openpathsampling.analysis.tis.StandardTransitionProbability
- class openpathsampling.analysis.tis.StandardTransitionProbability(transition, tcp_method, ctp_method)[source]
Calculate the transition probability according to the TCP/CTP split.
The transition probability is the probability that a path that starts from interface A_0 ends in some other state B, and is denoted P(B|A_0). What we call the “standard” approach to calculate this splits that probability into P(B|A_0) = P(B|A_m) P(A_m|A_0), where the first term in the product is the
ConditionalTransitionProbability
and the second term is determined by theTotalCrossingProbability
. In practice, one instance of this object is created for each transition.- Parameters
transition (
TISTransition
) – the transition to calculate the transition probability fortcp_method (
TotalCrossingProbability
) – the object to calculate the total crossing probability function; many details can be modified here including the details of the histograms that are generated or of the method used to combine the histogramsctp_method (
ConditionalTransitionProbability
) – the object to calculate the conditional transition probability (details on which ensembles and which states to analyze can be modified here)
Methods
__init__
(transition, tcp_method, ctp_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[, ensembles])Perform the analysis, using steps as input.
combine_results
(result_1, result_2)Combine two sets of results from this analysis.
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.
from_dict
(dct)Reconstruct an object from a dictionary representaiton
from_intermediate_results
(tcp, ctp)Calculate results from intermediates.
from_weighted_trajectories
(input_dict)Calculate results from a 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
reverse_uuid
()ruuid
(uid)set_observer
(active)(De-)Activate observing creation of storable objects
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
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
progress