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

Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.

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 native contacts analysis method