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 <[email protected]> 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; > } > > } > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
