exception when performing API MolSearch against polymer

Hi,

When we run the attached java code against the attached mol file, we see the below exception.  Is there a way to run the query as to prevent this problem?

We are using java version "1.5.0_17" and JChem 5.4.1.1.

Many thanks for any guidance.

Cheers,

Andrew

 

chemaxon.sss.search.SearchException: An error occured during search:java.lang.ArrayIndexOutOfBoundsException: -1

  Query:Cl

  Target:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7"

          elementType="* C C * C O O"

          formalCharge="0 0 0 0 0 -1 0"

          sgroupRef="0 sg1 sg1 0 sg1 sg1 sg1"

          x2="0.32999999999999874 -0.44000000000000083 0.33000000000000007 1.87 -0.4399999999999995 0.33000000000000096 -1.9799999999999995"

          y2="2.8578838324886475 1.5242047106606114 0.1905255888325761 0.19052558883257698 -1.1431535329954596 -2.4768326548234953 -1.1431535329954596"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a5" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a5 a6" order="1" />

        <bond atomRefs2="a5 a7" order="2" />

      </bondArray>

      <molecule id="sg1" role="SruSgroup" title="n" molID="m2"

         atomRefs="a2 a3 a5 a6 a7 a8" correspondence="" bondList="" connect="ht">

        <MBracket type="SQUARE" orientation="SINGLE">

          <MPoint x="-2.7499999999999996" y="3.017190917350883" />

          <MPoint x="-2.3649999999999993" y="3.017190917350883" />

          <MPoint x="-2.3649999999999993" y="-3.2468326548234954" />

          <MPoint x="-2.7499999999999996" y="-3.2468326548234954" />

        </MBracket>

        <MBracket type="SQUARE" orientation="SINGLE">

          <MPoint x="6.82" y="-3.2468326548234954" />

          <MPoint x="6.4350000000000005" y="-3.2468326548234954" />

          <MPoint x="6.4350000000000005" y="3.017190917350883" />

          <MPoint x="6.82" y="3.017190917350883" />

        </MBracket>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

 

 

Caused by:

-1

        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 polyprob.<init>(polyprob.java:53)

        at polyprob.main(polyprob.java:18)

Caused by: java.lang.ArrayIndexOutOfBoundsException: -1

        at chemaxon.sss.search.BracketComparator.setAtomsSgData(BracketComparator.java:239)

        at chemaxon.sss.search.BracketComparator.initSgroupData(BracketComparator.java:184)

        at chemaxon.sss.search.bracket.PolymerMatcher.removeStarAtoms(PolymerMatcher.java:245)

        at chemaxon.sss.search.bracket.PolymerMatcher.transform(PolymerMatcher.java:224)

        at chemaxon.sss.search.StructureSearch.transformPolymers(StructureSearch.java:1612)

        at chemaxon.sss.search.StructureSearch.transformPolymers(StructureSearch.java:1596)

        at chemaxon.sss.search.StructureSearch.handlePolymers(StructureSearch.java:1582)

        at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1477)

        at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:6308)

        at chemaxon.sss.search.StructureSearch.findFirstHit(StructureSearch.java:6297)

        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 Andrew,

 

It seems that the call convertToFrags() creates an inconsistent molecule. Probably it does not handle the brackets properly. My colleagues will check this function.

 

In the meantime, I suggest to use the search type:

 

so.setSearchType(SearchConstants.FULL_FRAGMENT);

 

on the original molecule. It would match to complete fragments only.

 

Best regards,

Szabolcs

Hi,

Thanks for the quick reply (and work-around suggestion) .. please let us know when/if the problematic function is fixed.

Best,

Andrew

Hi Andrew,

I am happy to inform you that in Marvin 5.6 released few days ago the method Molecule.convertToFrags() works correctly, the returned fragments will be
consistent molecules.

I would like to mention that this method separates the S-group in the molecule given in 'poly.mol' into two fragments and removes the disconnected repeating unit S-group (to keep the same functioning as before). If in cases like this you would like to keep separate fragments contained in the same S-groups in one fragment without removing the S-group, then please use instead of

Molecule frags[] = ((Molecule)mol.clone()).convertToFrags();

the following code:

Molecule clonedMolecule = (Molecule)mol.clone();


clonedMolecule.setGUIContracted(false);


Molecule frags[] = clonedMolecule.findFrags(Molecule.class, MoleculeGraph.FRAG_KEEPING_SGROUPS);

Best regards,

Zsuzsa

Thanks very much for the update!