The Vertex Adjacency Magnitude descriptor requires the number of heavy atom - heavy atom bonds as input. The current incorrect calculation retrieves the number of heavy atoms instead. Correct bond number estimation and test cases have been added based examples from MOE.
apply patches from diff doesn't work - this patch can be cherry picked from https://github.com/johnmay/cdk/compare/master-bootstrap
Looks good to me. I would have appreciated some pointers for me to see the correctness of the misinterpretation of the implementation before, but then again, I should just have read the paper...
Accepted and pushed.