contact_map.ContactMap

class contact_map.ContactMap(frame, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2)

Contact map (atomic and residue) for a single frame.

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

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

Methods

__init__(frame[, query, haystack, cutoff, …])	Initialize self.
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)
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
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_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_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	topology object for this system
use_atom_slice	Indicates if mdtraj.atom_slice() is used before calculating the contact map

all_atoms

all atom indices used in the contact map

Type:list of int

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)

contacts

contact dict for these contacts

Type:ContactsDict

cutoff

cutoff distance for contacts, in nanometers

Type:float

classmethod from_dict(dct)

Create object from dict.

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

See also

to_dict()

classmethod 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

classmethod from_json(json_string)

Create object from JSON string

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

See also

to_json()

haystack

indices of atoms to include as haystack

Type:list of int

haystack_residue_range

min and (max + 1) of haystack residue indices

Type:(int, int)

haystack_residues

residues for atoms in the haystack

Type:list

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

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_neighbors_ignored

number of neighbor residues (in same chain) to ignore

Type:int

query

indices of atoms to include as query

Type:list of int

query_residue_range

min and (max + 1) of query residue indices

Type:(int, int)

query_residues

residues for atoms in the query

Type:list

residue_ignore_atom_idxs

maps query residue index to atom indices to ignore

Type:dict

residue_query_atom_idxs

maps query residue index to atom indices in query

Type:dict

s_idx_to_idx(idx)

function to convert a sliced atom index back to real index

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

to_dict()

Convert object to a dict.

Keys should be strings; values should be (JSON-) serializable.

See also

from_dict()

to_json()

JSON-serialized version of this object.

See also

from_json()

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.

Type:mdtraj.Topology

use_atom_slice

Indicates if mdtraj.atom_slice() is used before calculating the contact map

Type:bool