contact_map.ContactFrequency

class contact_map.ContactFrequency(trajectory, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2, frames=None)

Contact frequency (atomic and residue) for a trajectory.

The contact frequency is defined as fraction of the trajectory that a certain contact is made. This object calculates this quantity for all contacts with atoms in the query residue, with “contact” defined as being within a certain cutoff distance.

Parameters

• trajectory (mdtraj.Trajectory) – Trajectory (segment) to analyze

• query (list of int) – Indices of the atoms to be included as query. Default None means all atoms.

• haystack (list of int) – Indices of the atoms to be included as haystack. Default None means all atoms.

• cutoff (float) – Cutoff distance for contacts, in nanometers. Default 0.45.

• n_neighbors_ignored (int) – Number of neighboring residues (in the same chain) to ignore. Default 2.

• frames (list of int) – The indices of the frames to use from the trajectory. Default all

__init__(trajectory, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2, frames=None)

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

Methods

__init__(trajectory[, query, haystack, …])	Initialize self.
add_contact_frequency(other)	Add results from other to the internal counter.
contact_map(trajectory, frame_number, …)	Returns atom and residue contact maps for the given frame.
convert_atom_contacts(atom_contacts)
from_dict(dct)	Create object from dict.
from_file(filename)	Load this object from a given file
from_json(json_string)	Create object from JSON string
idx_to_s_idx(idx)	function to convert a real atom index to a sliced one
most_common_atoms_for_contact(contact_pair)	Most common atom contacts for a given residue contact pair
most_common_atoms_for_residue(residue)	Most common atom contact pairs for contacts with the given residue
s_idx_to_idx(idx)	function to convert a sliced atom index back to real index
save_to_file(filename[, mode])	Save this object to the given file.
slice_trajectory(trajectory)
subtract_contact_frequency(other)	Subtracts results from other from internal counter.
to_dict()	Convert object to a dict.
to_json()	JSON-serialized version of this object.

Attributes

all_atoms	all atom indices used in the contact map
atom_contacts	Atoms pairs mapped to fraction of trajectory with that contact
contacts	contact dict for these contacts
cutoff	cutoff distance for contacts, in nanometers
haystack	indices of atoms to include as haystack
haystack_residue_range	min and (max + 1) of haystack residue indices
haystack_residues	residues for atoms in the haystack
n_frames	Number of frames in the mapped trajectory
n_neighbors_ignored	number of neighbor residues (in same chain) to ignore
query	indices of atoms to include as query
query_residue_range	min and (max + 1) of query residue indices
query_residues	residues for atoms in the query
residue_contacts	Residue pairs mapped to fraction of trajectory with that contact
residue_ignore_atom_idxs	maps query residue index to atom indices to ignore
residue_query_atom_idxs	maps query residue index to atom indices in query
topology	mdtraj.Topology: topology object for this system
use_atom_slice	Indicates if mdtraj.atom_slice() is used before calculating the contact map