contact_map.ContactTrajectory¶

class contact_map.ContactTrajectory(trajectory, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2)[source]¶

Track all the contacts over a trajectory, frame-by-frame.

Internally, this has a single-frame ContactFrequency for each frame of the trajectory.

Parameters:

trajectory (mdtraj.Trajectory) – the trajectory to calculate contacts for
query (list of int) – Indices of the atoms to be included as query. Default None means all heavy, non-water atoms.
haystack (list of int) – Indices of the atoms to be included as haystack. Default None means all heavy, non-water 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)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(trajectory[, query, haystack, …])	Initialize self.
`contact_frequency`()	Create a `ContactFrequency` from this contact trajectory
`count`(value)
`from_contact_maps`(maps)
`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
`index`(value, [start, [stop]])	Raises ValueError if the value is not present.
`join`(others)	Concatenate ContactTrajectory instances
`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
`rolling_frequency`([window_size, step])	`RollingContactFrequency` iterator for this trajectory
`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.

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_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_neighbors_ignored`	number of neighbor residues (in same chain) to ignore
`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`
`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_frequency()[source]¶: Create a ContactFrequency from this contact trajectory

contacts¶

contact dict for these contacts

Type:	`ContactsDict`

count(value) → integer -- return number of occurrences of value¶

cutoff¶

cutoff distance for contacts, in nanometers

Type:	float

classmethod from_dict(dct)[source]¶

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

index(value[, start[, stop]]) → integer -- return first index of value.¶

Raises ValueError if the value is not present.

Supporting start and stop arguments is optional, but recommended.

classmethod join(others)[source]¶

Concatenate ContactTrajectory instances

Parameters:	others (List[:class:.ContactTrajectory]) – contact trajectories to concatenate
Returns:	concatenated contact trajectory
Return type:	`ContactTrajectory`

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_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

rolling_frequency(window_size=1, step=1)[source]¶

RollingContactFrequency iterator for this trajectory

Parameters:	window_size (int) – the number of frames in the window step (int) – the number of frames between successive starting points of the window (like the `step` parameter in a Python slice object)
Returns:	windowed iterator for this trajectory
Return type:	`RollingContactFrequency`

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()[source]¶

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