contact_map.DaskContactFrequency¶

class contact_map.DaskContactFrequency(client, filename, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2, **kwargs)[source]¶

Dask-based parallelization of contact frequency.

The contact frequency is the fraction of a trajectory that a contact is made. See ContactFrequency for details. This implementation parallelizes the contact frequency calculation using dask.distributed, which must be installed separately to use this object.

Notes

The interface for this object closely mimics that of the ContactFrequency object, with the addition requiring the dask.distributed.Client as input. However, there is one important difference. Whereas ContactFrequency takes an mdtraj.Trajectory object as input, DaskContactFrequency takes a file name, plus any extra kwargs that MDTraj needs to load the file.

Parameters:

client (dask.distributed.Client) – Client object connected to the dask network.
filename (str) – Name of the file where the trajectory is located. File must be accessible by all workers in the dask network.
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__(client, filename, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2, **kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(client, filename[, query, …])	Initialize self.
`add_contact_frequency`(other)	Add results from other to the internal counter.
`from_contacts`(atom_contacts, …[, query, …])
`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`()	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_range`	return an tuple with the (min, max+1) of 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
`parameters`
`query`	indices of atoms to include as query
`query_range`	return an tuple with the (min, max+1) of 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
`run_info`
`topology`	topology object for this system
`use_atom_slice`	Indicates if mdtraj.atom_slice() is used before calculating the contact map

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

all_atoms¶

all atom indices used in the contact map

Type:	list of int

atom_contacts¶: Atoms pairs mapped to fraction of trajectory with that contact

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_range¶: return an tuple with the (min, max+1) of haystack

haystack_residue_range¶

min and (max + 1) of haystack residue indices

Type:	(int, int)

haystack_residues¶

residues for atoms in the haystack

Type:	list

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¶

number of neighbor residues (in same chain) to ignore

Type:	int

query¶

indices of atoms to include as query

Type:	list of int

query_range¶: return an tuple with the (min, max+1) of query

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_contacts¶: Residue pairs mapped to fraction of trajectory with that contact

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_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