Add movie-making scripts

[jchodera]

I've added a movie-making script so @bas-rustenburg can see if I've made some sort of proton indexing error.

[codecov-io]

Codecov Report

Merging #96 into master will decrease coverage by 6.79%. The diff coverage is n/a.

@@            Coverage Diff            @@
##           master      #96     +/-   ##
=========================================
- Coverage   72.26%   65.46%   -6.8%     
=========================================
  Files          35       19     -16     
  Lines        3897     2951    -946     
=========================================
- Hits         2816     1932    -884     
+ Misses       1081     1019     -62

Impacted Files	Coverage Δ
protons/tests/test_explicit.py	84.43% <0%> (-11.3%)	:arrow_down:
protons/tests/test_integrators.py	69.56% <0%> (-9.65%)	:arrow_down:
protons/tests/test_ligands.py	29.72% <0%> (-1.25%)	:arrow_down:
protons/tests/test_record.py	93.22% <0%> (ø)	:arrow_up:
protons/__init__.py	100% <0%> (ø)	:arrow_up:
protons/app/metadatareporter.py
protons/tests/test_simulation.py
protons/app/cnstphgbforces.py
protons/app/topology.py
protons/app/calibration.py
... and 33 more

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[jchodera]

@bas-rustenburg : I've updated my movie-making scripts. It would be great to instead work these into something we could more easily automate for making movies, and this may or may not be a stand-alone script. With pymol installed via conda, it might be possible to call PyMOL from Python to make these movies rather than the other way around. Or we could figure out how to use nglview, which seems to be much more modern.

[jchodera]

Note that I haven't had a chance to update these movie making scripts to use your new format for proton_states, so it might be useful to keep these scripts around and start from scratch with nglview.

Take away messages:

• Pausing the trajectory to fade the proton in and out is a good way to call attention to the protonation state action
• For the complex, rendering just the ligand and titratable residues is probably the best bet for highlighting interesting events