Strategies for adding protons to arbitrary components

[jchodera]

@rafwiewiora pointed out that Amber's reduce program has a nice solution to protonating arbitrary residues from the PDB. It uses a dictionary of all HET components in the PDB (presumably from the Ligand Expo with definitions of protons for anything you might find in the PDB.

[swails]

It's not ours. It's Michael Word's (he's at OpenEye, I think). We just bundle it because we find it useful:

See here: http://kinemage.biochem.duke.edu/software/reduce.php

[peastman]

This was implemented in #295.