IMP Reference Guide  develop.a3ebfe92e8,2023/01/27 The Integrative Modeling Platform
IMP::isd::NormalSigmaPCRestraint Class Reference

A Penalized Complexity prior on sigma of a normal distribution. More...

#include <IMP/isd/NormalSigmaPCRestraint.h>

Inheritance diagram for IMP::isd::NormalSigmaPCRestraint:

## Detailed Description

A Penalized Complexity prior on sigma of a normal distribution.

The Penalized Complexity (PC) prior on sigma minimizes the complexity (and resulting risk of over-fitting) introduced by deviation from a delta function ( $$\sigma=0$$) to a normal distribution. Its density is

$p(\sigma) = \frac{-\log\alpha}{\sigma_u} \alpha^{\sigma / \sigma_u},$

where $$\sigma_u$$ is a user-specified value of $$\sigma$$ that indicates a 'tail event', a value that it is unexpected to exceed, and $$\alpha = p(\sigma > \sigma_u)$$ is the density in the tail.

See Also
PenalizedComplexityPrior
Note
The prior is related by a change of variables to the PC prior on the precision tau in Simpson et al. Stat Sci. (2017) 32(1): 1. arXiv: 1403.4630, which is a type 2 Gumbel distribution.

Definition at line 37 of file NormalSigmaPCRestraint.h.

## Public Member Functions

NormalSigmaPCRestraint (Model *m, ParticleIndex spi, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%")

NormalSigmaPCRestraint (Scale s, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%")

virtual IMP::ModelObjectsTemp do_get_inputs () const override

double get_alpha () const

double get_probability () const

Scale get_sigma () const

double get_sigma_upper () const

virtual std::string get_type_name () const override

virtual ::IMP::VersionInfo get_version_info () const override
Get information about the module and version of the object. More...

virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override
Return the unweighted score for the restraint. More...

Public Member Functions inherited from IMP::Restraint
Restraint (Model *m, std::string name)
Create a restraint and register it with the model. More...

Restraintcreate_current_decomposition () const
Decompose this restraint into constituent terms for the current conf. More...

Restraintcreate_decomposition () const
Decompose this restraint into constituent terms. More...

virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
Create a scoring function with only this restraint. More...

virtual RestraintInfoget_dynamic_info () const

bool get_is_aggregate () const
Return whether this restraint wraps a number of other restraints. More...

double get_last_last_score () const
Get the unweighted score from the last-but-one time it was evaluated. More...

virtual double get_last_score () const

double get_score () const

virtual RestraintInfoget_static_info () const

bool get_was_good () const

double evaluate (bool calc_derivs) const

double evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_if_good (bool calc_derivatives) const

double evaluate_if_below (bool calc_derivatives, double max) const

virtual double unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Return the unweighted score, taking moving particles into account. More...

virtual double unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
The function calling this will treat any score >= max as bad. More...

virtual double unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

void set_weight (Float weight)

Float get_weight () const

double get_maximum_score () const

void set_maximum_score (double s)

Public Member Functions inherited from IMP::ModelObject
ModelObject (Model *m, std::string name)

bool get_has_dependencies () const
Return whether this object has dependencies computed. More...

bool get_has_required_score_states () const
Return whether score states are computed. More...

ModelObjectsTemp get_inputs () const

ModelObjectsTemps get_interactions () const
Get the interacting sets induced by this ModelObject. More...

Modelget_model () const

ModelObjectsTemp get_outputs () const

const ScoreStatesTempget_required_score_states () const
Get the score states that are ancestors of this in the dependency graph. More...

void set_has_dependencies (bool tf)
Either invalidate the dependencies or ensure they are correct. More...

void set_has_required_score_states (bool tf)
Compute the required score states. More...

Public Member Functions inherited from IMP::Object
virtual void clear_caches ()

CheckLevel get_check_level () const

LogLevel get_log_level () const

void set_check_level (CheckLevel l)

void set_log_level (LogLevel l)
Set the logging level used in this object. More...

void set_was_used (bool tf) const

void show (std::ostream &out=std::cout) const

const std::string & get_name () const

void set_name (std::string name)

## Additional Inherited Members

Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const

virtual void do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

virtual Restraints do_create_current_decomposition () const

virtual Restraints do_create_decomposition () const

ModelObjectsTemp do_get_outputs () const override

Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const

virtual void handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::Object
Object (std::string name)
Construct an object with the given name. More...

virtual void do_destroy ()

Protected Attributes inherited from IMP::Restraint
bool is_aggregate_

## Member Function Documentation

 virtual IMP::ModelObjectsTemp IMP::isd::NormalSigmaPCRestraint::do_get_inputs ( ) const
overridevirtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::ModelObject.

 virtual ::IMP::VersionInfo IMP::isd::NormalSigmaPCRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 66 of file NormalSigmaPCRestraint.h.

 virtual double IMP::isd::NormalSigmaPCRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

The documentation for this class was generated from the following file: