openpathsampling.FullBootstrapping

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

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)[source]

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