Detailed Description

Calculate score based on fit to EM map.

Definition at line 32 of file PCAFitRestraint.h.

Public Member Functions
	PCAFitRestraint (kernel::ParticlesTemp ps, DensityMap *em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key=atom::Mass::get_mass_key())
	Constructor. More...

unsigned int	add_particle (kernel::Particle *obj)

void	add_particles (const kernel::Particles &objs)

void	clear_particles ()

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

bool	get_has_particles ()

unsigned int	get_number_of_particles () const

kernel::Particle *	get_particle (unsigned int i) const

kernel::Particles	get_particles () 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	remove_particle (kernel::Particle *d)

void	remove_particles (const kernel::Particles &d)

void	reserve_particles (unsigned int sz)

void	set_particles (const kernel::Particles &ps)

void	set_particles_order (const kernel::Particles &objs)

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::em::PCAFitRestraint::PCAFitRestraint	(	kernel::ParticlesTemp	ps,
		DensityMap *	em_map,
		float	threahold,
		float	max_pca_size_diff,
		float	max_angle_diff,
		float	max_centroid_diff,
		FloatKey	weight_key = `atom::Mass::get_mass_key()`
	)

Constructor.

Parameters

[in]	ps	The particles participating in the fitting score
[in]	em_map	The density map used in the fitting score
[in]	threahold	consider all voxels above this value for PCA calculation
[in]	weight_key	the name of the weight attribute of the particles
[in]	max_pca_size_diff
[in]	max_angle_diff
[in]	max_centroid_diff

Member Function Documentation

virtual IMP::kernel::ModelObjectsTemp IMP::em::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.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 53 of file PCAFitRestraint.h.

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

PCAFitRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation