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

#include <IMP/isd/GaussianEMRestraint.h>

Inheritance diagram for IMP::isd::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 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...

virtual IMP::kernel::ModelObjectsTemp	do_get_inputs () const

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

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

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

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

void	show (std::ostream &out) const

virtual double	unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const

Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::Model *m, std::string name)

void	add_score_and_derivatives (ScoreAccumulator sa) const
	Perform the actual restraint scoring. More...

Restraint *	create_current_decomposition () const
	Decompose this restraint into constituent terms for the current conf. More...

Restraint *	create_decomposition () const
	Decompose this restraint into constituent terms. More...

virtual ScoringFunction *	create_scoring_function (double weight=1.0, double max=NO_MAX) const
	Create a scoring function with only this restraint. 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::kernel::ModelObject
	ModelObject (kernel::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...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_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::base::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::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

Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

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`,
		std::string	name = `"GaussianEMRestraint%1%"`
	)

Setup the GaussianEMRestraint.

Parameters

[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::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::kernel::ModelObjectsTemp IMP::isd::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::kernel::ModelObject.

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

Returns exp(score)

Definition at line 102 of file GaussianEMRestraint.h.

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

Get restraint slope.

Definition at line 116 of file GaussianEMRestraint.h.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 122 of file GaussianEMRestraint.h.

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

Set restraint slope.

Definition at line 113 of file GaussianEMRestraint.h.

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

GaussianEMRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation