Adding functions to get and add missing bonds

[dprada]

The need of adding two functions to get and add missing bonds from/to a molecular system arises when working with the demo files coming from NGLView is checked: the gro file has no bonds and the pdb bonds are not properly processed.

The way to include or detect covalent bonds should be similar to what is included in pytraj and probably in ParmED (this last library should be checked).

These two functions should be added to the module build.

[dprada]

I have already a first half-cooked draft of these functions in my forked repo.