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.

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

Methods

__init__(trajectory[, query, haystack, …])
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.
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
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
save_to_file(filename[, mode])	Save this object to the given file.
subtract_contact_frequency(other)	Subtracts results from other from internal counter.
to_dict()
to_json()	JSON-serialized version of this object.

add_contact_frequency(other)

Add results from other to the internal counter.

Parameters:other (ContactFrequency) – contact frequency made from the frames to remove from this contact frequency

atom_contacts

Atoms pairs mapped to fraction of trajectory with that contact

contact_map(trajectory, frame_number, residue_query_atom_idxs, residue_ignore_atom_idxs)

Returns atom and residue contact maps for the given frame.

Parameters:

• frame (mdtraj.Trajectory) – the desired frame (uses the first frame in this trajectory)
• residue_query_atom_idxs (dict) –
• residue_ignore_atom_idxs (dict) –

Returns:

• atom_contacts (collections.Counter)
• residue_contact (collections.Counter)

cutoff

float – cutoff distance for contacts, in nanometers

from_dict(dct)

Create object from dict.

Parameters:dct (dict) – dict-formatted serialization (see to_dict for details)

See also

to_dict()

from_file(filename)

Load this object from a given file

Parameters:filename (string) – the file to read from Returns:the reloaded object Return type:ContactObject

See also

save_to_file()

save to a file

from_json(json_string)

Create object from JSON string

Parameters:json_string (str) – JSON-serialized version of the object

See also

to_json()

haystack

list of int – indices of atoms to include as haystack

most_common_atoms_for_contact(contact_pair)

Most common atom contacts for a given residue contact pair

Parameters:contact_pair (length 2 list of Residue or int) – the residue contact pair for which the most common atom contact pairs will be calculated Returns:Atom contact pairs for the residue contact pair, in order of frequency. Referring to the list as l, each element of the list l[e] consists of two parts: l[e][0] is a list containing the two MDTraj Atom objects that make up the contact, and l[e][1] is the measure of how often the contact occurs. Return type:list

most_common_atoms_for_residue(residue)

Most common atom contact pairs for contacts with the given residue

Parameters:residue (Residue or int) – the Residue object or index representing the residue for which the most common atom contact pairs will be calculated Returns:Atom contact pairs involving given residue, order of frequency. Referring to the list as l, each element of the list l[e] consists of two parts: l[e][0] is a list containing the two MDTraj Atom objects that make up the contact, and l[e][1] is the measure of how often the contact occurs. Return type:list

n_frames

Number of frames in the mapped trajectory

n_neighbors_ignored

int – number of neighbor residues (in same chain) to ignore

query

list of int – indices of atoms to include as query

residue_contacts

Residue pairs mapped to fraction of trajectory with that contact

residue_ignore_atom_idxs

dict – maps query residue index to atom indices to ignore

residue_query_atom_idxs

dict – maps query residue index to atom indices in query

save_to_file(filename, mode='w')

Save this object to the given file.

Parameters:

• filename (string) – the file to write to
• mode ('w' or 'a') – file writing mode. Use ‘w’ to overwrite, ‘a’ to append. Note that writing by bytes (‘b’ flag) is automatically added.

See also

from_file()

load from generated file

subtract_contact_frequency(other)

Subtracts results from other from internal counter.

Note that this is intended for the case that you’re removing a subtrajectory of the already-calculated trajectory. If you want to compare two different contact frequency maps, use ContactDifference.

Parameters:other (ContactFrequency) – contact frequency made from the frames to remove from this contact frequency

to_json()

JSON-serialized version of this object.

See also

from_json()

topology

mdtraj.Topology – topology object for this system

The topology includes information about the atoms, how they are grouped into residues, and how the residues are grouped into chains.