calling IsotopeFactory.getInstance(atom.getBuilder()).configure(atom); leads to a NullPointerException whenever the Atom's symbol isn't recognized. This should be something more sensible.
Ralf, I created a patch. Please review:
My rebuttal would be that in cdk-1.4.x throwing CDKException is not possible, as that would change the API... with the IllegalArgumentException I did not have to change the API by adding a throws clause...
Mmmm... wrong report... never mind that previous comment. That should have gone somewhere else :/
Oh, OK. that is reasonable.
Fixed by patch