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 usingdask.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 thedask.distributed.Client
as input. However, there is one important difference. WhereasContactFrequency
takes anmdtraj.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.
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)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_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_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
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
run_info
topology
mdtraj.Topology
: topology object for this systemuse_atom_slice
Indicates if mdtraj.atom_slice() is used before calculating the contact map