openpathsampling.ensemble.TISEnsemble

class openpathsampling.ensemble.TISEnsemble(initial_states, final_states, interface, orderparameter=None, cv_max=None, lambda_i=None)[source]

An ensemble for TIS (or AMS).

Begin in initial_states, end in either initial_states or final_states, and cross interface.

initial_states

Volume(s) that only the first or last frame may be in

Type

openpathsampling.volume.Volume or list of openpathsampling.volume.Volume

final_states

Volume(s) that only the last frame may be in

Type

openpathsampling.volume.Volume or list of openpathsampling.volume.Volume

interface

Volume which the trajectory must exit to be accepted

Type

openpathsampling.volume.Volume

orderparameter

CV to be used as order parameter for this

Type

openpathsampling.collectivevariable.CollectiveVariable

__init__(initial_states, final_states, interface, orderparameter=None, cv_max=None, lambda_i=None)[source]

A path volume defines a set of paths.

Methods

__init__(initial_states, final_states, interface)

A path volume defines a set of paths.

args()

Return a list of args of the __init__ function of a class

base()

Return the most parent class actually derived from StorableObject

can_append(trajectory[, trusted])

Returns true, if the trajectory so far can still be in the ensemble if it is appended by a frame.

can_prepend(trajectory[, trusted])

Returns true, if the trajectory so far can still be in the ensemble if it is prepended by a frame.

check(trajectory)

Alias for __call__

check_reverse(trajectory[, trusted])

See __call__; same thing, but potentially in reverse frame order

count_weaks()

Return number of objects subclassed from StorableObject still in memory

descendants()

Return a list of all subclassed objects

extend_sample_from_trajectories(...[, ...])

Generate a sample in the ensemble by extending parts of trajectories

find_first_subtrajectory(trajectory)

Return the first sub-trajectory that matches the ensemble

find_last_subtrajectory(trajectory)

Return the last sub-trajectory that matches the ensemble

fix_name()

Set the objects name to be immutable.

from_dict(dct)

Reconstruct an object from a dictionary representaiton

get_sample_from_trajectories(trajectories[, ...])

Generate a sample in the ensemble by testing trajectories

get_uuid()

idx(store)

Return the index which is used for the object in the given store.

iter_extendable_slices(trajectory[, ...])

Return an iterator over maxiaml slices of extendable subtrajectories

iter_split(trajectory[, max_length, ...])

Return iterator over subtrajectories satisfying the given ensemble.

iter_valid_slices(trajectory[, max_length, ...])

Return an iterator over slices of subtrajectories matching the ensemble

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

split(trajectory[, max_length, min_length, ...])

Return list of subtrajectories satisfying the given ensemble.

split_sample_from_trajectories(trajectories)

Generate a sample in the ensemble by searching for sub-parts

strict_can_append(trajectory[, trusted])

Returns true if the trajectory can be the beginning of a trajectory in the ensemble.

strict_can_prepend(trajectory[, trusted])

Returns true if the trajectory can be the end of a trajectory in the ensemble.

to_dict()

Convert object into a dictionary representation

trajectory_summary(trajectory)

Return dict with info on how this ensemble "sees" the trajectory.

trajectory_summary_str(trajectory)

Returns a string with the results of the trajectory_summary function.

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.

extendable_sub_ensembles

is_named

True if this object has a custom name.

name

Return the current name of the object.

observe_objects