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Re: [Cdk-user] CDK Descriptors Concurrent Modification Exception
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From: Rajarshi G. <raj...@gm...> - 2012-03-23 16:02:09
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The descriptor code is not thread safe. I think there was some work
sometime back on going through and making classes threadsafe, but I
don't think it to the descriptors
On Fri, Mar 23, 2012 at 11:20 AM, lochana menikarachchi
<loc...@ya...> wrote:
> Following code run into concurrent modification exception when ran in more
> than 1 thread. Any ideas??
>
> ExecutorService eservice = Executors.newFixedThreadPool(threads);
> CompletionService <List<String>> cservice = new
> ExecutorCompletionService <List<String>> (eservice);
> int k=0;
> for (IAtomContainer mol : mols3D)
> {
> DescCalculator dc = new DescCalculator(mol);
> cservice.submit(dc);
> k=k+1;
>
> }
>
> ---------------------------------------------------------------------------------
>
> public class DescCalculator implements Callable<List<String>>{
>
> private IAtomContainer mol;
>
> DescCalculator(IAtomContainer mol_)
> {
> this.mol = mol_;
> }
>
> @Override
> public List<String> call() {
> List<String> dataItems = new ArrayList<String>();
> try
> {
> DescriptorEngine engine = new
> DescriptorEngine(DescriptorEngine.MOLECULAR);
> List<String> classNames = engine.getDescriptorClassNames();
> List<String> removeList = new ArrayList();
>
> removeList.add("org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor");
> classNames.removeAll(removeList);
> List<IDescriptor> instances =
> engine.instantiateDescriptors(classNames);
> engine.setDescriptorInstances(instances);
> ArrayList<IMolecularDescriptor> descriptors = new ArrayList();
> for (Object object : instances)
> {
> IMolecularDescriptor descriptor = (IMolecularDescriptor) object;
> descriptors.add(descriptor);
> }
> String title = (String) mol.getProperty("PUBCHEM_COMPOUND_CID");
> dataItems.add(title);
> int ndesc = 0;
> for (IMolecularDescriptor descriptor : descriptors) {
> DescriptorValue value = descriptor.calculate(mol);
> if (value.getException() != null) {
> for (int i = 0; i < value.getNames().length; i++) {
> dataItems.add("NA");
> }
> continue;
> }
>
> IDescriptorResult result = value.getValue();
> if (result instanceof DoubleResult) {
> dataItems.add(String.valueOf(((DoubleResult)
> result).doubleValue()));
> } else if (result instanceof IntegerResult) {
> dataItems.add(String.valueOf(((IntegerResult)
> result).intValue()));
> } else if (result instanceof DoubleArrayResult) {
> for (int i = 0; i < ((DoubleArrayResult)
> result).length(); i++) {
> dataItems.add(String.valueOf(((DoubleArrayResult)
> result).get(i)));
> }
> } else if (result instanceof IntegerArrayResult) {
> for (int i = 0; i < ((IntegerArrayResult)
> result).length(); i++) {
> dataItems.add(String.valueOf(((IntegerArrayResult)
> result).get(i)));
> }
> }
>
> ndesc++;
> }
>
> }
> catch(Exception e)
> {
> e.printStackTrace();
> }
> return dataItems;
> }
>
> }
>
>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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