Corrected the covalent radius implementation in element.

Did the python side correctly (aside from some comments),
however the .pxd code was not included in the commit.
Coordinates stored on an Atom now as a numpy array.

Originally a list, however a numpy array is more flexible.
The parsed output from cclib produces these in a numpy
array, and as such the fromXYZ method also uses a numpy
array.
Saving coordinates onto an atom now given as a numpy array.

These were originally provided as a list, however the
numpy array is more flexible.
Parse the mopac output file using the parse method

Was already implemented, so just using an existing method
instead of redoing it.
Check the optimized geometry connectivity in gaussian

Previously done with mopac, now including the method
for gaussian.