contact_map.ContactTrajectory¶
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class
contact_map.
ContactTrajectory
(trajectory, query=None, haystack=None, cutoff=0.45, n_neighbors_ignored=2)[source]¶ Track all the contacts over a trajectory, frame-by-frame.
Internally, this has a single-frame
ContactFrequency
for each frame of the trajectory.Parameters: - trajectory (mdtraj.Trajectory) – the trajectory to calculate contacts for
- query (list of int) – Indices of the atoms to be included as query. Default
None
means all heavy, non-water atoms. - haystack (list of int) – Indices of the atoms to be included as haystack. Default
None
means all heavy, non-water 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. contact_frequency
()Create a ContactFrequency
from this contact trajectorycount
(value)from_contact_maps
(maps)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 index
(value, [start, [stop]])Raises ValueError if the value is not present. join
(others)Concatenate ContactTrajectory instances 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 rolling_frequency
([window_size, step])RollingContactFrequency
iterator for this trajectorysave_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_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
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
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contact_frequency
()[source]¶ Create a
ContactFrequency
from this contact trajectory
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contacts
¶ contact dict for these contacts
Type: ContactsDict
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count
(value) → integer -- return number of occurrences of value¶
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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)¶ 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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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
Supporting start and stop arguments is optional, but recommended.
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classmethod
join
(others)[source]¶ Concatenate ContactTrajectory instances
Parameters: others (List[:class:.ContactTrajectory]) – contact trajectories to concatenate Returns: concatenated contact trajectory Return type: ContactTrajectory
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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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query
¶ indices of atoms to include as query
Type: list of int
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rolling_frequency
(window_size=1, step=1)[source]¶ RollingContactFrequency
iterator for this trajectoryParameters: Returns: windowed iterator for this trajectory
Return type:
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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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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