resonance plugin problem

When I submit the compound below to the following code, I get a NullPointerException:





ResonancePlugin resPlugin = new ResonancePlugin();


resPlugin.setMolecule(molecule);


resPlugin.run();





Here's the trace:





java.lang.NullPointerException


at chemaxon.calculations.Tautomerization.setFixTBonds(Tautomerization.java:5576)


at chemaxon.calculations.Tautomerization.isAllowedDelocalization(Tautomerization.java:5116)


at chemaxon.calculations.Tautomerization.isNewADCombination(Tautomerization.java:4888)


at chemaxon.calculations.Tautomerization.createCombinedTautomers(Tautomerization.java:2669)


at chemaxon.calculations.Tautomerization.calculateDACouples(Tautomerization.java:3494)


at chemaxon.calculations.Tautomerization.createDACouples(Tautomerization.java:3441)


at chemaxon.marvin.calculations.MultiformPlugin.run(MultiformPlugin.java:267)


at com.prenhall.epoch.mechanisms.MechRuleFunctions.pKaCheck(MechRuleFunctions.java:694)








Are we doing anything wrong? We're still using the JChem 3.2 prerelease from August 17, so perhaps you have fixed this problem already.

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31"           elementType="C C N C C N N C C N C N O O O C C H H C C C O C O C C C O C O"           formalCharge="0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"           mrvMap="0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"           x3="-7.116840057580488 -6.225410233848155 -9.73236209370845 -11.066031434756708 -11.066031434756708 -9.73236209370845 -8.39869275266019 -8.39869275266019 -12.399700775804966 -13.733370116853225 -13.733370116853225 -12.399700775804966 -12.399700775804966 -14.971786444264971 -7.160276425248444 -8.851616938772537 -7.5179378169444995 -7.661840057580488 -6.3460936660871505 -4.647287296353373 -5.2154044105734005 -3.088478270335642 -5.058665163938606 -5.060921126441357 -6.478003782989465 -6.349315301007441 -7.376612618560189 -4.907266049296443 -6.510695950042446 -6.47850825574415 -7.549152643323181"           y3="-1.2233147957972115 -0.1690381696871306 1.9369092211769825 1.1668922806179438 -0.3731416005001371 -1.1431585410591794 -0.3731416005001371 1.1668922806179438 1.9369092211769825 1.1668922806179438 -0.3731416005001371 -1.1431585410591794 3.366909221176982 -1.0881416005001405 1.8818922806179437 3.9454808593914787 3.175480859391479 -2.1672824859222497 -1.9940611872905483 -1.103659618807372 -2.5593293948310523 -1.1767787606429403 -0.4368086952114538 -0.3354420680020782 0.44095232868461753 4.589097028741461 5.7665484178219 5.185524680797321 3.822364878406848 3.7262179345428947 2.5159980743350623"           z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.4269874761813843 1.4376326302433107 1.3662899315774495 0.32294413937543 2.7233773696402594 -1.0249728243669325 1.4269874761813843 1.4376326302433107 1.3662899315774495 0.32294413937543 2.7233773696402594 -1.0249728243669325"           />       <bondArray>         <bond atomRefs2="a1 a7" order="1" />         <bond atomRefs2="a1 a18" order="1" />         <bond atomRefs2="a1 a19" order="1" />         <bond atomRefs2="a3 a4" order="2" />         <bond atomRefs2="a3 a8" order="1" />         <bond atomRefs2="a3 a16" order="1" />         <bond atomRefs2="a5 a4" order="1" />         <bond atomRefs2="a9 a4" order="1" />         <bond atomRefs2="a5 a6" order="2" />         <bond atomRefs2="a12 a5" order="1" />         <bond atomRefs2="a6 a7" order="1" />         <bond atomRefs2="a7 a8" order="1" />         <bond atomRefs2="a8 a15" order="2" />         <bond atomRefs2="a9 a10" order="1" />         <bond atomRefs2="a9 a13" order="2" />         <bond atomRefs2="a10 a11" order="1" />         <bond atomRefs2="a11 a12" order="1" />         <bond atomRefs2="a11 a14" order="2" />         <bond atomRefs2="a16 a17" order="1" />         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a23 a2" order="1" />         <bond atomRefs2="a2 a25" order="2" />         <bond atomRefs2="a24 a20" order="1" />         <bond atomRefs2="a20 a21" order="1" />         <bond atomRefs2="a20 a22" order="1" />         <bond atomRefs2="a20 a23" order="1" />         <bond atomRefs2="a29 a17" order="1" />         <bond atomRefs2="a17 a31" order="2" />         <bond atomRefs2="a30 a26" order="1" />         <bond atomRefs2="a26 a27" order="1" />         <bond atomRefs2="a26 a28" order="1" />         <bond atomRefs2="a26 a29" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

Hi,





Yes, this error has already been fixed.





Thanks.


Jozsi