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
¶ 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
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
- trajectory (