contact_map.ContactDifference¶

class contact_map.ContactDifference(positive, negative)[source]¶

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)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(positive, negative)	Initialize self.
`contact_map`(args, *kwargs)
`from_contacts`(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.

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

contacts¶

contact dict for these contacts

Type:	`ContactsDict`

cutoff¶

cutoff distance for contacts, in nanometers

Type:	float

classmethod from_dict(dct)[source]¶: Create object from dict. :param dct: dict-formatted serialization (see to_dict for details) :type dct: dict

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

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_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

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.