schwancr-contact

I made a couple changes to #298.

1. Fixed the python 2.6  bug in test_element.py
1. Changed the return value of `compute_contact_distances` to also return the residue indices used
2. Changed the name of `make_square` to `squareform` (it's sort of like the scipy function `scipy.spatial.distance.squareform`), and changed its arguments to necessarily accept both of the outputs of `compute_contact_distances`.
2. Added some tests, and changed some docstrings.