Detailed Description

Calculate score based on fit to EM map.

The score is a function of the cross correlation between the EM map and the map simulated from the particles. This is calculated by means of a double sum over the two sets of voxels.

Note: In most cases it is faster to approximate the two maps with a Gaussian Mixture Model and to use that for the scoring, with isd::GaussianEMRestraint.

Definition at line 39 of file FitRestraint.h.

Public Member Functions
	FitRestraint (ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN)
	Constructor. More...

unsigned int	add_particle (Particle *obj)

void	add_particles (const Particles &objs)

void	clear_particles ()

virtual IMP::ModelObjectsTemp	do_get_inputs () const override

void	erase_particle (unsigned int i)

bool	get_has_particles ()

SampledDensityMap *	get_model_dens_map () const
	Return the predicted density map of the model. More...

unsigned int	get_number_of_particles () const

Particle *	get_particle (unsigned int i) const

Particles	get_particles () const

float	get_scale_factor () 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	remove_particle (Particle *d)

void	remove_particles (const Particles &d)

void	reserve_particles (unsigned int sz)

void	set_particles (const Particles &ps)

void	set_particles_order (const Particles &objs)

void	set_scale_factor (float scale)

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)

Public Attributes
list	particles
	A Python list of Particles More...

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::em::FitRestraint::FitRestraint	(	ParticlesTemp	ps,
		DensityMap *	em_map,
		FloatPair	norm_factors = `FloatPair(0., 0.)`,
		FloatKey	weight_key = `atom::Mass::get_mass_key()`,
		float	scale = `1`,
		bool	use_rigid_bodies = `true`,
		KernelType	kt = `GAUSSIAN`
	)

Constructor.

Parameters

[in]	ps	The particles participating in the fitting score
[in]	em_map	The density map used in the fitting score
[in]	norm_factors	if set, they are used as normalization factors for the cross correlation calculations. This is relevant when the cross-correlation score of the entire system is decomposed.
[in]	weight_key	the name of the weight attribute of the particles
[in]	scale	multiply the fitting restraint score and derivatives by this value
[in]	use_rigid_bodies	if some of the particles are part of a rigid body, use the rigid body for faster calculations
[in]	kt	KernelType to use for simulating density from particles

Note: Rigid-bodies are interpolated and not resampled if use_rigid_bodies option is selected. This significantly reduces the running time but is less accurate. If the user prefers to get more accurate results, provide its members as input particles and not the rigid body.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::em::FitRestraint::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.

SampledDensityMap* IMP::em::FitRestraint::get_model_dens_map ( ) const

Return the predicted density map of the model.

Definition at line 67 of file FitRestraint.h.

virtual ::IMP::VersionInfo IMP::em::FitRestraint::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 73 of file FitRestraint.h.

virtual double IMP::em::FitRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const

overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

Member Data Documentation

list IMP::em::FitRestraint::particles

A Python list of Particles

Note: This class member is only available in Python.

Definition at line 73 of file FitRestraint.h.

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

FitRestraint.h

Detailed Description

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation