ArrayIndexOutOfBoundsException in StructureSearch.initMolecu

The code:

Code:

public static boolean matchPrecise_JChem(Molecule respMol,             Molecule authMol) throws MolFileException {         try {             MolSearch s1 = new MolSearch();             s1.setSearchType(SearchConstants.PERFECT);             // required for comparing nonaromatized aromatic rings             s1.setOption(SearchConstants.OPTION_VAGUE_BOND,                 SearchConstants.VAGUE_BOND_OFF);             s1.setOption(SearchConstants.OPTION_STEREO_MODEL,                 SearchConstants.STEREO_MODEL_GLOBAL); // JChem 3.2.2             s1.setTarget(respMol);             s1.setQuery(authMol);             System.out.println("matchPrecise_JChem: Match resp "                     + respMol.toFormat("mrv"));             System.out.println("matchPrecise_JChem: Match struct "                     + authMol.toFormat("mrv"));             boolean res1 = s1.isMatching();             println("matchPrecise_JChem: search result is " + res1);             return res1;         } catch (SearchException e2) {             System.out.println("Error in matchPrecise_JChem ");             e2.printStackTrace();             throw new MolFileException("MolFile error " + e2.getMessage());         }     } // matchPrecise_JChem(Molecule, Molecule)

The log output:

Code:

matchPrecise_JChem: Match resp <?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6"           elementType="C C C C C O"           x2="49.467529296875 48.133859955826736 50.801198637923264 52.13486797897153 53.46853732001979 52.13486797897153"           y2="61.61229187672355 60.84227493616451 60.84227493616451 61.61229187672355 60.84227493616451 63.15229187672355"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a1 a3" order="2" />         <bond atomRefs2="a4 a3" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a4 a6" order="2" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument> matchPrecise_JChem: Match struct <?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6"           elementType="C C C C C O"           formalCharge="0 0 0 0 0 1"           x2="61.75486633925228 60.1691904674423 63.088535680300545 64.42220502134882 65.75587436239707 64.42220502134882"           y2="61.7246171332027 61.14205823097373 60.95460019264365 61.7246171332027 60.95460019264365 63.2646171332027"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a1 a3" order="2" />         <bond atomRefs2="a4 a3" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a4 a6" order="2">           <bondStereo>C</bondStereo>         </bond>       </bondArray>     </molecule>   </MChemicalStruct> </MDocument> java.lang.ArrayIndexOutOfBoundsException: -1         at chemaxon.sss.search.StructureSearch.initMolecule(StructureSearch.java:1873)         at chemaxon.sss.search.StructureSearch.initSearch(StructureSearch.java:1430)         at chemaxon.sss.search.StructureSearch.findFirst0(StructureSearch.java:5163)         at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:5656)         at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:5648)         at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:856)         at com.prenhall.epoch.chem.MolFunctions.matchPrecise_JChem(MolFunctions.java:211)         at com.prenhall.epoch.chem.MolFunctions.areResonanceStructures(MolFunctions.java:2064)

We're using JChem 3.2.4. Any ideas what's going wrong? The code and the substrates look fine to me.

I could not reproduce the error using the molecules in your post. Would you send the original source of these molecules?





Tamás

They were not entered in Marvin as such, but as part of a much larger document that was then parsed.





I've fiddled around with the code, and I am no longer generating the errors. They seemed to go away when I stopped replacing H atoms with pseudoatoms. (But in the particular example above, there *were* no pseudoatoms.) Anyway, I'll let you know if they pop up again.

I came across another error that I think may be the source of the above-reported one.





In the command below, the value of mol is converted to an empty Molecule. Not null, because you can still do operations like mol.toFormat("mrv"). But empty. I was under the impression that an operation that generated a new variable type would not affect the original variable's value. However, cloning the molecule and fragmenting the clone solves the problem.

Code:

Molecule[] c = mol.convertToFrags();

I think I might have had this command prior to sending a Molecule to the method described above, and that may be why there was a search error.

Hm, will see, just debugging the undo process, certainly something is fishy about cloning...

Apparently managed to fix the original undo bug - will a second look at the converToFrags() problem. Bob; does it come forward only for reactions or for any molecules?

We don't use reactions as you define them, so molecules only.

Bob,





I quote from the apidoc of Molecule.convertToFrags():

Quote:

Warning: Atoms are removed from the original molecule object to the created fragments, therefore the original molecule becomes inconsistent.

http://www.chemaxon.com/jchem/doc/api/chemaxon/struc/Molecule.html#convertToFrags()





So I recommend to clone the molecule before calling Molecule.convertToFrags(), if you still want to use it to any purpose afterwards.





Regards,


Szabolcs

Sorry, I just realized that you wrote the same above.





In summary: yes, that is the correct solution.