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.

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

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

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.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () 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)

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)

Protected Attributes
base::Pointer < DerivativeCalculator >	derivative_calculator_

base::Pointer < RigidBodiesProfileHandler >	handler_

base::Pointer< ProfileFitter < ChiScore > >	profile_fitter_

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...

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

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation