openpathsampling.engines.gromacs.ExternalMDSnapshot

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

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)[source]

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.