The storedata() method in the CMLCoreModule calls storeAtomData() and storeBondData() to configure the CDK molecule with the read in atom/bond data. Both methods used to call newAtomData() and newBondData() at the end of the store methods, resetting all variables. This behavior makes extending/overriding the methods counter intuitive in custom CML conventions.
Moving the newAtom/BondData() methods outside the storeAtom/BondData() methods ensures that the methods only do what the methods names say and enable usage of the methods in custom conventions.
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