IMP::em2d::Em2DRestraint Class Reference

#include <IMP/em2d/Em2DRestraint.h>

Inheritance diagram for IMP::em2d::Em2DRestraint:

Public Member Functions
	Em2DRestraint ()
virtual void	do_show (std::ostream &out) const
RegistrationResults	get_registration_results () const
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)
Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (Model *m, std::string name)
void	add_score_and_derivatives (ScoreAccumulator sa) const
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
ContainersTemp	get_input_containers () const
ParticlesTemp	get_input_particles () const
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 (Model *m, std::string name)
ModelObjectsTemp	get_inputs () const
ModelObjectsTemps	get_interactions () const
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
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)

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < Em2DRestraint > >	Em2DRestraintsTemp
Related Functions inherited from IMP::kernel::Restraint
typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > >	RestraintsTemp
Related Functions inherited from IMP::kernel::ModelObject
typedef IMP::base::Vector < IMP::base::WeakPointer < ModelObject > >	ModelObjectsTemp
Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

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
virtual void	do_update_dependencies ()

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 Em2DRestraint.h.

Constructor & Destructor Documentation

IMP::em2d::Em2DRestraint::Em2DRestraint

(

)

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

Definition at line 53 of file Em2DRestraint.h.

Member Function Documentation

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 132 of file 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 122 of file 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 evalute the similarity between particles and projections
params	All the parameters required for the restraint

Definition at line 61 of file Em2DRestraint.h.

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Friends And Related Function Documentation

typedef IMP::base::Vector<IMP::base::WeakPointer< Em2DRestraint > > Em2DRestraintsTemp

related

Pass a set of objects.

Definition at line 139 of file Em2DRestraint.h.

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

• Em2DRestraint.h