Hb - Coarse Summary

Added in the generation of coarse summary for bonds between residues.
Streamlined Post-Processing

Removed some of the old cut-offs that we no longer look at.
Adjacent Rings Fix

Added in check such that we don't measure the distance between things
that are next to each other. For obvious reasons.
Ion Distances

Quick script to measure the distance between different ions in the
system and the peptide. It outputs a histogram, contact count, miniumum
and average distances for each ion type, as well as a raw ion distance
with time.