openpathsampling.engines.openmm.Snapshot

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

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

engine

reference to the engine used to generate the snapshot

__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`	returns: box_vectors -- the box_vectors of the configuration. The coordinates are wrapped in a
`cls`	Return the class name as a string
`coordinates`	returns: coordinates -- the atomic coordinates of the configuration. The coordinates are
`descriptor`
`instantaneous_temperature`	returns: instantaneous_temperature -- instantaneous temperature from the kinetic energy of this snapshot
`kinetics`	Descriptor class to handle proxy objects in attributes
`masses`	returns: masses -- atomic masses (with openmm.unit attached) in units of mass
`masses_per_mole`	returns: masses_per_mole -- atomic masses (with openmm.unit attached) in units of mass/mole
`md`	returns: md -- the actual trajectory object. Can be used with all functions from mdtraj
`n_degrees_of_freedom`	returns: n_degrees_of_freedom -- number of degrees of freedom in this system (after accounting for
`observe_objects`
`reversed`	Get the reversed copy.
`statics`	Descriptor class to handle proxy objects in attributes
`topology`
`velocities`	The velocities in the configuration.
`xyz`	returns: xyz -- atomic coordinates without dimensions. Be careful.