def __init__(self, subchanges=None, samples=None, mover=None,
details=None, input_samples=None):
StorableObject.__init__(self)
self._lazy = {}
self._len = None
self._collapsed = None
self._results = None
self._trials = None
self._accepted = None
self.mover = mover
if subchanges is None:
self.subchanges = []
else:
self.subchanges = subchanges
if samples is None:
self.samples = []
else:
self.samples = samples
if input_samples is None:
self.input_samples = []
else:
self.input_samples = input_samples
self.details = details
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, subchanges=None, samples=None, mover=None,
details=None, input_samples=None):
StorableObject.__init__(self)
self._lazy = {}
self._len = None
self._collapsed = None
self._results = None
self._trials = None
self._accepted = None
self.mover = mover
if subchanges is None:
self.subchanges = []
else:
self.subchanges = subchanges
if samples is None:
self.samples = []
else:
self.samples = samples
if input_samples is None:
self.input_samples = []
else:
self.input_samples = input_samples
self.details = details
def __init__(self):
super(MoveChangeStore, self).__init__(
MoveChange,
json=False
)
self._cached_all = False
self.class_list = StorableObject.objects()
def __init__(self):
super(MoveChangeStore, self).__init__(
MoveChange,
json=False
)
self._cached_all = False
self.class_list = StorableObject.objects()
def __init__(self, trajectory=None):
"""
Create a simulation trajectory object
Parameters
----------
trajectory : :obj:`Trajectory` or list of :obj:`openpathsampling.engines.BaseSnapshot`
if specified, make a deep copy of specified trajectory
"""
# Initialize list.
list.__init__(self)
StorableObject.__init__(self)
if trajectory is not None:
if type(trajectory) is Trajectory:
self.extend(trajectory.iter_proxies())
else:
self.extend(trajectory)
def __init__(self, trajectory=None):
"""
Create a simulation trajectory object
Parameters
----------
trajectory : :obj:`Trajectory` or list of :obj:`openpathsampling.engines.BaseSnapshot`
if specified, make a deep copy of specified trajectory
"""
# Initialize list.
list.__init__(self)
StorableObject.__init__(self)
if trajectory is not None:
if type(trajectory) is Trajectory:
self.extend(trajectory.iter_proxies())
else:
self.extend(trajectory)
def _get_id(self, idx, obj):
if self.reference_by_uuid:
uuid = self.vars['uuid'][int(idx / 2)]
else:
if idx in self.proxy_index:
uuid = self.proxy_index[int(idx / 2)]
else:
return
if idx & 1:
uuid = StorableObject.ruuid(uuid)
obj.__uuid__ = uuid
def _get_id(self, idx, obj):
if self.reference_by_uuid:
uuid = self.vars['uuid'][int(idx / 2)]
if idx & 1:
uuid = StorableObject.ruuid(uuid)
else:
if idx in self.proxy_index:
uuid = self.proxy_index[idx]
elif idx ^ 1 in self.proxy_index:
uuid = StorableObject.ruuid(self.proxy_index[idx ^ 1])
else:
return
obj.__uuid__ = uuid
if idx & 1:
if obj._reversed:
obj._reversed.__uuid__ = uuid
uuid = StorableObject.ruuid(uuid)
obj.__uuid__ = uuid
def __init__(self, contents):
StorableObject.__init__(self)
frozenset.__init__(contents)
self._dimensions = dict(self)
self._cls = self._dimensions['class']
del self._dimensions['class']
def __init__(self, contents):
StorableObject.__init__(self)
frozenset.__init__(contents)
self._dimensions = dict(self)
self._cls = self._dimensions['class']
del self._dimensions['class']
def rev_id(obj):
return StorableObject.ruuid(UUIDReversalDict.id(obj))
