openpathsampling.FullBootstrapping

class openpathsampling.FullBootstrapping(transition, snapshot, storage=None, engine=None, extra_interfaces=None, extra_ensembles=None, forbidden_states=None, initial_max_length=None)

Takes a snapshot as input; gives you back a sampleset with trajectories for every ensemble in the transition.

This includes

Parameters:

• transition (TISTransition) – the TIS transition to fill by bootstrapping

• snapshot (Snapshot) – the initial snapshot

• storage (Storage) – storage file to record the steps (optional)

• engine (DynamicsEngine) – MD engine to use for dynamics

• extra_interfaces (list of Volume) – additional interfaces to make into TIS ensembles (beyond those in the transition)

• extra_ensembles (list of Ensemble) – additional ensembles to sample after the TIS ensembles

• forbidden_states (list of Volume) – regions that are disallowed during the initial trajectory. Note that these region are allowed during the interface sampling

• initial_max_length (int) – maximum length of the initial A->A trajectory

__init__(transition, snapshot, storage=None, engine=None, extra_interfaces=None, extra_ensembles=None, forbidden_states=None, initial_max_length=None)

Methods

__init__(transition, snapshot[, storage, ...])
args()	Return a list of args of the __init__ function of a class
attach_default_hooks()
attach_hook(hook[, hook_for])	Attach a hook class or method to this simulation.
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
empty_hooks()	Return a hook dictionary with no hooks.
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()
run([max_ensemble_rounds, ...])	Run the simulator for a number of steps
run_hooks(hook_name, **kwargs)	Run the hooks for the given hook_name
ruuid(uid)
save_initial_step()	Save the initial state as an MCStep to the storage
set_observer(active)	(De-)Activate observing creation of storable objects
sync_storage()	Will sync all collective variables and the storage to disk
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
calc_name
cls	Return the class name as a string
default_name	Return the default name.
hook_names
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects