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ArrayIndexOutOfBoundsException from getParity
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Brendan

Joined: 12 Jul 2012
Posts: 44

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Link to postPosted: Thu Aug 16, 2012 11:01 amPost subject: ArrayIndexOutOfBoundsException from getParity Reply with quote

Hi,

I am using JChem 5.10.2.

I have imported a number of molecule using the MolImporter class, and proceeded to run structure checker on them. I got the following for one molecule:

java.lang.ArrayIndexOutOfBoundsException: -1
    at chemaxon.core.calculations.Parity.getParity(Parity.java:629)
    at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:3505)
    at chemaxon.fixers.WedgeCleanFixer.fix(WedgeCleanFixer.java:38)
    at chemaxon.checkers.runner.BasicCheckerRunner.fix(BasicCheckerRunner.java:131)

I have attached the troubled molecule. I'd appreciate some guidance on what is causing this issue, and if I (or you) can resolve it. I do not get the same exception when using the Structure Checker standalone software.

Cheers,

Brendan




 Filename: troubled_molecule.sdf    Filesize: 7.95 KB    Downloaded: 179 Time(s)
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Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

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Link to postPosted: Thu Aug 16, 2012 11:46 amPost subject: Reply with quote

Hi,

Could you attach your Java code?

Zsolt

Brendan

Joined: 12 Jul 2012
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Link to postPosted: Thu Aug 16, 2012 11:51 amPost subject: Reply with quote

Zsolt wrote:

Hi,

Could you attach your Java code?

Zsolt

 

Hi Zsolt,

I don't really want to upload large amounts of code. I am not doing anything particulalry complicated though. This is the nuts and bolts:

public void checkStructure(Molecule molecule) {

       CheckerRunner checkerRunner = new BasicCheckerRunner(checkerConfigurationReader);
       checkerRunner.setMolecule(molecule);
       List<StructureCheckerResult> results = checkerRunner.checkAndWait();
       for (StructureCheckerResult result : results) {
                Boolean success = checkerRunner.fix(result);
       }

}


Brendan

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

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Link to postPosted: Tue Sep 04, 2012 2:32 pmPost subject: Reply with quote

Thanks.

We can reproduce the error, and we will fix it. Fix can be expected in Marvin 5.11.x or in 5.12 version.

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