Fix issue q2mm/q2mm#40 (#41)
Fix issue q2mm/q2mm#40 (#41)

See q2mm/q2mm#40 (I hope that the magic GitHub Markdown turns that into a link).
Also, I got rid of some blank spaces.

Anyway, it turns out that Schrodinger's [getBond()](http://content.schrodinger.com/Docs/r2015-4/python_api/api/schrodinger.structure.Structure-class.html#getBond)
function can return None. Personally, I would have made that raise an exception
of some sort, but I mean, I didn't write it. Anyway, here's an example.

Ex.) Don't take this syntax too literally. It's just an illustration.

N-P (single bond)
bond = merge.getBond(N, P)
print(bond)
>>> bond(1, 2)

N P (no bond)
bond = merge.getBond(N, P)
print(bond)
>>> None

The code now checks for this behavior and adds the bond if it's missing.
Q2MM/q2mm,Q2MM/q2mm,ericchansen/q2mm,arosale4/q2mm,ericchansen/q2mm,arosale4/q2mm