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

Creates a restraint between two Gaussian Mixture Models, "model" and "density". More...

#include <IMP/bayesianem/GaussianEMRestraint.h> Inheritance diagram for IMP::bayesianem::GaussianEMRestraint:

## Detailed Description

Creates a restraint between two Gaussian Mixture Models, "model" and "density".

This restrains two sets of GMMs with a density overlap function. The function is correlation of the two GMMs $$f_M$$ and $$f_D$$:

$\frac{2\int{f_M(x)f_D(x)dx}}{\int{f_M^2(x)+f_D^2(x)dx}}$

Where the integral is the "overlap function" given by:

$ov(f_M,f_D) = \sum_{i=1}^{N_M} \sum_{j=1}^{N_D} \frac{1}{(2 \pi)^{3/2}|\Sigma_{Mi}+\Sigma_{Dj}|^{1/2}}\exp\left [-\frac{1}{2}(\boldsymbol\mu_{Mi} - \boldsymbol\mu_{Dj})^\top (\Sigma_{Mi}+\Sigma_{Dj})^{-1} (\boldsymbol\mu_{Mi} - \boldsymbol \mu_{Dj})\right ]$

Note
Source: Greenberg, Pellarin, Sali. In preparation.

Definition at line 77 of file bayesianem/GaussianEMRestraint.h.

## Public Member Functions

GaussianEMRestraint (Model *mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model=true, bool backbone_slope=false, std::string name="GaussianEMRestraint%1%")
Setup the GaussianEMRestraint. More...

void compute_initial_scores ()
Pre-calculate the density-density and model-model scores. More...

void debug ()

virtual IMP::ModelObjectsTemp do_get_inputs () const

RestraintInfoget_dynamic_info () const

ParticleIndexes const get_indexes ()

Floats const get_log2 ()

double get_probability () const
Returns exp(score) More...

Float get_slope ()
Get restraint slope. More...

RestraintInfoget_static_info () 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...

void set_density_filename (std::string density_fn)
Set the filename corresponding to the density GMM particles. More...

void set_slope (Float s)
Set restraint slope. More...

void show (std::ostream &out) const

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 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

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::bayesianem::GaussianEMRestraint::GaussianEMRestraint ( Model * mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model = true, bool backbone_slope = false, std::string name = "GaussianEMRestraint%1%" )

Setup the GaussianEMRestraint.

Parameters
 [in] mdl the Model object to operate on [in] model_ps particles for the model GMM [in] density_ps particles for the density GMM [in] global_sigma Particle to modulate the uncertainty [in] model_cutoff_dist Cutoff for the model-model interactions [in] density_cutoff_dist Cutoff for model-density interactions [in] slope Gentle term to move all particles to the density [in] update_model (DEPRECATED) update model each cycle [in] backbone_slope Limit the slope only to backbone particles [in] name Name of this restraint
Note
the model and density particles must be set up as Gaussian

## Member Function Documentation

 void IMP::bayesianem::GaussianEMRestraint::compute_initial_scores ( )

Pre-calculate the density-density and model-model scores.

This is automatically called by the constructor. You only need to call it manually if you change Gaussian variances

 virtual IMP::ModelObjectsTemp IMP::bayesianem::GaussianEMRestraint::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.

 RestraintInfo* IMP::bayesianem::GaussianEMRestraint::get_dynamic_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

 double IMP::bayesianem::GaussianEMRestraint::get_probability ( ) const

Returns exp(score)

Definition at line 103 of file bayesianem/GaussianEMRestraint.h.

 Float IMP::bayesianem::GaussianEMRestraint::get_slope ( )

Get restraint slope.

Definition at line 134 of file bayesianem/GaussianEMRestraint.h.

 RestraintInfo* IMP::bayesianem::GaussianEMRestraint::get_static_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

 virtual ::IMP::VersionInfo IMP::bayesianem::GaussianEMRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 148 of file bayesianem/GaussianEMRestraint.h.

 void IMP::bayesianem::GaussianEMRestraint::set_density_filename ( std::string density_fn )

Set the filename corresponding to the density GMM particles.

If the density GMM particles were read from a file, this method can be used to tell the restraint so that it can track this information back to the original EM density file, which is useful for deposition.

Definition at line 112 of file bayesianem/GaussianEMRestraint.h. Here is the call graph for this function:

 void IMP::bayesianem::GaussianEMRestraint::set_slope ( Float s )

Set restraint slope.

Definition at line 131 of file bayesianem/GaussianEMRestraint.h.

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