AV.h File Reference

#include <IMP/bff/bff_config.h>
#include <IMP/decorator_macros.h>
#include <IMP/Decorator.h>
#include <IMP/algebra/Vector3D.h>
#include <IMP/algebra/Transformation3D.h>
#include <IMP/core/XYZ.h>
#include <IMP/log.h>
#include <IMP/bff/PathMap.h>
#include <string>
#include <cmath>
#include <vector>
#include <limits>
#include <iostream>
#include <IMP/bff/internal/json.h>
#include <IMP/bff/internal/InverseSampler.h>
#include <IMP/bff/internal/Histogram.h>

Include dependency graph for AV.h:

Go to the source code of this file.

Classes
class	AVPairDistanceMeasurement
	Container for experimental distance measurement. More...
class	AV
	A decorator for a particle with accessible volume (AV). More...

Enumerations
enum	DyePairMeasures {   DYE_PAIR_DISTANCE_E , DYE_PAIR_DISTANCE_MEAN , DYE_PAIR_DISTANCE_MP , DYE_PAIR_EFFICIENCY ,   DYE_PAIR_DISTANCE_DISTRIBUTION , DYE_PAIR_XYZ_DISTANCE }
	Different types of distances between two accessible volumes. More...

Functions
	IMP_DECORATORS (AV, AVs, ParticlesTemp)
template<typename T >
T	fret_efficiency (T distance, double forster_radius)
	Computes the FRET efficiency given the distance and Forster radius.
template<typename T >
T	distance_fret (double fret_efficiency, double forster_radius)
	Computes the distance between two volumes given the FRET efficiency and Forster radius.
IMPBFFEXPORT double	av_distance (const AV &a, const AV &b, double forster_radius=52.0, int distance_type=DYE_PAIR_DISTANCE_MEAN, int n_samples=10000)
	Computes the distance to another accessible volume.
IMPBFFEXPORT std::vector< double >	av_random_points (const AV &av1, int n_samples=10000)
IMPBFFEXPORT std::vector< double >	av_random_distances (const AV &av1, const AV &av2, int n_samples=10000)
	Random sampling over AV/AV distances.
IMPBFFEXPORT std::vector< double >	av_distance_distribution (const AV &av1, const AV &av2, std::vector< double > axis, int n_samples=10000)
	Compute the distance to another accessible volume.
IMPBFFEXPORT IMP::ParticleIndex	search_labeling_site (const IMP::core::Hierarchy &hier, std::string json_str="", const nlohmann::json &json_data=nlohmann::json())
	Find the particle index of a labeling site.

Enumeration Type Documentation

DyePairMeasures

enum DyePairMeasures

Different types of distances between two accessible volumes.

Enumerator
DYE_PAIR_DISTANCE_E
DYE_PAIR_DISTANCE_MEAN	Mean FRET averaged distance R_E.
DYE_PAIR_DISTANCE_MP	Mean distance <R_DA>
DYE_PAIR_EFFICIENCY	Distance between AV mean positions.
DYE_PAIR_DISTANCE_DISTRIBUTION	Mean FRET efficiency.
DYE_PAIR_XYZ_DISTANCE	Distance distribution. Distance between XYZ of dye particles

Function Documentation

av_distance()

IMPBFFEXPORT double av_distance	(	const AV &	a,
		const AV &	b,
		double	forster_radius = 52.0,
		int	distance_type = DYE_PAIR_DISTANCE_MEAN,
		int	n_samples = 10000
	)

Computes the distance to another accessible volume.

Parameters

a	The first accessible volume.
b	The second accessible volume.
forster_radius	The Forster radius.
distance_type	The type of distance to compute.
n_samples	The number of samples to use for distance computation.

Returns

The distance between the two accessible volumes.

av_distance_distribution()

IMPBFFEXPORT std::vector< double > av_distance_distribution	(	const AV &	av1,
		const AV &	av2,
		std::vector< double >	axis,
		int	n_samples = 10000
	)

Compute the distance to another accessible volume.

av_random_distances()

IMPBFFEXPORT std::vector< double > av_random_distances	(	const AV &	av1,
		const AV &	av2,
		int	n_samples = 10000
	)

Random sampling over AV/AV distances.

av_random_points()

IMPBFFEXPORT std::vector< double > av_random_points	(	const AV &	av1,
		int	n_samples = 10000
	)

distance_fret()

template<typename T >

T distance_fret ( double  fret_efficiency, double  forster_radius  )

inline

Computes the distance between two volumes given the FRET efficiency and Forster radius.

Template Parameters

T	The type of the distance.

Parameters

fret_efficiency	The FRET efficiency.
forster_radius	The Forster radius.

Returns

The distance between the two volumes.

fret_efficiency()

template<typename T >

T fret_efficiency ( T  distance, double  forster_radius  )

inline

Computes the FRET efficiency given the distance and Forster radius.

Template Parameters

T	The type of the distance.

Parameters

distance	The distance between the two volumes.
forster_radius	The Forster radius.

Returns

The FRET efficiency.

IMP_DECORATORS()

IMP_DECORATORS	(	AV	,
		AVs	,
		ParticlesTemp
	)

search_labeling_site()

IMPBFFEXPORT IMP::ParticleIndex search_labeling_site	(	const IMP::core::Hierarchy &	hier,
		std::string	json_str = "",
		const nlohmann::json &	json_data = nlohmann::json()
	)

Find the particle index of a labeling site.

This function searches for the particle index of a labeling site in a given hierarchy.

Parameters

[in]	hier	The hierarchy in which the labeling site is searched.
[in]	json_str	The JSON string containing the FPS.json position (optional).
[in]	json_data	The JSON data containing the FPS.json position (optional).

Returns

The particle index of the labeling site.

Note

If both json_str and json_data are provided, json_str will be used.