Detailed Description

A restraint for fast scoring of Particles vs. em2d class averages.

The restraint fits the particles into the 2D images by alignment of principal components of each of the particles projections with principal components of the 2D class average. Therefore, the particle set should comprise all subunits that are in the image. The aligned projections are scored against 2D class averages using cross correlation score. This is a fast alignment and scoring that works well for negative stain EM class averages.

Definition at line 31 of file d/PCAFitRestraint.h.

Public Member Functions
	PCAFitRestraint (kernel::Particles particles, const std::vector< std::string > &image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=false)
	Constructor. More...

IMP::kernel::ModelObjectsTemp	do_get_inputs () const

unsigned int	get_projection_number () const

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_projection_number (unsigned int n)

double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const

void	write_best_projections (std::string file_name, bool evaluate=false)

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::em2d::PCAFitRestraint::PCAFitRestraint	(	kernel::Particles	particles,
		const std::vector< std::string > &	image_files,
		double	pixel_size,
		double	resolution = `10.0`,
		unsigned int	projection_number = `100`,
		bool	reuse_direction = `false`
	)

Constructor.

Parameters

[in]	particles	The particles participating in the score, need to have XYZ, radius and mass
[in]	image_file_names	2D class averages filenames in PGM text format
[in]	pixel_size	Pixel size in Angstrom
[in]	resolution	Estimated resolution of the images
[in]	projection_number	Number of projections to generate and fit to images. The lower the number, the faster the evaluation, but also less accurate.

Member Function Documentation

IMP::kernel::ModelObjectsTemp IMP::em2d::PCAFitRestraint::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.

Definition at line 60 of file d/PCAFitRestraint.h.

virtual ::IMP::base::VersionInfo IMP::em2d::PCAFitRestraint::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 61 of file d/PCAFitRestraint.h.

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

d/PCAFitRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation