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

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

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.