Renaming of <Protons/> ffxml block for consistency.

[bas-rustenburg]

https://github.com/choderalab/protons/blob/master/examples/Ligand%20example/imidazole.xml#L24

@jchodera notes: For example, we have <Residue> denote a residue, <Atom> denotes an atom. The <Protons> tag doesn't denote a proton, but a block of information defining parameters for different titration states.

The suggestion is to rename <TitrationStates/>. Potentially could come up with a term that encompasses tautomers as well, since @wiederm is using the code for that purpose.

Todo:

• Modify the setup code that generates the files
• Modify the code that reads the blocks
• Update any example files (can probably just use sed).