contact_map.ContactFrequency¶
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class
contact_map.
ContactFrequency
(trajectory, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2)[source]¶ Contact frequency (atomic and residue) for a trajectory.
The contact frequency is defined as fraction of the trajectory that a certain contact is made. This object calculates this quantity for all contacts with atoms in the query residue, with “contact” defined as being within a certain cutoff distance.
Parameters: - trajectory (mdtraj.Trajectory) – Trajectory (segment) to analyze
- 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.
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__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. add_contact_frequency
(other)Add results from other to the internal counter. 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 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. 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 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 topology
topology object for this system use_atom_slice
Indicates if mdtraj.atom_slice() is used before calculating the contact map -
add_contact_frequency
(other)[source]¶ Add results from other to the internal counter.
Parameters: other ( ContactFrequency
) – contact frequency made from the frames to remove from this contact frequency
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all_atoms
¶ all atom indices used in the contact map
Type: list of int
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atom_contacts
¶ Atoms pairs mapped to fraction of trajectory with that contact
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contacts
¶ contact dict for these contacts
Type: ContactsDict
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classmethod
from_dict
(dct)[source]¶ Create object from dict.
Parameters: dct (dict) – dict-formatted serialization (see to_dict for details) See also
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classmethod
from_file
(filename)[source]¶ 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
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classmethod
from_json
(json_string)¶ Create object from JSON string
Parameters: json_string (str) – JSON-serialized version of the object See also
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haystack
¶ indices of atoms to include as haystack
Type: list of int
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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 listl[e]
consists of two parts:l[e][0]
is a list containing the two MDTraj Atom objects that make up the contact, andl[e][1]
is the measure of how often the contact occurs.Return type: list
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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 listl[e]
consists of two parts:l[e][0]
is a list containing the two MDTraj Atom objects that make up the contact, andl[e][1]
is the measure of how often the contact occurs.Return type: list
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n_frames
¶ Number of frames in the mapped trajectory
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query
¶ indices of atoms to include as query
Type: list of int
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residue_contacts
¶ Residue pairs mapped to fraction of trajectory with that contact
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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
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subtract_contact_frequency
(other)[source]¶ Subtracts results from other from internal counter.
Note that this is intended for the case that you’re removing a subtrajectory of the already-calculated trajectory. If you want to compare two different contact frequency maps, use
ContactDifference
.Parameters: other ( ContactFrequency
) – contact frequency made from the frames to remove from this contact frequency
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to_dict
()[source]¶ Convert object to a dict.
Keys should be strings; values should be (JSON-) serializable.
See also
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to_json
()¶ JSON-serialized version of this object.
See also
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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