AVNetworkRestraint Class Reference

A restraint that uses an annotated volumetric network to score particle distances. More...

#include <AVNetworkRestraint.h>

Inheritance diagram for AVNetworkRestraint:

Collaboration diagram for AVNetworkRestraint:

Public Member Functions
	AVNetworkRestraint (const IMP::core::Hierarchy &hier, std::string fps_json_fn, std::string name="AVNetworkRestraint%1%", std::string score_set="", int n_samples=50000)
	Constructs an AVNetworkRestraint object.
double	get_probability () const
	Returns exp(score).
const IMP::bff::AVs	get_used_avs ()
	Returns the used Atom::AVs.
const std::map< std::string, AVPairDistanceMeasurement >	get_used_distances ()
	Returns the used experimental distances.
double	get_model_distance (std::string position1_name, std::string position2_name, double forster_radius, int distance_type) const
	Returns the model distance (or FRET efficiency) between two dyes.
ParticleIndexes const	get_indexes ()
	Returns the particle indexes of the AVs.
virtual double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override
	Evaluates the restraint.
virtual IMP::ModelObjectsTemp	do_get_inputs () const override
	Returns the inputs required by the restraint.
void	show (std::ostream &out) const
	Prints a description of the restraint.

Detailed Description

A restraint that uses an annotated volumetric network to score particle distances.

The AVNetworkRestraint class represents a restraint that utilizes an annotated volumetric network to score distances between particles. It is designed to be used with the IMP library.

The restraint is initialized with a hierarchy, a filename of a fps.json file, a name, and an optional score set. The hierarchy is used to obtain the particles involved in the restraint. The fps.json file contains the annotated volumetric network data. The name parameter is used to assign a name to the restraint. The score set parameter specifies the name of the score in the fps.json file to be used for scoring. If no score set is provided, all distances are used for scoring.

Constructor & Destructor Documentation

AVNetworkRestraint()

AVNetworkRestraint::AVNetworkRestraint	(	const IMP::core::Hierarchy &	hier,
		std::string	fps_json_fn,
		std::string	name = "AVNetworkRestraint%1%",
		std::string	score_set = "",
		int	n_samples = 50000
	)

Constructs an AVNetworkRestraint object.

Parameters

[in]	hier	The hierarchy used to obtain particles.
[in]	fps_json_fn	The filename of the fps.json file.
[in]	name	The name of this restraint. Default is "AVNetworkRestraint%1%".
[in]	score_set	The name of the score in the fps.json file. If not provided, all distances are used for scoring.

Member Function Documentation

do_get_inputs()

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

overridevirtual

Returns the inputs required by the restraint.

Returns

The inputs required by the restraint.

get_indexes()

ParticleIndexes const AVNetworkRestraint::get_indexes ( )

inline

Returns the particle indexes of the AVs.

Returns

The particle indexes.

get_model_distance()

double AVNetworkRestraint::get_model_distance	(	std::string	position1_name,
		std::string	position2_name,
		double	forster_radius,
		int	distance_type
	)		const

Returns the model distance (or FRET efficiency) between two dyes.

Parameters

[in]	position1_name	The name of the first dye position.
[in]	position2_name	The name of the second dye position.
[in]	forster_radius	The Förster radius.
[in]	distance_type	The type of distance calculation.

Returns

The model distance (or FRET efficiency) between the two dyes.

get_probability()

double AVNetworkRestraint::get_probability ( ) const

inline

Returns exp(score).

Returns

The exponential of the score.

get_used_avs()

const IMP::bff::AVs AVNetworkRestraint::get_used_avs

(

)

Returns the used Atom::AVs.

Returns

The used Atom::AVs.

get_used_distances()

const std::map< std::string, AVPairDistanceMeasurement > AVNetworkRestraint::get_used_distances ( )

inline

Returns the used experimental distances.

Returns

The used experimental distances.

show()

void AVNetworkRestraint::show ( std::ostream &  out ) const

inline

Prints a description of the restraint.

Parameters

[in]

out

The output stream.

unprotected_evaluate()

virtual double AVNetworkRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator *  accum ) const

overridevirtual

Evaluates the restraint.

Parameters

[in]

accum

The derivative accumulator.

Returns

The score of the restraint.

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

• /Users/tpeulen/dev/imp.bff/include/AVNetworkRestraint.h