openpathsampling.analysis.tis.TISAnalysis

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

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)[source]

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