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IMP Reference Guide  develop.0ea7f7a4db,2020/10/23
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
 
double get_alpha () const
 
double get_probability () const
 
Scale get_sigma () const
 
double get_sigma_upper () const
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. 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
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () const
 
bool get_was_good () 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
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- 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 ()
 

Member Function Documentation

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

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
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 66 of file NormalSigmaPCRestraint.h.


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