#include <IMP/em2d/Em2DRestraint.h>

Inheritance diagram for IMP::em2d::Em2DRestraint:

Detailed Description

This restraint ensures that a set of particles are similar to a set of EM images. The restraint generates projections of the model that are then compared with the EM images. The projections are generated from the radius of its particles. In the case of atoms, the radius is generated automatically. For other particles the radius has to be provided.

Definition at line 32 of file em2d/Em2DRestraint.h.

Public Member Functions
	Em2DRestraint (Model *m)

virtual IMP::ModelObjectsTemp	do_get_inputs () const override

RegistrationResults	get_registration_results () const

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_coarse_registration_mode (bool opt)

void	set_fast_mode (unsigned int n)

void	set_images (const em2d::Images em_images)

void	set_particles (SingletonContainer *particles_container)

void	set_variance_images (const em2d::Images variance_images)

void	setup (ScoreFunction *score_function, const Em2DRestraintParameters &params)

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...

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 RestraintInfo *	get_dynamic_info () const

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

virtual RestraintInfo *	get_static_info () 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...

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::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 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::em2d::Em2DRestraint::Em2DRestraint ( Model * m )

Creates the restraint. You are not done yet by creating the restraint. After creating it, you need to call the setup() function

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::em2d::Em2DRestraint::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.

RegistrationResults IMP::em2d::Em2DRestraint::get_registration_results ( ) const

Get the registration results for each of the images after finishing the optimization. Obviously, requesting the results before optimizing is an error

Returns: A list of registration results

Definition at line 131 of file em2d/Em2DRestraint.h.

virtual ::IMP::VersionInfo IMP::em2d::Em2DRestraint::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 138 of file em2d/Em2DRestraint.h.

void IMP::em2d::Em2DRestraint::set_coarse_registration_mode ( bool opt )

If the value provided to this function is true, restraint operates only using a coarse registration scheme (maximizing the cross correlation coefficient). This option (which is set to false by default) can speed the evaluation of the restraint by a order of magnitude, but the values obtained are not going to be less accurate. You could want to activate it at the beginning of an optimization.

Parameters

opt	true if you want to use the coarse mode

Definition at line 121 of file em2d/Em2DRestraint.h.

void IMP::em2d::Em2DRestraint::set_fast_mode ( unsigned int n )

Sets fast mode for computing the restraint. This mode only makes sense it the set_coarse_registration_mode option is false. This option only optimizes some coarse results (those given by the argument) to get the refined value. This option is very fast compared to a full optimization, and almost always is a good idea to use it with 1-5 results. This mode is still significantly slow compared to set_coarse_registration_mode(), but the values optimized are optimum.

Parameters

n	The number of images to optimize

void IMP::em2d::Em2DRestraint::set_images ( const em2d::Images em_images )

Sets the EM images to use as restraints

Parameters

em_images The images

void IMP::em2d::Em2DRestraint::set_particles ( SingletonContainer * particles_container )

Sets the particles used to compute projections.

Parameters

particles_container All the particles must be in the container

void IMP::em2d::Em2DRestraint::set_variance_images ( const em2d::Images variance_images )

Sets the variance images of EM images. This is useful if the image is a class average Note: Not all the scoring function use this data Sets the variance images for class averages. If class averages are used as restraints, it is possible to use the variance images to assign a standard deviation (error) for each of the pixels in a class average.

Parameters

variance_images

Note: Not all the scoring functions use the variance images; This function is functional as is tested, but has not been tested in a real application yet.

void IMP::em2d::Em2DRestraint::setup	(	ScoreFunction *	score_function,
		const Em2DRestraintParameters &	params
	)

Initializes the restraint

Parameters

score_function	Scoring function to use to evaluate the similarity between particles and projections
params	All the parameters required for the restraint

Definition at line 60 of file em2d/Em2DRestraint.h.

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virtual double IMP::em2d::Em2DRestraint::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:

em2d/Em2DRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation