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