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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)
void add_score_and_derivatives (ScoreAccumulator sa) const
 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)

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
- 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

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

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: