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

the topology object associated with the class

Type

mdtraj.Topology

atom_pairs

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

Type

list

minimum_distances

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

Type

list

__init__(trajectory, query, haystack)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(trajectory, query, haystack)

Initialize self.

Attributes

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