NullPointerException with AsymmetricAtomCount 5.2.4

Hi,

took me some time to figure that out and reminds me that every software writer

should have a deep JUNIT testing framework applied when coding in JAVA. Well,

I never went to that class and so its my bad (that will teach me something!).

I had some 10-100 liner running in JCHEM 4.x and it worked like charm, this is

jchem.version=5.2.4 and this is a bug regarding AsymmetricAtomCount.

C:\>cxcalc AsymmetricAtomCount "CIH"
id      Asymmetric atom count
1       4

and now the error, you can see with CIH (cysteinylisoleucylhistidine) it works.

and with "C" (methane) epic fail.

C:\>cxcalc AsymmetricAtomCount "C"
Error at molecule: 1 ID = 1
java.lang.NullPointerException
java.lang.NullPointerException
        at chemaxon.calculations.TopologyAnalyser.asymmetricAtomCount(TopologyAnalyser.java:393)
        at chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAsymmetricAtomCount(TopologyAnalyserPlugin.java:1130)
        at chemaxon.marvin.calculations.TopologyAnalyserPlugin.getResult(TopologyAnalyserPlugin.java:1576)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getResults(CalculatorPluginOutput.java:299)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:279)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getCachedResults(CalculatorPluginOutput.java:210)
        at chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit.getResult(DefaultPluginWorkUnit.java:52)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:91)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.WorkUnitProcessorBase.process(WorkUnitProcessorBase.java:200)
        at chemaxon.util.concurrent.processors.WorkUnitProcessorBase$Worker.call(WorkUnitProcessorBase.java:403)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
id      Asymmetric atom count
1
Exception in thread "main" java.util.concurrent.ExecutionException: java.lang.NullPointerException
        at chemaxon.marvin.Calculator.outputOnlyPlugin(Calculator.java:1469)
        at chemaxon.marvin.Calculator.consume(Calculator.java:1404)
        at chemaxon.marvin.Calculator.run(Calculator.java:1134)
        at chemaxon.marvin.Calculator.run(Calculator.java:1096)
        at chemaxon.marvin.Calculator.main(Calculator.java:1667)
Caused by: java.lang.NullPointerException
        at chemaxon.calculations.TopologyAnalyser.asymmetricAtomCount(TopologyAnalyser.java:393)
        at chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAsymmetricAtomCount(TopologyAnalyserPlugin.java:1130)
        at chemaxon.marvin.calculations.TopologyAnalyserPlugin.getResult(TopologyAnalyserPlugin.java:1576)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getResults(CalculatorPluginOutput.java:299)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:279)
        at chemaxon.marvin.plugin.CalculatorPluginOutput.getCachedResults(CalculatorPluginOutput.java:210)
        at chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit.getResult(DefaultPluginWorkUnit.java:52)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:91)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.WorkUnitProcessorBase.process(WorkUnitProcessorBase.java:200)
        at chemaxon.util.concurrent.processors.WorkUnitProcessorBase$Worker.call(WorkUnitProcessorBase.java:403)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)

I first thought there was some change in the API or I made some wrong assignments,

or the molhandler was deprecated or however importing "ClC1CCCCC1Br" is not OK.

package examples;

import chemaxon.formats.MolFormatException;
import chemaxon.marvin.calculations.TopologyAnalyserPlugin;
import chemaxon.marvin.plugin.PluginException;
import chemaxon.struc.Molecule;
import chemaxon.util.MolHandler;

public class AssymetricError {
    public static void main(String[] args) throws   PluginException, MolFormatException {

        // somehow the "C" cxsmiles evokes error in getAsymmetricAtomCount
        // ok: ClC1CCCCC1Br
        // FAIL: C
        
        MolHandler mh = new MolHandler("C");
        Molecule target = mh.getMolecule();

        // create plugins - what is faster direct or plugin?
        TopologyAnalyserPlugin topologyplugin = new TopologyAnalyserPlugin();

        // set the input molecule
        topologyplugin.setMolecule(target);

        try {
            // run the calculation
            topologyplugin.run();
            int myAromaticRingCount = topologyplugin.getAromaticRingCount();
            int myassymetricringcount = topologyplugin.getAsymmetricAtomCount();
            double tempbalabanindex = topologyplugin.getBalabanIndex();
            System.out.println("ARC: " + myAromaticRingCount + " AssyRC: " + myassymetricringcount + " Balaban: "+ tempbalabanindex );

        } catch (PluginException e) {
            e.printStackTrace();
            System.exit(1);
        }// end catch
    } 
}

Exception in thread "main" java.lang.NullPointerException
    at chemaxon.calculations.TopologyAnalyser.asymmetricAtomCount(TopologyAnalyser.java:393)
    at chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAsymmetricAtomCount(TopologyAnalyserPlugin.java:1130)
    at examples.AssymetricError.main(AssymetricError.java:30)

OH: and another problem with the CODE boxes, they somehow cut off the code,

which is not very nice...

the line above was:

chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAsymmetricAtomCount(TopologyAnalyserPlugin.java:1130)

but I can only see

chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAsymmetricAtomCount(TopologyAnalyserPl

But this is a browser (JAVAScript flaw) because my screen is 1920x1200 and my

DPI settings are 130%, but guess what it worked since 5 years just recently when

this new editor was introduced it started cutting off text.

Cheers

Tobias

Thank you for reporting the issue. You are absolutely right, unit testing is very important and we do it regularly, however, its quality always depends on the test cases added to the unit tests. Negative examples are sometimes forgotten.

However, this problem has been corrected in 5.2.5. I think, the easiest way to figure out if an issue has been corrected in a later version or not is to visit our archive here where you can run applets of many Marvin versions.

Hi,

thanks for the link, thats very nice, I guess within v5 there should be no problem with

the new lics.

Cheers

Tobias