Chen-Roux ions scheme

[bas-rustenburg]

This still needed to be merged into master, since it is needed for production runs.

Implementation of ion selection from Chen-Roux 2015 paper, extended to deal with ligands/charge changes larger than one unit. Key thing is that alchemical charges are only added/deleted in one direction, as recommended by Chen and Roux, as opposed to creation/destruction of opposite charges.

The proposal mechanism is called OneDirectionChargeProposal.

Also adds tests that actually ensure that accumulation of ions doesn't happen. Large improvement over old test is that the ion scheme is tested without actually having to run a simulation. Much faster now, and doesn't require CUDA (or OpenMM really). It uses a fictional MC chain of protonation states from realistic residue types and keeps track of what salt would have been added/removed to maintain charge neutrality.

Should be good to merge if builds pass.

[codecov-io]

Codecov Report

Merging #115 into master will decrease coverage by 1.17%. The diff coverage is 86.87%.

@@            Coverage Diff             @@
##           master     #115      +/-   ##
==========================================
- Coverage   64.91%   63.74%   -1.18%     
==========================================
  Files          37       37              
  Lines        4923     4967      +44     
==========================================
- Hits         3196     3166      -30     
- Misses       1727     1801      +74

Impacted Files	Coverage Δ
protons/tests/test_ligands.py	41.46% <ø> (+10.48%)	:arrow_up:
protons/tests/test_explicit.py	94.44% <100%> (+4.94%)	:arrow_up:
protons/tests/test_implicit.py	22% <100%> (-69.9%)	:arrow_down:
protons/app/driver.py	85.16% <100%> (-0.41%)	:arrow_down:
protons/app/proposals.py	67.11% <74.39%> (+17.11%)	:arrow_up:
protons/app/analysis.py	7.53% <0%> (-0.32%)	:arrow_down:

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