openpathsampling.engines.openmm.MDSnapshot

class openpathsampling.engines.openmm.MDSnapshot(velocities=None, coordinates=None, box_vectors=None, engine=None)[source]

A fast MD snapshot, which does not proxy the coordinates/velocities.

velocities

atomic velocities

Type

numpy.ndarray, shape=(atoms, 3), dtype=numpy.float32

coordinates

atomic coordinates

Type

numpy.ndarray, shape=(atoms, 3), dtype=numpy.float32

engine

reference to the engine used to generate the snapshot

Type

openpathsampling.DynamicsEngine

__init__(velocities=None, coordinates=None, box_vectors=None, engine=None)

Methods

__init__([velocities, coordinates, …])

args()

Return a list of args of the __init__ function of a class

base()

Return the most parent class actually derived from StorableObject

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[, velocities, coordinates, …])

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

Attributes

ACTIVE_LONG

CREATION_COUNT

INSTANCE_UUID

base_cls

Return the base class

base_cls_name

Return the name of the base class

cls

Return the class name as a string

descriptor

observe_objects

reversed

Get the reversed copy.

topology

xyz

returns

xyz – atomic coordinates without dimensions. Be careful.