contact_map.MinimumDistanceCounter¶

class contact_map.MinimumDistanceCounter(trajectory, query, haystack)[source]¶

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)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(trajectory, query, haystack) Initialize self.

Attributes

`atom_count`	map from atom pair to the number of times that pair is the minimum distance
`atom_history`	list of atom pairs when represent the minimum distance at each frame of the trajectory
`residue_count`	map from residue pair to the number of times that pair is the minimum distance
`residue_history`	list of residue pairs when represent the minimum distance at each frame of the trajectory

atom_count¶

map from atom pair to the number of times that pair is the minimum distance

Type:	`collections.Counter`

atom_history¶

list of atom pairs when represent the minimum distance at each frame of the trajectory

Type:	list of 2-tuples

residue_count¶

map from residue pair to the number of times that pair is the minimum distance

Type:	`collections.Counter`

residue_history¶

list of residue pairs when represent the minimum distance at each frame of the trajectory

Type:	list of 2-tuples