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
.Methods
__init__
(positive, negative)Initialize self.
contact_map
(*args, **kwargs)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 systemuse_atom_slice
Indicates if mdtraj.atom_slice() is used before calculating the contact map