Classes
class	DistributionSampler

class	mt19937_RG

class	RandomGenerator
	Random number generator system. More...

class	ReservoirSampler
	Simple container for keeping K random values. More...

class	standard_RG
	Generator based on rand() < clib > function. More...

class	uniform_RG
	Uniform random number generator. More...

class	WeightedReservoirItem

class	WeightedReservoirSampler

class	WeightedSampler

Typedefs
typedef platform::Size	Size

typedef utility::pointer::shared_ptr < RandomGenerator >	RandomGeneratorOP

typedef utility::pointer::shared_ptr < uniform_RG >	uniform_RG_OP

typedef utility::pointer::shared_ptr < uniform_RG const >	uniform_RG_COP

Functions
static void	lshift128 (w128_t out, const w128_t in, int shift)

static uint32_t	ini_func1 (uint32_t x)

static uint32_t	ini_func2 (uint32_t x)

static int	sformat_idxof (int i)

static void	do_recursion (w128_t r, w128_t a, w128_t b, w128_t c, w128_t *lung)

static RandomGeneratorOP	random_generator (0)

RandomGenerator &	rg ()
	Return the one-per-thread "singleton" random generator. More...

double	uniform ()
	Generate a random number between 0 and 1. Threadsafe since each thread uses its own random generator. More...

double	gaussian ()
	Generate a random number pulled from a standard normal – i.e. mean of zero and standard deviation of 1. Threadsafe since each thread uses its own random generator. More...

int	random_range (int low, int high)
	Return a number uniformly drawn from the inclusive range between low and high. Threadsafe since each thread uses its own random generator. More...

uniform_RG_OP	createRG (string const &type)
	uniform_RG factory More...

template<typename T >
xyzVector< T >	random_point_on_unit_sphere (RandomGenerator &RG)

template<typename T >
T	random_rotation_angle (T rot_mag, RandomGenerator &RG)
	gamma-distribution-like random angle generation, rot_mag makes exactly the same sense as in gaussian_move More...

template<typename T >
xyzVector< T >	random_translation (T trans_mag, RandomGenerator &RG)
	produce a random translation in xyz space More...

template<typename T >
platform::Size	binary_search_cdf (utility::vector1< T > const &cdf, T urn)
	Return the index in the CDF array such that it is smaller than or equal to the uniform-random-number (urn) and that the next entry in the array is larger than urn. The CDF ought to represent the exclusive cumulative sum of the probabilities of some discrete set so that the width for entry i – the gap between entry i and entry i+1 should be the probability of entry i. More...

template<typename T >
platform::Size	pick_random_index_from_cdf (utility::vector1< T > const &cdf, RandomGenerator &RG)
	Choose an element from an array of positions representing the cumulative distribution function for some target distribution. This uses binary search to quickly find the target index. If any position has the same probability as the preceeding position, then its index won't be returned. More...

template<class T >
void	random_permutation (utility::vector1< T > &vect, RandomGenerator &rg)

template<class T >
void	random_permutation (utility::vector0< T > &vect, RandomGenerator &rg)

template<class T >
void	random_permutation (std::vector< T > &vect, RandomGenerator &rg)

template<typename RandomAccessIterator >
void	random_permutation (RandomAccessIterator first, RandomAccessIterator last, RandomGenerator &rg)
	randomly shuffle elements of a sequence More...

xyzVector< Real >	random_vector_spherical ()

xyzVector< Real >	random_vector_unit_cube ()

xyzVector< Real >	random_vector ()

xyzVector< Real >	random_normal ()

Quaternion< Real >	random_unit_quaternion ()

xyzMatrix< Real >	random_rotation ()

xyzTransform< Real >	random_xform ()

xyzTransform< Real >	gaussian_random_xform (Real const &angsd, Real const &movsd)

numeric::Real	reservoir_sample_accept_prob (numeric::Size n_wanted, numeric::Size n_seen)
	Returns the probability that the Nth value in a sequence should be accepted using the reservoir sampling criterion. More...

template<typename T >
utility::vector1< T >	reservoir_sample (utility::vector1< T > const &vec, numeric::Size n_wanted, RandomGenerator &rg=numeric::random::rg())

Typedef Documentation

typedef utility::pointer::shared_ptr< RandomGenerator > numeric::random::RandomGeneratorOP

typedef platform::Size numeric::random::Size

typedef utility::pointer::shared_ptr< uniform_RG const > numeric::random::uniform_RG_COP

typedef utility::pointer::shared_ptr< uniform_RG > numeric::random::uniform_RG_OP

Function Documentation

template<typename T >

platform::Size numeric::random::binary_search_cdf	(	utility::vector1< T > const &	cdf,
		T	urn
	)

Return the index in the CDF array such that it is smaller than or equal to the uniform-random-number (urn) and that the next entry in the array is larger than urn. The CDF ought to represent the exclusive cumulative sum of the probabilities of some discrete set so that the width for entry i – the gap between entry i and entry i+1 should be the probability of entry i.

References test.T007_TracerIO::T.

Referenced by pick_random_index_from_cdf().

uniform_RG_OP numeric::random::createRG ( string const & type )

uniform_RG factory

References utility_exit_with_message.

Referenced by numeric::random::RandomGenerator::set_seed().

static void numeric::random::do_recursion	(	w128_t *	r,
		w128_t *	a,
		w128_t *	b,
		w128_t *	c,
		w128_t *	lung
	)

inlinestatic

This function represents the recursion formula.

Parameters

r	output
a	a 128-bit part of the internal state array
b	a 128-bit part of the internal state array
c	a 128-bit part of the internal state array
lung	a 128-bit part of the internal state array

References DSFMT_HIGH_CONST, DSFMT_LOW_MASK, DSFMT_MSK1, DSFMT_MSK2, DSFMT_SL1, DSFMT_SL2, DSFMT_SR1, DSFMT_SR2, lshift128(), W128_T::u, and x().

Referenced by numeric::random::mt19937_RG::gen_rand_all().

double numeric::random::gaussian ( )

Generate a random number pulled from a standard normal – i.e. mean of zero and standard deviation of 1. Threadsafe since each thread uses its own random generator.

References numeric::random::RandomGenerator::gaussian(), and rg().

Referenced by gaussian_random_xform(), and random_vector_spherical().

numeric::xyzTransform< numeric::Real > numeric::random::gaussian_random_xform	(	Real const &	angsd,
		Real const &	movsd
	)

References gaussian(), and numeric::rotation_matrix_degrees().

static uint32_t numeric::random::ini_func1 ( uint32_t x )

inlinestatic

This function represents a function used in the initialization by init_by_array

Parameters

x	32-bit integer

Returns: 32-bit integer

Referenced by numeric::random::mt19937_RG::init_by_array().

static uint32_t numeric::random::ini_func2 ( uint32_t x )

inlinestatic

This function represents a function used in the initialization by init_by_array

Parameters

x	32-bit integer

Returns: 32-bit integer

Referenced by numeric::random::mt19937_RG::init_by_array().

static void numeric::random::lshift128	(	w128_t *	out,
		const w128_t *	in,
		int	shift
	)

inlinestatic

This function simulates SIMD 128-bit left shift by the standard C. The 128-bit integer given in in is shifted by (shift * 8) bits. This function simulates the LITTLE ENDIAN SIMD.

Parameters

out	the output of this function
in	the 128-bit data to be shifted
shift	the shift value

References W128_T::u.

Referenced by do_recursion().

template<typename T >

platform::Size numeric::random::pick_random_index_from_cdf	(	utility::vector1< T > const &	cdf,
		RandomGenerator &	RG
	)

Choose an element from an array of positions representing the cumulative distribution function for some target distribution. This uses binary search to quickly find the target index. If any position has the same probability as the preceeding position, then its index won't be returned.

References binary_search_cdf(), test.T007_TracerIO::T, and numeric::random::RandomGenerator::uniform().

static RandomGeneratorOP numeric::random::random_generator ( 0 )

static

Referenced by rg().

numeric::xyzVector< numeric::Real > numeric::random::random_normal ( )

References random_vector_spherical().

template<class T >

void numeric::random::random_permutation	(	utility::vector1< T > &	vect,
		RandomGenerator &	rg
	)

References test.T200_Scoring::ii, test.T007_TracerIO::T, and numeric::random::RandomGenerator::uniform().

Referenced by run_pep_prep().

template<class T >

void numeric::random::random_permutation	(	utility::vector0< T > &	vect,
		RandomGenerator &	rg
	)

References test.T200_Scoring::ii, test.T007_TracerIO::T, and numeric::random::RandomGenerator::uniform().

template<class T >

void numeric::random::random_permutation	(	std::vector< T > &	vect,
		RandomGenerator &	rg
	)

References test.T200_Scoring::ii, test.T007_TracerIO::T, and numeric::random::RandomGenerator::uniform().

template<typename RandomAccessIterator >

void numeric::random::random_permutation	(	RandomAccessIterator	first,
		RandomAccessIterator	last,
		RandomGenerator &	rg
	)

randomly shuffle elements of a sequence

References numeric::random::RandomGenerator::uniform().

template<typename T >

xyzVector< T > numeric::random::random_point_on_unit_sphere ( RandomGenerator & RG )

inline

generate uniformly distributed vector on the unit sphere

Author: Zhe Zhang; Justin R. Porter generate uniformly distributed unit vector a random normal distribution of coordinates gives a uniform distribution of directions. same functionality as the commented random_point_on_unit_sphere(), but simpler algorithm rename as random_uniform_distributed_direction()?; Zhe Zhang

References numeric::random::RandomGenerator::gaussian(), and numeric::xyzVector< typename >::normalized().

int numeric::random::random_range	(	int	low,
		int	high
	)

Return a number uniformly drawn from the inclusive range between low and high. Threadsafe since each thread uses its own random generator.

References numeric::random::RandomGenerator::random_range(), and rg().

Referenced by numeric::random::ReservoirSampler< T >::add_value(), CoupledMovesProtocol::apply(), DatabaseIOBenchmark::run(), run(), and FragmentAssemblyMover::run().

numeric::xyzMatrix< numeric::Real > numeric::random::random_rotation ( )

References numeric::xyzMatrix< typename >::cols(), random_unit_quaternion(), numeric::Quaternion< typename >::w(), numeric::Quaternion< typename >::x(), numeric::Quaternion< typename >::y(), and numeric::Quaternion< typename >::z().

Referenced by random_xform().

template<typename T >

T numeric::random::random_rotation_angle	(	T	rot_mag,
		RandomGenerator &	RG
	)

inline

gamma-distribution-like random angle generation, rot_mag makes exactly the same sense as in gaussian_move

generate axis and angle for axis-angle rotation for random rotation move in R/RT degrees of freedom. rotation axis: uniformly distributed on unit sphere, rotation angle: chosen to mimic the distribution of rotation angles obtained from gaussian distrbuted Euler angles (core/kinematics/Jump.cc), which is a gamma-distribution-like distribution

Note: gaussian distributed Euler angles do not give unbiased sampling in rotational space by applying this angle to a uniformly chosen rotation axis unbiased rotational sampling is achieved

Author: Zhe Zhang Justin R. Porter

References numeric::random::RandomGenerator::gaussian(), numeric::rotation_axis(), test.T007_TracerIO::T, numeric::x_rotation_matrix_degrees(), numeric::y_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().

template<typename T >

xyzVector< T > numeric::random::random_translation	(	T	trans_mag,
		RandomGenerator &	RG
	)

inline

produce a random translation in xyz space

Author: Zhe Zhang; Justin R. Porter

References numeric::random::RandomGenerator::gaussian().

numeric::Quaternion< numeric::Real > numeric::random::random_unit_quaternion ( )

References numeric::constants::d::pi_2, and uniform().

Referenced by random_rotation().

numeric::xyzVector< numeric::Real > numeric::random::random_vector ( )

References random_vector_spherical().

numeric::xyzVector< numeric::Real > numeric::random::random_vector_spherical ( )

References gaussian().

Referenced by random_normal(), random_vector(), and random_xform().

numeric::xyzVector< numeric::Real > numeric::random::random_vector_unit_cube ( )

References uniform().

numeric::xyzTransform< numeric::Real > numeric::random::random_xform ( )

References random_rotation(), and random_vector_spherical().

template<typename T >

utility::vector1< T > numeric::random::reservoir_sample	(	utility::vector1< T > const &	vec,
		numeric::Size	n_wanted,
		RandomGenerator &	rg = `numeric::random::rg()`
	)

References basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::mp::mutate_relax::iter, numeric::random::RandomGenerator::random_range(), reservoir_sample_accept_prob(), rg(), and numeric::random::RandomGenerator::uniform().

numeric::Real numeric::random::reservoir_sample_accept_prob	(	numeric::Size	n_wanted,
		numeric::Size	n_seen
	)

inline

Returns the probability that the Nth value in a sequence should be accepted using the reservoir sampling criterion.

If we've seen N values and we want to keep K of them, the probability of the Nth value being accepted is min(K/N,1.0).

References min().

Referenced by numeric::random::ReservoirSampler< T >::add_value(), and reservoir_sample().

RandomGenerator & numeric::random::rg ( )

Return the one-per-thread "singleton" random generator.

References random_generator().

Referenced by PerformanceBenchmark::execute(), gaussian(), gen_pep_bb_sequential(), main(), make_1mer_frags(), mutate_random_residue(), random_range(), randomly_open_pose_loop(), reservoir_sample(), myMC::roll(), run_pep_prep(), RunPepSpec(), basic::database::safely_read_from_database(), set_pep_csts(), and uniform().

static int numeric::random::sformat_idxof ( int i )

inlinestatic

This function simulate a 32-bit array index overlapped to 64-bit array of LITTLE ENDIAN in BIG ENDIAN machine.

Referenced by numeric::random::mt19937_RG::init_by_array(), and numeric::random::mt19937_RG::setSeed().

double numeric::random::uniform ( )

Generate a random number between 0 and 1. Threadsafe since each thread uses its own random generator.

References rg(), and numeric::random::RandomGenerator::uniform().

Referenced by numeric::random::ReservoirSampler< T >::add_value(), CoupledMovesProtocol::apply(), numeric::random::WeightedReservoirSampler< T >::consider_sample(), main(), make_1mer_frags(), mutate_random_residue(), numeric::random::RandomGenerator::random_range(), random_unit_quaternion(), random_vector_unit_cube(), randomly_open_pose_loop(), myMC::roll(), FragmentAssemblyMover::run(), run_pep_prep(), basic::database::safely_read_from_database(), numeric::random::DistributionSampler< T >::sample(), and set_pep_csts().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation