The getCyclicBonds() rountine in ConnectionTableTool,
calls CMLBondSet in its calculation, which throws a
CMLException when trying to add a bond that is
already in the Set (called from getRingNucleiBondSets
()) - unfortunately this seems to throw an exception
whenever you try to do any calculations on a molecule
with any rings.
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I believe this to have been fixed over the last few weeks.
In general it will help to have a unit test that throws errors like this.
P.