Hi,
I'm calculating partial charge with cdk using the code below. But for some
molecule, it throws some exceptions. I don't know what goes wrong. Can
anyone help? A example molecule is attached. Thanks.
String path = "example.sdf";
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
IteratingSDFReader sdfr = new IteratingSDFReader(new FileReader(path),
bldr);
while (sdfr.hasNext())
{
IAtomContainer mol= sdfr.next();
PartialTChargeMMFF94Descriptor ptc= new
PartialTChargeMMFF94Descriptor();
PiElectronegativityDescriptor pen=new PiElectronegativityDescriptor();
SigmaElectronegativityDescriptor sen=new SigmaElectronegativityDescriptor();
DescriptorValue pt=ptc.calculate(a, mol);
IDescriptorResult v_1=pt.getValue();
DescriptorValue pe=pen.calculate(a, mol);
IDescriptorResult v_2=pe.getValue();
DescriptorValue se=sen.calculate(a, mol);
IDescriptorResult v_3=se.getValue();
}
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