openpathsampling.analysis.tis.TISAnalysis

class openpathsampling.analysis.tis.TISAnalysis(network, flux_method, transition_probability_methods)

Generic class for TIS analysis. One of these for each network.

In general, the TIS rate is split into the flux and the transition probability.

Parameters:

• network (TransitionNetwork) – the reaction network to be analyzed

• flux_method (flux calculation method) – the method to use to calculate the flux; typical classes are MinusMoveFlux and DictFlux

• transition_probability_methods (dict of Transition to method) – the method for calculating the transition probability (one for each transition).

__init__(network, flux_method, transition_probability_methods)

Methods

__init__(network, flux_method, ...)
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
calculate(steps)	Perform the analysis, using steps as input.
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.
flux(from_state[, through_interface])	Flux from a volume and through and interface.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
from_weighted_trajectories(input_dict)	Calculate results from weighted trajectories dictionary.
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
rate(from_state, to_state)	Rate for the transition between two states
rate_matrix([steps])	Calculate the rate matrix.
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
state_fluxes(from_state)	All fluxes associated with a given initial state.
to_dict()	Convert object into a dictionary representation
transition_probability(from_state, to_state)	Transition probability between two states.

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.
flux_matrix	float}: keys are (state, interface); values are the associated flux
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects
transition_probability_matrix	matrix of transition probabilities