Release 0.0.1a5

[bas-rustenburg]

This PR merges previously developed features back into master and prepares for a release.

Notable new features

• Carboxylic acid MC sampling for dummy atoms
• Single proton asp and glu residues (as opposed to GL4 and AS4)
• Implicit solvent force field xml files (OBC2)
• Updated SAMS implementation with 4 stages, and more internal tracking of variables for analysis
• Updated analysis functions that handle multiple netCDF4 files
• Merging of the Calibration and Simulation class
• Script for parameterizing a ligand based on Epik calculations
• Script for preparing a constant-pH simulation/calibration
• Script for running sequential constant-pH simulations/calibrations