)C(O)=O)C(O)=O |&1:1,2,w:1.0,2.2|

  Target:OC(C(O)C(O)=O)C(O)=O

 

Caused by:

64

        at chemaxon.sss.search.MolSearch.getWrapperSearchException(MolSearch.java:697)

        at chemaxon.sss.search.MolSearch.findFirstHit(MolSearch.java:732)

        at chemaxon.sss.search.MolSearch.findAllHits(MolSearch.java:795)

        at chemaxon.sss.search.Search.findAll(Search.java:649)

        at debug.<init>(debug.java:37)

        at debug.main(debug.java:18)

Caused by: java.lang.ArrayIndexOutOfBoundsException: 64

        at chemaxon.sss.search.StructureSearch.hasEnoughBondsForStereo(StructureSearch.java:4694)

        at chemaxon.sss.search.StructureSearch.compareChiralities0(StructureSearch.java:5330)

        at chemaxon.sss.search.StructureSearch.compareChiralities(StructureSearch.java:5196)

        at chemaxon.sss.search.StructureSearch.testChiralityInTheMiddle(StructureSearch.java:5427)

        at chemaxon.sss.search.StructureSearch.isCompatibleIdx(StructureSearch.java:5505)

        at chemaxon.sss.search.StructureSearch.findNextSNforThisQN(StructureSearch.java:5575)

        at chemaxon.sss.search.StructureSearch.findNext0(StructureSearch.java:6527)

        at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6334)

        at chemaxon.sss.search.StructureSearch.findFirstHit(StructureSearch.java:6288)

        at chemaxon.sss.search.MolSearch.findNextEnumeratedHit(MolSearch.java:1024)

        at chemaxon.sss.search.MolSearch.findNextFilteredHit(MolSearch.java:877)

        at chemaxon.sss.search.MolSearch.findFirstHit(MolSearch.java:724)

        ... 4 more

Hi,

 

Thank you for the detailed bug report !

We could reproduce the problem and my colleagues will start working on it after the holidays.

They will get back to you here with their findings and the estimated time when the bugfix will be available in a future version.

Meanwhile I have noticed that your query is a bit strange:

"OC(C(O)C(O)=O)C(O)=O |&1:1,2,w:1.0,2.2|"

Enhanced stereo AND groups are designed to be used with UP or DOWN wedges - with wiggly bonds I guess they are superfluous. Please see:

http://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html#mdl_enhanced_stereo

If you let us know what do you want to achieve we may give you some advice. 

Nevertheless the following query only containing the wiggly bonds throws the same exception, so we will have to investigate and fix anyway:

"OC(C(O)C(O)=O)C(O)=O |w:1.0,2.2|"

Thank you again for the report.

 

Best regards,

 

Szilard

Hi,

Thanks for the quick reply, and also for catching my notation/smiles mistake .. I really should have used "O[C@H]([C@@H](O)C(O)=O)C(O)=O |&1:1,2|" to indicate the mixture of "both up" and "both down" structures .. the revised structure does not cause an exception.

Thanks again for the help.

Happy holidays,

Andrew

Hi Andrew,

We are happy that you could avoid the exception this way. We fixed this bug, so the original query will work as well. This will be released in 5.4.1.

Bye,

Robert