def __init__(self, trajectory=None):
"""
Create a simulation trajectory object
Parameters
----------
trajectory : Trajectory
if specified, make a deep copy of specified trajectory
"""
# Initialize list.
list.__init__(self)
StorableObject.__init__(self)
self.path_probability = None # For future uses
if trajectory is not None:
# Try to make a copy out of whatever container we were provided
if hasattr(trajectory, 'atom_indices'):
self.atom_indices = trajectory.atom_indices
else:
self.atom_indices = None
if type(trajectory) is Trajectory:
self.extend(trajectory.iter_proxies())
else:
self.extend(trajectory)
else:
self.atom_indices = None
def __init__(self):
super(PathMoveChangeStore, self).__init__(
PathMoveChange,
json=False
)
self._cached_all = False
self.class_list = StorableObject.objects()
def __init__(self, subchanges=None, samples=None, mover=None, details=None):
StorableObject.__init__(self)
self._len = None
self._collapsed = None
self._results = None
self._trials = None
self._accepted = None
self.mover = mover
if subchanges is None:
self.subchanges = list()
else:
self.subchanges = subchanges
if samples is None:
self.samples = list()
else:
self.samples = samples
self.details = details
def update_class_list(self):
self.class_list = StorableObject.objects()