openpathsampling.high_level.transition.TISTransition

class openpathsampling.high_level.transition.TISTransition(stateA, stateB, interfaces, orderparameter=None, name=None, name_suffix='')[source]

Transition using TIS ensembles.

The additional information from the TIS ensembles allows us to set up all the analysis (assuming we built these are proper TIS ensembles, which we DO in the intitialization!)

Parameters
  • stateA (Volume) – Volume for the state from which the transition begins

  • stateB (Volume) – Volume for the state in which the transition ends

  • interfaces (list of Volume) – Volumes for the interfaces

  • orderparameter (CollectiveVariable) – order parameter to be used in the analysis (does not need to be the parameter which defines the interfaces, although it usually is)

  • name (string) – name for the transition

__init__(stateA, stateB, interfaces, orderparameter=None, name=None, name_suffix='')[source]

Methods

__init__(stateA, stateB, interfaces[, …])

args()

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

base()

Return the most parent class actually derived from StorableObject

conditional_transition_probability(steps, …)

This transition’s conditional transition probability for a given ensemble.

copy([with_results])

copy_analysis_from(other)

count_weaks()

Return number of objects subclassed from StorableObject still in memory

crossing_probability(ensemble[, n_blocks])

Return the crossing probability for the given ensemble.

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

pathlength_histogram(ensemble)

Return the pathlength histogram for the given ensemble.

rate(steps[, flux, outer_ensemble, …])

Calculate the rate for this transition.

reverse_uuid()

ruuid(uid)

set_observer(active)

(De-)Activate observing creation of storable objects

to_dict()

Convert object into a dictionary representation

total_crossing_probability([steps, method, …])

Return the total crossing probability using method

Attributes

ACTIVE_LONG

CREATION_COUNT

INSTANCE_UUID

all_ensembles

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