# openpathsampling.shooting.GaussianBiasSelector

class openpathsampling.shooting.GaussianBiasSelector(collectivevariable, alpha=1.0, l_0=0.5)[source]

A selector that biases according to a Gaussian along specified CollectiveVariable, with mean l_0 and width parameter alpha. That is, for snapshot $$x$$ and CV $$\lambda$$, the selection probability for each frame is weighted according to the function

$P_\text{sel}(x) \propto \exp(-\alpha (\lambda(x) - l_0)^2)$

Note that normalization here depends on the trajectory that the snapshot is a part of: the sum of the probabilities for all frames is 1, which gives a different normalization constant than the standard Gaussian distribution normalization, and exact probabilities for selecting a given snapshot will change depending on the trajectory it is a part of.

Parameters
• collectivevariable (CollectiveVariable) – the axis to use for the Gaussian

• alpha (float) – the width of the Gaussian

• l_0 (float) – the center of the Gaussian

__init__(collectivevariable, alpha=1.0, l_0=0.5)[source]

Methods

 __init__(collectivevariable[, alpha, l_0]) args() Return a list of args of the __init__ function of a class base() Return the most parent class actually derived from StorableObject count_weaks() Return number of objects subclassed from StorableObject still in memory descendants() Return a list of all subclassed objects f(snapshot, trajectory) Returns the unnormalized proposal probability of a snapshot 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 pick(trajectory) Returns the index of the chosen snapshot within trajectory probability(snapshot, trajectory) probability_ratio(snapshot, old_trajectory, ...) reverse_uuid() ruuid(uid) set_observer(active) (De-)Activate observing creation of storable objects sum_bias(trajectory) Returns the unnormalized probability probability of a trajectory. 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