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	mdtraj.Topology: topology object for this system
use_atom_slice	Indicates if mdtraj.atom_slice() is used before calculating the contact map