contact_map.ContactDifference

class contact_map.ContactDifference(positive, negative)

Contact map comparison (atomic and residue).

This can compare single frames or entire trajectories (or even mix the two!) While this can be directly instantiated by the user, the more common way to make this object is by using the - operator, i.e., diff = map_1 - map_2.

__init__(positive, negative)

Methods

__init__(positive, negative)
contact_map(*args, **kwargs)
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.
to_dict()	Convert object to a dict.
to_json()	JSON-serialized version of this object.

cutoff

float – cutoff distance for contacts, in nanometers

classmethod 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_neighbors_ignored

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

query

list of int – indices of atoms to include as query

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

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

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.