Distances and contacts

The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays.

• Atom-wise distances between matching AtomGroups
• All distances between two selections
• All distances within a selection

MDAnalysis.analysis.contacts contains functions and a class to analyse the fraction of native contacts over a trajectory.

• Fraction of native contacts over a trajectory
• Q1 vs Q2 contact analysis
• Contact analysis: number of contacts within a cutoff
• Write your own contacts analysis method