openpathsampling.engines.Trajectory

class openpathsampling.engines.Trajectory(trajectory=None)

Simulation trajectory. Essentially a python list of snapshots

__init__(trajectory=None)

Create a simulation trajectory object

Parameters:

trajectory (Trajectory or list of openpathsampling.engines.BaseSnapshot) – if specified, make a deep copy of specified trajectory

Methods

__init__([trajectory])	Create a simulation trajectory object
append(object, /)	Append object to the end of the list.
args()	Return a list of args of the __init__ function of a class
as_proxies()	Returns all contains all actual elements
base()	Return the most parent class actually derived from StorableObject
clear()	Remove all items from list.
contains_symmetric(item)	Test whether a snapshot or its reversed is in a trajectory
copy()	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
extend(iterable)	Extend list by appending elements from the iterable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_as_proxy(item)	Get an actual contained element
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
index(value[, start, stop])	Return first index of value.
index_symmetric(value)	Return index of a snapshot or its reversed inside a trajectory
insert(index, object, /)	Insert object before index.
is_correlated(other[, time_reversal])	Checks if two trajectories share a common snapshot
iter_proxies()	Returns an iterator over all actual elements
map(fnc[, allow_fast])	This runs a function and tries to be fast.
objects()	Returns a dictionary of all storable objects
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse()	Reverse IN PLACE.
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
shared_configurations(other[, time_reversal])	Returns a set of shared snapshots
shared_subtrajectory(other[, time_reversal])	Returns a subtrajectory which only contains frames present in other
sort(*[, key, reverse])	Sort the list in ascending order and return None.
subtrajectory_indices(subtrajectories)	Returns a list of lists of indices for frames from subtrajectories.
summarize_by_volumes(label_dict)	Summarize trajectory based on number of continuous frames in volumes.
summarize_by_volumes_str(label_dict[, delimiter])	Return string version of the volumes visited by this trajectory.
to_dict()	Convert object into a dictionary representation
to_mdtraj([topology])	Construct a mdtraj.Trajectory object from the Trajectory itself
unique_subtrajectory(other)	Returns a subtrajectory which contains frames not present in other

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
engine
n_snapshots	Return the number of frames in the trajectory.
observe_objects
reversed	Returns a reversed (shallow) copy of the trajectory itself.
snapshots
topology	Return a Topology object representing the topology of the current view of the trajectory