openpathsampling.engines.openmm.Snapshot

class openpathsampling.engines.openmm.Snapshot(statics=None, kinetics=None, is_reversed=False, engine=None)

The standard snapshot for MD, based on statics and kinetics proxies.

engine

reference to the engine used to generate the snapshot

Type:

openpathsampling.DynamicsEngine

__init__(statics=None, kinetics=None, is_reversed=False, engine=None)

Methods

__init__([statics, kinetics, is_reversed, ...])
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
construct([coordinates, box_vectors, ...])	Construct a new snapshot from numpy arrays
copy()	Returns a shallow copy of the instance itself.
copy_to(target)
copy_with_replacement(**kwargs)
count_weaks()	Return number of objects subclassed from StorableObject still in memory
create_empty()
create_reversed()
descendants()	Return a list of all subclassed objects
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
init_copy(self[, statics, kinetics, ...])
init_empty()
objects()	Returns a dictionary of all storable objects
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
to_dict()	Convert object into a dictionary representation
trajectory_box_vectors(traj)
trajectory_coordinates(traj)
trajectory_velocities(traj)

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
box_vectors
cls	Return the class name as a string
coordinates
descriptor
instantaneous_temperature
kinetics	Descriptor class to handle proxy objects in attributes
masses
masses_per_mole
md
n_degrees_of_freedom
observe_objects
reversed	Get the reversed copy.
statics	Descriptor class to handle proxy objects in attributes
topology
velocities	The velocities in the configuration.
xyz