Deprecate ContactMap (allowing rename ContactFrequency => ContactMap)

[dwhswenson]

First step of #82.

Also, note that the correct warning to use here is FutureWarning, which will actually show for users (DeprecationWarning will not). I learned that from this SO answer, written by a very brilliant author. I would argue that basic interactive use of Contact Map Explorer in a Jupyter notebook counts as "application", not "library."

[dwhswenson]

Codeclimate complains about:

• contact_map.py being too long (well, it'll be shorter when we remove ContactMap! plus, as stated before, I intend to split things out of it in a PR dedicated to that process)
• the changes for deprecating classmethods look like repeated code. While writing the code, I actually thought about writing a decorator to avoid that repetition, but it seemed like overkill for code that's going to be removed in a near-future release.

Marking both as wontfix.

[sroet]

Looks good in general,

small comments on the examples:

• in the contact_map.ipynb there are still a couple references to ContactMap (an import and some text in the list residue contacts section
• The without_atom_slice notebook still references contactMap (as the only bad case), so there might need to be some alteration of the text there (as the example can't get our code to be slower than without atomslice). Maybe try adding a map for a single frame?
  frame_contacts = ContactFrequency(traj[0], query=used_atoms, haystack=used_atoms)

[dwhswenson]

• in the contact_map.ipynb there are still a couple references to ContactMap (an import and some text in the list residue contacts section

Fixed.

• The without_atom_slice notebook still references contactMap (as the only bad case), so there might need to be some alteration of the text there (as the example can't get our code to be slower than without atomslice). Maybe try adding a map for a single frame?

I probably should have actually read the text instead of just removing every bit of code that said ContactMap.... anyway, I think what's there now illustrates the original point.

[sroet]

LGTM, feel free to merge