The rotatable bond count descriptor should not include C-N amides and terminal hydrogen- and hetero-atoms for the extended Lipinki's rule of five implementation (see Veber, D.F. et al., 2002. Journal of medicinal chemistry, 45(12), pp.2615–23). The parameters for the rotatable bond counts descriptor have been modified to that end and an option has been added to exclude simple C-N amides (ignoring tautomeric or charged constitutions).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>