Remove the usage of some deprecated classes.

This pull request replaces the following deprecated classes:
org.openscience.cdk.nonotify.NNAtomContainer
org.openscience.cdk.nonotify.NNChemFile
org.openscience.cdk.nonotify.NNMolecule
org.openscience.cdk.nonotify.NNMoleculeSet

It also replaces, where possibly, org.openscience.cdk.interfaces.IMolecule with org.openscience.cdk.interfaces.IAtomContainer