IMP  2.0.1
The Integrative Modeling Platform
IMP::isd::MarginalNOERestraint Class Reference

Apply an NOE distance restraint between two particles. More...

#include <IMP/isd/MarginalNOERestraint.h>

+ Inheritance diagram for IMP::isd::MarginalNOERestraint:

Public Member Functions

 MarginalNOERestraint ()
 Create the restraint. More...
 
void add_contribution (Particle *p1, Particle *p2, double Iexp)
 
void add_contribution (PairContainer *pc, double Iexp)
 
virtual void do_show (std::ostream &out) const
 
double get_log_gammahat () const
 
unsigned get_number_of_contributions () const
 
double get_probability () const
 
double get_SS () const
 
- Public Member Functions inherited from IMP::isd::ISDRestraint
 ISDRestraint (std::string name)
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 
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
 
ContainersTemp get_input_containers () const
 
ParticlesTemp get_input_particles () const
 
virtual double get_last_score () const
 
double get_score () 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::kernel::ModelObject
 ModelObject (Model *m, std::string name)
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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::kernel::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
virtual void do_update_dependencies ()
 

Detailed Description

Marginal of the NOE lognormal model. Since restraint is complicated, pass individual particles to add_contribution() command. Supports ambiguous NOEs and derivatives.

\[p(D|X,I) = SS^{-\frac{N-1}{2}} \quad SS = \sum_{i=1}^N \log^2\left(\frac{V_i^{exp}}{d_i^{-6}(X) \hat{\gamma}}\right) \quad \hat{\gamma} = \left(\prod_{i=1}^N \frac{V_i^{exp}}{d_i^{-6}}\right)^{1/N} \]

Definition at line 31 of file MarginalNOERestraint.h.

Constructor & Destructor Documentation

IMP::isd::MarginalNOERestraint::MarginalNOERestraint ( )

Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.

Definition at line 45 of file MarginalNOERestraint.h.

Member Function Documentation

virtual void IMP::isd::MarginalNOERestraint::do_show ( std::ostream &  out) const
virtual

This macro declares the basic needed methods: evaluate and show


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