IMP Reference Guide  develop.27926d84dc,2024/04/13 The Integrative Modeling Platform
IMP::isd::GaussianEMRestraint Class Reference

Restraint between two Gaussian Mixture Models, "model" and "density". More...

#include <IMP/isd/GaussianEMRestraint.h>

Inheritance diagram for IMP::isd::GaussianEMRestraint:

## Detailed Description

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 43 of file isd/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, bool local=false, std::string name="GaussianEMRestraint%1%")
Setup the GaussianEMRestraint. More...

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

virtual IMP::ModelObjectsTemp do_get_inputs () const override

double get_cross_correlation_coefficient () const
Get cross correlation between the model and the map. More...

RestraintInfoget_dynamic_info () const override

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

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

RestraintInfoget_static_info () const override

virtual std::string get_type_name () const override

virtual ::IMP::VersionInfo get_version_info () const override
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 override
Return the unweighted score for the restraint. More...

Public Member Functions inherited from IMP::Restraint
Restraint (Model *m, std::string name)
Create a restraint and register it with the model. More...

Restraint ()
Default constructor. 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...

bool get_is_aggregate () const
Return whether this restraint wraps a number of other restraints. More...

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

double evaluate (bool calc_derivs) const

double evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double evaluate_if_good (bool calc_derivatives) const

double evaluate_if_below (bool calc_derivatives, double max) const

virtual double unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Return the unweighted score, taking moving particles into account. More...

virtual double unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
The function calling this will treat any score >= max as bad. More...

virtual double unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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 override

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 ()

Protected Attributes inherited from IMP::Restraint
bool is_aggregate_

## Constructor & Destructor Documentation

 IMP::isd::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, bool local = 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 (currently unused) [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] local Only consider density particles that are within the specified cutoff of the model particles (experimental) [in] name Name of this restraint
Note
the model and density particles must be set up as Gaussian

## Member Function Documentation

 void IMP::isd::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::isd::GaussianEMRestraint::do_get_inputs ( ) const
overridevirtual

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.

 double IMP::isd::GaussianEMRestraint::get_cross_correlation_coefficient ( ) const

Get cross correlation between the model and the map.

This CCC is that calculated from the last scoring function evaluation; calling this function before the score is calculated results in undefined behavior.

Definition at line 84 of file isd/GaussianEMRestraint.h.

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

Reimplemented from IMP::Restraint.

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

Returns exp(score)

Definition at line 75 of file isd/GaussianEMRestraint.h.

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 Float IMP::isd::GaussianEMRestraint::get_slope ( )

Get restraint slope.

Definition at line 107 of file isd/GaussianEMRestraint.h.

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

Reimplemented from IMP::Restraint.

 virtual ::IMP::VersionInfo IMP::isd::GaussianEMRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 119 of file isd/GaussianEMRestraint.h.

 void IMP::isd::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 93 of file isd/GaussianEMRestraint.h.

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

Set restraint slope.

Definition at line 104 of file isd/GaussianEMRestraint.h.

 virtual double IMP::isd::GaussianEMRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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