openpathsampling.engines.gromacs.ExternalMDSnapshot

class openpathsampling.engines.gromacs.ExternalMDSnapshot(file_name=None, file_position=None, engine=None)

Snapshot for external MD engines

Internally, this only stores the file_name and the file_position. All specific details (positions, velocities, box vectors) are loaded from file when requested.

engine

reference to the engine used to generate the snapshot

Type:

openpathsampling.DynamicsEngine

file_name

Type:

str

file_position

Type:

int

Parameters:

• file_name (str) – the name of the external file where the positions/velocities/etc. reside

• file_position (int) – position within the file; the engine should be able to load data for this specific snapshot based on this number

• engine (DynamicsEngine) – the engine associated with this snapshot

__init__(file_name=None, file_position=None, engine=None)

Methods

__init__([file_name, file_position, engine])
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
clear_cache()	Remove internal details from snapshot.
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[, engine, ...])
init_empty()
internalize()	Return a version of this snapshot with storable details.
load_details()	Cache coords, velocities, box vectors from the external file
objects()	Returns a dictionary of all storable objects
reverse_uuid()
ruuid(uid)
set_details(xyz, velocities, box_vectors)	Set coords, velocities, and box vectors.
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
box_vectors
cls	Return the class name as a string
coordinates
descriptor
observe_objects
reversed	Get the reversed copy.
topology
velocities
xyz	returns: xyz -- atomic coordinates without dimensions.