 IMP Reference Guide  develop.1a04b19ae7,2021/11/27 The Integrative Modeling Platform
IMP::isd::LognormalAmbiguousRestraint Class Reference

#include <IMP/isd/LognormalAmbiguousRestraint.h> Inheritance diagram for IMP::isd::LognormalAmbiguousRestraint:

## Detailed Description

A restraint for ambiguous cross-linking MS data. $$z_i$$ is the discrete classifier, $$\sigma_G$$ is the uncertainty estimate for good data points, $$\sigma_B$$ is the uncertainty estimate for bad data points, $$k_i$$ is the index of the restraint to be picked up from the ambiguous set, and $$\lambda_0$$ is the maximum length for the cross-linker.

Usage: Construct the ambiguous set using LognormalAmbiguousRestraint( $$z_i$$, $$\sigma_G$$, $$\sigma_B$$, $$k_i$$, $$\lambda_0$$). Pass individual cross-linked particles to add_contribution(part0, part1). The marginal likelihood is modeled by a sigmoid function:

$p(D|X,I) = \frac{1}{\lambda_0+\sigma(\sqrt(\pi/2)-1)} [1+\theta(r_k-\lambda_0+\sigma)[\exp(-\frac{(r_k- \lambda_0+\sigma)^2}{2\sigma^2})]]$

where $$\sigma=z_i\sigma_G+(1-z_i)\sigma_B$$ and $$r_k$$ is the distance between part0 and part1.

Definition at line 45 of file LognormalAmbiguousRestraint.h.

## Public Member Functions

LognormalAmbiguousRestraint (Particle *p1, Particle *p2, Particle *ki, Particle *sigmaG)
Create the restraint. More...

void add_contribution (double lexp, Particle *omega)

virtual IMP::ModelObjectsTemp do_get_inputs () const

void draw_k_from_posterior (double kt)

unsigned get_number_of_contributions () const

double get_probability () 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)

Perform the actual restraint scoring. More...

void add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) 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
Create a scoring function with only this restraint. More...

virtual RestraintInfoget_dynamic_info () const

virtual 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

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) 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 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 ()

## Constructor & Destructor Documentation

 IMP::isd::LognormalAmbiguousRestraint::LognormalAmbiguousRestraint ( Particle * p1, Particle * p2, Particle * ki, Particle * sigmaG )

Create the restraint.

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

## Member Function Documentation

 virtual IMP::ModelObjectsTemp IMP::isd::LognormalAmbiguousRestraint::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::LognormalAmbiguousRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 79 of file LognormalAmbiguousRestraint.h.

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