AV.h File Reference

Simple Accessible Volume decorator. More...

#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/Value.h>
#include <IMP/value_macros.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>

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

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::bff
	Bayesian Fluorescence Framework.

Typedefs
typedef IMP::Vector < AVPairDistanceMeasurement >	IMP::bff::AVPairDistanceMeasurements
typedef IMP::Vector< AV >	IMP::bff::AVs

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

Functions
double	IMP::bff::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. More...
std::vector< double >	IMP::bff::av_distance_distribution (const AV &av1, const AV &av2, std::vector< double > axis, int n_samples=10000)
	Compute the distance to another accessible volume. More...
std::vector< double >	IMP::bff::av_random_distances (const AV &av1, const AV &av2, int n_samples=10000)
	Random sampling over AV/AV distances. More...
std::vector< double >	IMP::bff::av_random_points (const AV &av1, int n_samples=10000)
template<typename T >
T	IMP::bff::distance_fret (double fret_efficiency, double forster_radius)
	Computes the distance between two volumes given the FRET efficiency and Forster radius. More...
template<typename T >
T	IMP::bff::fret_efficiency (T distance, double forster_radius)
	Computes the FRET efficiency given the distance and Forster radius. More...
IMP::ParticleIndex	IMP::bff::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. More...

Detailed Description

Simple Accessible Volume decorator.

Authors

Thomas-Otavio Peulen Copyright 2007-2022 IMP Inventors. All rights reserved.

Definition in file AV.h.