openpathsampling.engines.Topology

class openpathsampling.engines.Topology(n_atoms, n_spatial=3)

Topology is the object that contains all information about the structure of the system to be simulated.

n_atoms

number of atoms

Type:

int

n_spatial

number of spatial dimensions, default is 3

Type:

int

__init__(n_atoms, n_spatial=3)

Methods

__init__(n_atoms[, n_spatial])
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
fix_name()	Set the objects name to be immutable.
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.
named(name)	Name an unnamed object.
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
default_name	Return the default name.
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects