contact_map.MinimumDistanceCounter

class contact_map.MinimumDistanceCounter(trajectory, query, haystack)

Count how often each atom pair is the minimum distance.

Parameters:

• trajectory (mdtraj.Trajectory) – trajectory to be analyzed
• query (list) – list of the (integer) atom indices to use as the query
• haystack (list) – list of the (integer) atom indices to use as the haystack

topology

mdtraj.Topology – the topology object associated with the class

atom_pairs

list – list of 2-tuples representing atom index pairs to use when looking for the minimum distance

minimum_distances

list – the minimum distance between query group and haystack group at each frame of the trajectory

__init__(trajectory, query, haystack)

Methods

__init__(trajectory, query, haystack)

atom_count

collections.Counter – map from atom pair to the number of times that pair is the minimum distance

atom_history

list of 2-tuples – list of atom pairs when represent the minimum distance at each frame of the trajectory

residue_count

collections.Counter – map from residue pair to the number of times that pair is the minimum distance

residue_history

list of 2-tuples – list of residue pairs when represent the minimum distance at each frame of the trajectory