The :mod:`MDAnalysis.analysis.distances` module provides functions to rapidly compute distances. These largely take in coordinate arrays.
.. toctree:: :maxdepth: 1 /examples/analysis/distances_and_contacts/distances_between_atomgroups /examples/analysis/distances_and_contacts/distances_between_selections /examples/analysis/distances_and_contacts/distances_within_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.
:mod:`MDAnalysis.analysis.contacts` contains functions and a class to analyse the fraction of native contacts over a trajectory.
.. toctree:: :maxdepth: 1 /examples/analysis/distances_and_contacts/contacts_native_fraction /examples/analysis/distances_and_contacts/contacts_q1q2 /examples/analysis/distances_and_contacts/contacts_within_cutoff /examples/analysis/distances_and_contacts/contacts_custom