#1360 LengthOverBreadthDescriptor yields only NaNs

[Martin Gütlein]

Hi,

The LengthOverBreadthDescriptor returns only NaNs, even with 3D input data.

ISimpleChemObjectReader reader = new ReaderFactory().createReader(new FileReader(
                "/tmp/30_random_cpdbas_compounds.ob3d.sdf"));
        IChemFile content = (IChemFile) reader.read((IChemObject) new ChemFile());
        for (IAtomContainer mol : ChemFileManipulator.getAllAtomContainers(content))
        {
            IMolecularDescriptor desc = new LengthOverBreadthDescriptor();
            System.out.println(desc.calculate(mol).getValue());
        }
        reader.close();

[John May]

You need make sure the mass is set for the centre of mass calc.

Isotopes.getInstance().configureAtoms(mol);

The error was written to the exception:

System.out.println(desc.calculate(mol).getException());

You also need to tell the MDL reader to load as 3D. I don't know how it's done on the reader factory.

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
MDLV2000Reader     rdr  = new MDLV2000Reader(new FileReader("../30_random_cpdbas_compounds.ob3d.sdf"));

// config reader
Properties prop = new Properties();
prop.setProperty("ForceReadAs3DCoordinates", "true");
PropertiesListener listener = new PropertiesListener(prop);
rdr.addChemObjectIOListener(listener);
rdr.customizeJob();

IMolecularDescriptor desc = new LengthOverBreadthDescriptor(); // outside of loop

// mem efficient iter
IAtomContainer mol;
while ((mol = rdr.read(bldr.newInstance(IAtomContainer.class,0,0,0,0))) != null)
{
    Isotopes.getInstance().configureAtoms(mol);
    System.out.println(desc.calculate(mol).getValue());
}
reader.close();