[Cdk-devel] several questions about CDK

[<sha...@ho...>]

I'm learning CDK APIs now. And when I use CDK to make some sample 
applications, I encounter some problems.
1.For some molecules, after I use 
HydrogenAdder.addImplicitHydrogensToSatisfyValency method, exception will 
occured when using SMILESWriter to write the molecule to disk. 
I debug the source code and find the problem below:
  when using SMILESWriter, CanonicalLabeler.createInvarLabel method will be 
invoked. The following code may have a problem.

inv.append((int)Math.abs(a.getFormalCharge)));      //Hydrogen count
inv.append(a.getHydrogenCount());
vect.add(new InvPair(Long.parseLong(inv.toString()), a));

a.getHydrogenCount()  will return a negative. thus 
Long.parseLong(inv.toString())  will have an exception. 

2.When I use PDBReader or PDBWriter to read or write a molecule, I never 
get a normal result. I just don't know why. And I wonder how should I use 
the two classes. 

3.When I use class RuleOfFiveDescriptor to descript a molecule, I always 
get a 0 in weight. The code is followed: 
        IMolecularDescriptor mw = new WeightDescriptor();
        Object[] mwparams = {new String("")};
        mw.setParameters(mwparams);
        double mwvalue = 
((DoubleResult)mw.calculate(mol).getValue()).doubleValue();

I'd appreciate for any of your help.

With best regards
           Jimmy

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