Calculate score based on fit to SAXS profile. More...

#include <IMP/saxs/Restraint.h>

Inheritance diagram for IMP::saxs::Restraint:

Public Member Functions
	Restraint (const kernel::Particles &particles, const Profile *exp_profile, FormFactorType ff_type=HEAVY_ATOMS)
	Constructor. More...

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

Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::Model *m, std::string name)

	Restraint (std::string name="Restraint %1%")

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 (kernel::Model *m, std::string name)

	ModelObject (std::string name)

virtual void	do_set_model (kernel::Model *)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

virtual void	do_destroy ()

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
virtual double	const

Protected Member Functions
void	compute_profile (Profile *model_profile)

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...

	Object ()

Protected Attributes
base::Pointer < DerivativeCalculator >	derivative_calculator_

FormFactorType	ff_type_

kernel::Particles	particles_

base::Pointer< ProfileFitter < ChiScore > >	profile_fitter_

std::vector< kernel::Particles >	rigid_bodies_

std::vector< core::RigidBody >	rigid_bodies_decorators_

base::PointerMember< Profile >	rigid_bodies_profile_

Detailed Description

The restraint takes rigid bodies into account, in order to speed up the calculations. Rigid body should be gived as single RigidBody Particle. Other, non-rigid body Particles can also be given.

The shape of a rigid body is assumed to be defined by the set of atom::Hierarchy leaves of the atom::Hierarchy rooted at the rigid body particle.

Algorithmic details:: The distances between the atoms of rigid body do not change, therefore their contribution to the profile is pre-computed and stored.

Definition at line 42 of file saxs/Restraint.h.

Constructor & Destructor Documentation

IMP::saxs::Restraint::Restraint	(	const kernel::Particles &	particles,
		const Profile *	exp_profile,
		FormFactorType	ff_type = `HEAVY_ATOMS`
	)

Parameters

[in]	particles	The particles participating in the fitting score
[in]	exp_profile	The experimental profile used in the fitting score
[in]	ff_type	Type of the form factors for profile calculations: ALL_ATOMS - all atoms including hydrogens HEAVY_ATOMS - no hydrogens, all other atoms included CA_ATOMS - residue level, residue represented by CA

Member Function Documentation

virtual IMP::kernel::ModelObjectsTemp IMP::saxs::Restraint::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.

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

saxs/Restraint.h

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation