API Reference

Contact maps

contact_map.ContactCount(counter, object_f, …)	Return object when dealing with contacts (residue or atom).
ContactMap(frame[, query, haystack, cutoff, …])	Contact map (atomic and residue) for a single frame.
ContactFrequency(trajectory[, query, …])	Contact frequency (atomic and residue) for a trajectory.
ContactDifference(positive, negative)	Contact map comparison (atomic and residue).

Minimum Distance (and related)

MinimumDistanceCounter(trajectory, query, …)	Count how often each atom pair is the minimum distance.
NearestAtoms(trajectory, cutoff[, …])	Identify nearest atoms (within a cutoff) to an atom.