New features for scripts, and refactoring of ions and MC sampling code

[bas-rustenburg]

This adds several new features and fixes several bugs:

• Dispersion correction was added as an option to scripts.
• Charge neutralizing ion strategy can now be specified separately from the MC proposal code
• The ions are now explicitly associated with residue titration states, rather than the overall charge state of the system so that simultaneous residue changes can no longer cause inconsistencies in the composition of the solvent ions.
• The NCMCProtonDrive .update function has been updated internally for increased modularity.
• Based on the refactored internal structure, a strategy for calculating the weight of states without changing states (aka. importance sampling) was added.
  • This is a new argument to the constructor of the NCMC ProtonDrive and sub classes.
  • The ConstantPHSimulation class handles this internally with the same outward facing API.
  • The protons prep script has new options for specifying the exact state one wants to sample, or to prepare systems for every possible state.
• Tests for the new features (ions, importance sampling) and for the protons.scripts module were added.
• Compatibility fixes for the tautomer related features were added to ligands.py and driver.py

Minor changes:

• Formatting changes to @wiederm 's new tautomer sampling classes
• Small bugs in the test suite were fixed
• protons.scripts module scripts were updated to fix bugs identified in the new tests.

[bas-rustenburg]

Tests pass locally, and Marcus validated that his tautomer features still work as expected..