numeric Namespace Reference

Unit headers. More...

Namespaces
	alignment
	constants
	conversions
	coordinate_fitting
	crick_equations
	deriv
	expression_parser
	fourier
	geometry
	histograms
	interpolation
	kdtree
	kinematic_closure
	linear_algebra
	model_quality
	nls
	random
	statistics

Classes
class	ClusterOptions
class	AgglomerativeHierarchicalClusterer
class	SingleLinkClusterer
class	AverageLinkClusterer
class	CompleteLinkClusterer
class	AxisRotationSampler
class	BodyPosition
	Rigid body 3-D position/transform. More...
class	CalculatorParser
class	Calculator
class	ClusteringTreeNode
struct	CubicPolynomial
struct	SplineParameters
	SplineParameters is a simple struct for holding the cubic spline polynomials used in the etable to interpolate the lennard-jones attractive and LK-solvation terms to zero smoothly. These splines have exactly two knots to represent them, and the same x values are used for all the knots: thus the only parameters needed are the y values at the knots, and the second-derivatives for the polynomials at knots. More...
class	DiscreteIntervalEncodingTree
class	DietNode
class	EulerAngles
	Euler angles 3-D orientation representation. More...
class	HomogeneousTransform
class	HomogeneousTransform_Double
class	ColPointers
class	ColsPointer
class	ColVectors
class	RowPointers
class	RowsPointer
class	RowVectors
class	IntervalSet
class	IntervalSet_Double
struct	IOTraits
	Numerics input/output type traits. More...
struct	IOTraits< short int >
	Numerics input/output type traits short int specialization. More...
struct	IOTraits< int >
	Numerics input/output type traits int specialization. More...
struct	IOTraits< long int >
	: Numerics input/output type traits long int specialization More...
struct	IOTraits< unsigned short int >
	: Numerics input/output type traits unsigned short int specialization More...
struct	IOTraits< unsigned int >
	: Numerics input/output type traits unsigned int specialization More...
struct	IOTraits< unsigned long int >
	Numerics input/output type traits unsigned long int specialization. More...
struct	IOTraits< float >
	Numerics input/output type traits float Specialization. More...
struct	IOTraits< double >
	Numerics input/output type traits double specialization. More...
struct	IOTraits< long double >
	Numerics input/output type traits long double specialization. More...
class	MathMatrix
class	MathNTensor
class	MathNTensorBase
class	MathTensor
class	MathVector
class	MultiDimensionalHistogram
	a class for accumulating a histogram of one or more numeric variables More...
struct	NearestSelector
	Nearest function selector class for R non-integer or T integer. More...
struct	NearestSelector< R, T, true >
	Nearest function selector class for R integer and T non-integer. More...
struct	ModSelector
	Mod function selector class for non-integer types. More...
struct	ModSelector< T, true >
	Mod function selector class for integer types. More...
struct	ModuloSelector
	Modulo function selector class for non-integer types. More...
struct	ModuloSelector< T, true >
	Modulo function selector class for integer types. More...
struct	RemainderSelector
	Remainder function selector class for non-integer types. More...
struct	RemainderSelector< T, true >
	Remainder function selector class for integer types. More...
struct	FastRemainderSelector
	Fast remainder function selector class for non-integer types. More...
struct	FastRemainderSelector< T, true >
	Fast remainder function selector class for integer types. More...
struct	NumericTraits
	NumericTraits: Numeric type traits. More...
struct	NumericTraits< float >
	NumericTraits: Numeric type traits float specialization. More...
struct	NumericTraits< double >
	NumericTraits: Numeric type traits double specialization. More...
struct	NumericTraits< long double >
	NumericTraits: Numeric type traits long double specialization. More...
class	Polynomial_1d
class	Quaternion
	Unit quaternion 3-D orientation representation. More...
class	RocPoint
class	RocCurve
class	sphericalVector
	sphericalVector: Fast spherical-coordinate numeric vector More...
struct	urs_Quat
class	UniformRotationSampler
class	VoxelArray
class	VoxelGrid
class	xyzMatrix
	xyzMatrix: Fast 3x3 xyz matrix template More...
class	xyzTransform
struct	XformHash32
struct	XformHash64
struct	Xforms
class	Py_xyzTransform_double
class	xyzTriple
	Fast (x,y,z)-coordinate vector container. More...
class	xyzVector
	xyzVector: Fast (x,y,z)-coordinate numeric vector More...

Typedefs
typedef utility::pointer::shared_ptr< AxisRotationSampler >	AxisRotationSamplerOP
typedef utility::pointer::shared_ptr< AxisRotationSampler const >	AxisRotationSamplerCOP
typedef BodyPosition< float >	BodyPosition_float
typedef BodyPosition< double >	BodyPosition_double
typedef BodyPosition< long double >	BodyPosition_longdouble
typedef utility::pointer::shared_ptr< Calculator >	CalculatorOP
typedef utility::pointer::shared_ptr< ClusteringTreeNode >	ClusteringTreeNodeOP
typedef utility::pointer::weak_ptr< ClusteringTreeNode >	ClusteringTreeNodeAP
using	Vector = xyzVector< Real >
using	Length = Real
template<class T , numeric::Size N>
using	MathNTensorOP = utility::pointer::shared_ptr< MathNTensor< T, N > >
template<class T , numeric::Size N>
using	MathNTensorCOP = utility::pointer::shared_ptr< MathNTensor< T, N > const >
template<class T >
using	MathNTensorBaseOP = utility::pointer::shared_ptr< MathNTensorBase< T > >
template<class T >
using	MathNTensorBaseCOP = utility::pointer::shared_ptr< MathNTensorBase< T > const >
typedef utility::pointer::shared_ptr< Polynomial_1d >	Polynomial_1dOP
typedef utility::pointer::shared_ptr< Polynomial_1d const >	Polynomial_1dCOP
typedef Quaternion< float >	Quaternion_float
typedef Quaternion< double >	Quaternion_double
typedef Quaternion< long double >	Quaternion_longdouble
typedef utility::pointer::shared_ptr< RocPoint >	RocPointOP
typedef utility::pointer::shared_ptr< RocCurve >	RocCurveOP
using	Real = platform::Real
typedef platform::Size	Size
typedef platform::SSize	SSize
typedef utility::pointer::shared_ptr< UniformRotationSampler >	UniformRotationSamplerOP
typedef utility::pointer::shared_ptr< UniformRotationSampler const >	UniformRotationSamplerCOP
typedef xyzMatrix< bool >	xyzMatrix_bool
typedef xyzMatrix< short int >	xyzMatrix_short
typedef xyzMatrix< int >	xyzMatrix_int
typedef xyzMatrix< long int >	xyzMatrix_long
typedef xyzMatrix< unsigned short int >	xyzMatrix_ushort
typedef xyzMatrix< unsigned int >	xyzMatrix_uint
typedef xyzMatrix< unsigned long int >	xyzMatrix_ulong
typedef xyzMatrix< platform::Size >	xyzMatrix_Size
typedef xyzMatrix< platform::Size >	xyzMatrix_size_t
typedef xyzMatrix< platform::Size >	xyzMatrix_size
typedef xyzMatrix< float >	xyzMatrix_float
typedef xyzMatrix< double >	xyzMatrix_double
typedef xyzMatrix< long double >	xyzMatrix_long_double
typedef xyzMatrix< char >	xyzMatrix_char
typedef xyzMatrix< unsigned char >	xyzMatrix_uchar
typedef xyzMatrix< signed char >	xyzMatrix_schar
typedef xyzMatrix< platform::Real >	xyzMatrix_real
typedef xyzTransform< float >	Xformf
typedef xyzTransform< double >	Xform
typedef xyzTransform< numeric::Real >	xyzTransform_Real
typedef xyzTransform< float >	xyzTransform_float
typedef xyzTransform< double >	xyzTransform_double
typedef xyzTriple< bool >	xyzTriple_bool
typedef xyzTriple< short int >	xyzTriple_short
typedef xyzTriple< int >	xyzTriple_int
typedef xyzTriple< long int >	xyzTriple_long
typedef xyzTriple< unsigned short int >	xyzTriple_ushort
typedef xyzTriple< unsigned int >	xyzTriple_uint
typedef xyzTriple< unsigned long int >	xyzTriple_ulong
typedef xyzTriple< std::size_t >	xyzTriple_size_t
typedef xyzTriple< std::size_t >	xyzTriple_size
typedef xyzTriple< float >	xyzTriple_float
typedef xyzTriple< double >	xyzTriple_double
typedef xyzTriple< long double >	xyzTriple_longdouble
typedef xyzTriple< char >	xyzTriple_char
typedef xyzTriple< unsigned char >	xyzTriple_uchar
typedef xyzTriple< signed char >	xyzTriple_schar
typedef xyzVector< bool >	xyzVector_bool
typedef xyzVector< short int >	xyzVector_short
typedef xyzVector< int >	xyzVector_int
typedef xyzVector< long int >	xyzVector_long
typedef xyzVector< unsigned short int >	xyzVector_ushort
typedef xyzVector< unsigned int >	xyzVector_uint
typedef xyzVector< unsigned long int >	xyzVector_ulong
typedef xyzVector< std::size_t >	xyzVector_size_t
typedef xyzVector< std::size_t >	xyzVector_size
typedef xyzVector< float >	xyzVector_float
typedef xyzVector< double >	xyzVector_double
typedef xyzVector< long double >	xyzVector_long_double
typedef xyzVector< char >	xyzVector_char
typedef xyzVector< unsigned char >	xyzVector_uchar
typedef xyzVector< signed char >	xyzVector_schar
typedef xyzVector< Real >	xyzVector_real

Enumerations
enum	RocStatus { true_positive , true_negative , false_positive , false_negative }

Functions
template<class T >
void	get_cluster_data (utility::vector1< T > &data_in, ClusteringTreeNodeOP cluster, utility::vector1< T > &data_out)
template<typename T >
T	principal_angle (T const &angle)
	Principal value of angle in radians on ( -pi, pi ]. More...
template<typename T >
T	principal_angle_radians (T const &angle)
	Principal value of angle in radians on ( -pi, pi ]. More...
template<typename T >
T	principal_angle_degrees (T const &angle)
	Principal value of angle in degrees on ( -180, 180 ]. More...
template<typename T >
T	nonnegative_principal_angle (T const &angle)
	Positive principal value of angle in radians on [ 0, 2*pi ) More...
template<typename T >
T	nonnegative_principal_angle_radians (T const &angle)
	Positive principal value of angle in radians on [ 0, 2*pi ) More...
template<typename T >
T	nonnegative_principal_angle_degrees (T const &angle)
	Positive principal value of angle in degrees on [ 0, 360 ) More...
template<typename T >
T	nearest_angle (T const &angle, T const &base_angle)
	Nearest periodic value of angle to a base angle in radians. More...
template<typename T >
T	nearest_angle_radians (T const &angle, T const &base_angle)
	Nearest periodic value of angle to a base angle in radians. More...
template<typename T >
T	nearest_angle_degrees (T const &angle, T const &base_angle)
	Nearest periodic value of angle to a base angle in degrees. More...
template<typename T >
void	R2quat (xyzMatrix< T > const &R, Quaternion< T > &Q)
	Interconvert Quaternion <=> Rotation Matrix. More...
template<typename T >
void	quat2R (Quaternion< T > const &Q, xyzMatrix< T > &R)
	Interconvert Quaternion <=> Rotation Matrix. More...
template<typename T >
bool	operator== (BodyPosition< T > const &p1, BodyPosition< T > const &p2)
	BodyPosition == BodyPosition. More...
template<typename T >
bool	operator!= (BodyPosition< T > const &p1, BodyPosition< T > const &p2)
	BodyPosition != BodyPosition. More...
template<typename T >
std::ostream &	operator<< (std::ostream &stream, BodyPosition< T > const &p)
	stream << BodyPosition output operator More...
template<typename T >
std::istream &	operator>> (std::istream &stream, BodyPosition< T > &p)
	stream >> BodyPosition input operator More...
template<typename T >
std::istream &	read_row (std::istream &stream, T &x, T &y, T &z, T &t)
	Read an BodyPosition row from a stream. More...
void	do_add_symbol (CalculatorParser &cp, std::string name, double value)
double	do_abs (double a)
double	do_pow (double a, double b)
double	do_exp (double a)
double	do_ln (double a)
double	do_log10 (double a)
double	do_log2 (double a)
double	do_log (double a, double b)
double	do_sqrt (double a)
double	do_sin (double a)
double	do_cos (double a)
double	do_tan (double a)
double	do_max (std::vector< double > a)
double	do_min (std::vector< double > a)
double	do_mean (std::vector< double > a)
double	do_median (std::vector< double > a)
numeric::xyzVector< platform::Real >	rgb_to_hsv (platform::Real r, platform::Real b, platform::Real g)
	convert an RGB color to HSV More...
numeric::xyzVector< platform::Real >	rgb_to_hsv (numeric::xyzVector< platform::Real > rgb_triplet)
	convert and RGB color to HSV More...
numeric::xyzVector< platform::Real >	hsv_to_rgb (platform::Real h, platform::Real s, platform::Real v)
	convert an HSV color to RGB More...
numeric::xyzVector< platform::Real >	hsv_to_rgb (numeric::xyzVector< platform::Real > hsv_triplet)
	convert an HSV color to RGB More...
CubicPolynomial	cubic_polynomial_from_spline (platform::Real xlo, platform::Real xhi, SplineParameters const &sp)
	Compute cubic polynomial coefficients from a set of SplineParameters. More...
platform::Real	cubic_polynomial_deriv (platform::Real const x, CubicPolynomial const &cp)
	Evaluate derivative of cubic polynomial given x and polynomial coefficients. More...
platform::Real	eval_cubic_polynomial (platform::Real const x, CubicPolynomial const &cp)
	Evaluate cubic polynomial at value x given polynomial coefficients. More...
void	ccd_angle (utility::vector1< xyzVector< Real > > const &F, utility::vector1< xyzVector< Real > > const &M, xyzVector< Real > const &axis_atom, xyzVector< Real > const &theta_hat, Real &alpha, Real &S)
template<typename T >
std::ostream &	operator<< (std::ostream &stream, HomogeneousTransform< T > const &ht)
std::ostream &	operator<< (std::ostream &stream, HomogeneousTransform< double > const &ht)
template<class Value >
double	linear_interpolate (Value start, Value stop, unsigned curr_stage, unsigned num_stages)
	Linearly interpolates a quantity from start to stop over (num_stages + 1) stages. More...
template<typename T >
std::ostream &	operator<< (std::ostream &output, const IntervalSet< T > &interval)
template<typename T >
MathMatrix< T > &	operator+= (MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	add one matrix to another More...
template<typename T >
MathMatrix< T > &	operator-= (MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	subtract one matrix from another More...
template<typename T >
MathMatrix< T > &	operator/= (MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &)
	divide one matrix by another More...
template<typename T >
MathMatrix< T > &	operator+= (MathMatrix< T > &MATRIX_LHS, const T &VALUE)
	add scalar to matrix More...
template<typename T >
MathMatrix< T > &	operator-= (MathMatrix< T > &MATRIX_LHS, const T &VALUE)
	subtract scalar from matrix More...
template<typename T >
MathMatrix< T > &	operator*= (MathMatrix< T > &MATRIX_LHS, const T &SCALAR)
	multiply matrix with scalar More...
template<typename T >
MathMatrix< T > &	operator/= (MathMatrix< T > &MATRIX_LHS, const T &SCALAR)
	divide matrix by scalar More...
template<typename T >
bool	operator== (const MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	compare to matricess for equality More...
template<typename T >
bool	operator!= (const MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	compare to matrices for inequality More...
template<typename T >
bool	operator== (const MathMatrix< T > &MATRIX_LHS, const T &VALUE_RHS)
	compare if all items in matrix are equal to a given VALUE More...
template<typename T >
bool	operator== (const T &VALUE_LHS, const MathMatrix< T > &MATRIX_RHS)
	compare if all items in matrix are equal to a given VALUE More...
template<typename T >
bool	operator!= (const MathMatrix< T > &MATRIX_LHS, const T &VALUE_RHS)
	compare if all items in matrix are not equal to a given VALUE More...
template<typename T >
bool	operator!= (const T &VALUE_LHS, const MathMatrix< T > &MATRIX_RHS)
	compare if all items in matrix are not equal to a given VALUE More...
template<typename T >
MathMatrix< T >	operator+ (const MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	sum two matrixs of equal size More...
template<typename T >
MathMatrix< T >	operator- (const MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	subtract two matrixs of equal size More...
template<typename T >
MathMatrix< T >	operator* (const MathMatrix< T > &MATRIX_LHS, const MathMatrix< T > &MATRIX_RHS)
	multiply two matrixs of equal size by building the inner product yielding the scalar product More...
template<typename T >
MathMatrix< T >	operator+ (const MathMatrix< T > &MATRIX_LHS, const T &VALUE_RHS)
	add value to matrix More...
template<typename T >
MathMatrix< T >	operator+ (const T &VALUE_LHS, const MathMatrix< T > &MATRIX_RHS)
	add matrix to value More...
template<typename T >
MathMatrix< T >	operator- (const MathMatrix< T > &MATRIX_LHS, const T &VALUE_RHS)
	subtract value from matrix More...
template<typename T >
MathMatrix< T >	operator- (const T &VALUE_LHS, const MathMatrix< T > &MATRIX_RHS)
	subtract matrix from value More...
template<typename T >
MathMatrix< T >	operator* (const T &SCALAR_LHS, const MathMatrix< T > &MATRIX_RHS)
	multiply scalar with matrix More...
template<typename T >
MathMatrix< T >	operator* (const MathMatrix< T > &MATRIX_LHS, const T &SCALAR_RHS)
	multiply matrix with scalar More...
template<typename T >
MathVector< T >	operator* (const MathMatrix< T > &MATRIX_LHS, const MathVector< T > &VECTOR_RHS)
	multiply matrix with vector More...
template<typename T >
MathMatrix< T >	operator/ (const MathMatrix< T > &MATRIX_LHS, const T &SCALAR_RHS)
	divide matrix with scalar More...
template<typename T >
MathMatrix< T >	operator/ (const T &SCALAR_LHS, const MathMatrix< T > &MATRIX_RHS)
	divide scalar by matrix More...
template<class T , numeric::Size N>
MathNTensorOP< T, N >	deep_copy (MathNTensor< T, N > const &source)
template<class T , numeric::Size N>
bool	write_tensor_to_file_without_json (std::string const &filename, MathNTensor< T, N > const &tensor)
template<class T , numeric::Size N>
void	read_tensor_from_file (std::string const &filename_input, MathNTensor< T, N > &tensor, utility::json_spirit::mObject &json)
template<class T , numeric::Size N>
void	read_tensor_from_file (std::string const &filename, MathNTensor< T, N > &tensor)
template<class T , numeric::Size N>
bool	write_tensor_to_file (std::string const &filename, MathNTensor< T, N > const &tensor, utility::json_spirit::Value const &json_input)
template<class T , numeric::Size N>
bool	write_tensor_to_file (std::string const &filename, MathNTensor< T, N > const &tensor)
template<class T >
MathNTensorBaseOP< T >	deep_copy (MathNTensorBase< T > const &source)
template MathNTensorBaseOP< Real >	deep_copy (MathNTensorBase< Real > const &)
	Explicit template instantiation, apparently needed for PyRosetta. More...
template<typename T >
T	distance (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
T	proj_angl (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B, MathVector< T > const &VECTOR_C, MathVector< T > const &VECTOR_D)
template<typename T >
T	proj_angl (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B, MathVector< T > const &VECTOR_C)
template<typename T >
T	proj_angl (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
T	scalar_product (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
MathVector< T >	MakeVector (T const &X)
template<typename T >
MathVector< T >	MakeVector (T const &X, T const &Y)
template<typename T >
MathVector< T >	MakeVector (T const &X, T const &Y, T const &Z)
template<typename T >
MathVector< T >	operator- (MathVector< T > const &VECTOR)
template<typename T >
MathVector< T >	operator+ (MathVector< T > const &VECTOR)
template<typename T >
bool	operator== (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
bool	operator!= (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
bool	operator== (MathVector< T > const &VECTOR, T const &X)
template<typename T >
bool	operator!= (MathVector< T > const &VECTOR, T const &X)
template<typename T >
bool	operator== (T const &X, MathVector< T > const &VECTOR)
template<typename T >
bool	operator!= (T const &X, MathVector< T > const &VECTOR)
template<typename T >
MathVector< T >	operator+ (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
MathVector< T >	operator- (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
MathVector< T >	operator+ (MathVector< T > const &VECTOR, T const &X)
template<typename T >
MathVector< T >	operator- (MathVector< T > const &VECTOR, T const &X)
template<typename T >
MathVector< T >	operator+ (T const &X, MathVector< T > const &VECTOR)
template<typename T >
MathVector< T >	operator- (T const &X, MathVector< T > const &VECTOR)
template<typename T >
T	operator* (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
MathVector< T >	operator* (T const &X, MathVector< T > const &VECTOR)
template<typename T >
MathVector< T >	operator* (MathVector< T > const &VECTOR, T const &X)
template<typename T >
MathVector< T >	operator/ (MathVector< T > const &VECTOR, T const &X)
template<typename T >
MathVector< T >	operator/ (MathVector< T > const &VECTOR_A, MathVector< T > const &VECTOR_B)
template<typename T >
MathVector< T >	operator/ (T const &X, MathVector< T > const &VECTOR)
template<typename T >
MathVector< T >	operator^ (T const &X, MathVector< T > const &VECTOR)
std::ostream &	operator<< (std::ostream &os, MultiDimensionalHistogram const &mdhist)
short int	min (short int const a, short int const b)
	min( short int, short int ) More...
int	min (int const a, int const b)
	min( int, int ) More...
long int	min (long int const a, long int const b)
	min( long int, long int ) More...
unsigned short int	min (unsigned short int const a, unsigned short int const b)
	min( unsigned short int, unsigned short int ) More...
unsigned int	min (unsigned int const a, unsigned int const b)
	min( unsigned int, unsigned int ) More...
unsigned long int	min (unsigned long int const a, unsigned long int const b)
	min( unsigned long int, unsigned long int ) More...
float	min (float const a, float const b)
	min( float, float ) More...
double	min (double const a, double const b)
	min( double, double ) More...
long double	min (long double const a, long double const b)
	min( long double, long double ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c)
	min( a, b, c ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d)
	min( a, b, c, d ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e)
	min( a, b, c, d, e ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	min( a, b, c, d, e, f ) More...
short int	max (short int const a, short int const b)
	max( short int, short int ) More...
int	max (int const a, int const b)
	max( int, int ) More...
long int	max (long int const a, long int const b)
	max( long int, long int ) More...
unsigned short int	max (unsigned short int const a, unsigned short int const b)
	max( unsigned short int, unsigned short int ) More...
unsigned int	max (unsigned int const a, unsigned int const b)
	max( unsigned int, unsigned int ) More...
unsigned long int	max (unsigned long int const a, unsigned long int const b)
	max( unsigned long int, unsigned long int ) More...
float	max (float const a, float const b)
	max( float, float ) More...
double	max (double const a, double const b)
	max( double, double ) More...
long double	max (long double const a, long double const b)
	max( long double, long double ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c)
	max( a, b, c ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d)
	max( a, b, c, d ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e)
	max( a, b, c, d, e ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	max( a, b, c, d, e, f ) More...
template<typename T >
T	square (T const &x)
	square( x ) == x^2 More...
template<typename T >
T	cube (T const &x)
	cube( x ) == x^3 More...
template<typename T >
int	sign (T const &x)
	sign( x ) More...
template<typename S , typename T >
T	sign_transfered (S const &sigma, T const &x)
	Sign transfered value. More...
template<typename T >
T	abs_difference (T const &a, T const &b)
	Absolute difference. More...
template<typename R , typename T >
R	nearest (T const &x)
	nearest< R >( x ): Nearest R More...
template<typename T >
std::size_t	nearest_size (T const &x)
	nearest_size( x ): Nearest std::size_t More...
template<typename T >
SSize	nearest_ssize (T const &x)
	nearest_ssize( x ): Nearest SSize More...
template<typename T >
int	nearest_int (T const &x)
	nearest_int( x ): Nearest int More...
template<typename T >
int	nint (T const &x)
	nint( x ): Nearest int More...
template<typename T >
T	mod (T const &x, T const &y)
	x(mod y) computational modulo returning magnitude < | y | and sign of x More...
template<typename T >
T	modulo (T const &x, T const &y)
	x(mod y) mathematical modulo returning magnitude < | y | and sign of y More...
template<typename T >
T	remainder (T const &x, T const &y)
	Remainder of x with respect to division by y that is of smallest magnitude. More...
template<typename T >
T	fast_remainder (T const &x, T const &y)
	Remainder of x with respect to division by y that is of smallest magnitude. More...
template<typename T , typename S >
T	remainder_conversion (T const &t, S &s)
	Remainder and result of conversion to a different type. More...
template<typename T >
T	gcd (T const &m, T const &n)
	Greatest common divisor. More...
template<typename T >
bool	eq_tol (T const &x, T const &y, T const &r_tol, T const &a_tol)
	Equal within specified relative and absolute tolerances? More...
template<typename T >
bool	lt_tol (T const &x, T const &y, T const &r_tol, T const &a_tol)
	Less than within specified relative and absolute tolerances? More...
template<typename T >
bool	le_tol (T const &x, T const &y, T const &r_tol, T const &a_tol)
	Less than or equal within specified relative and absolute tolerances? More...
template<typename T >
bool	ge_tol (T const &x, T const &y, T const &r_tol, T const &a_tol)
	Greater than or equal within specified relative and absolute tolerances? More...
template<typename T >
bool	gt_tol (T const &x, T const &y, T const &r_tol, T const &a_tol)
	Greater than within specified relative and absolute tolerances? More...
template<typename T >
T	factorial (T const &N)
	Calculate the value of N!. More...
template<typename T >
xyzVector< T >	first_principal_component (utility::vector1< xyzVector< T > > const &coords)
	return the first principal component of the given set of points More...
template<typename T >
xyzMatrix< T >	principal_components (utility::vector1< xyzVector< T > > const &coords)
	return a matrix containing the first 3 principal components of the given set of points. Matrix columns are principal components, first column is first component, etc. More...
template<typename T >
xyzVector< T >	principal_component_eigenvalues (utility::vector1< xyzVector< T > > const &coords)
	return a vector containing the eigenvalues corresponding to the first 3 principal components of the given set of points. More...
template<typename T >
std::pair< xyzMatrix< T >, xyzVector< T > >	principal_components_and_eigenvalues (utility::vector1< xyzVector< T > > const &coords)
	return a pair containing a matrix of the first 3 principal components and a vector of the corresponding eigenvalues of the given set of points. More...
std::pair< utility::vector1< utility::vector1< Real > >, utility::vector1< Real > >	principal_components_and_eigenvalues_ndimensions (utility::vector1< utility::vector1< Real > > const &coords, bool const shift_center)
	Return a pair containing a matrix (vector of vectors) of all of the principal components and a vector of the corresponding eigenvalues of the given set of points in n-dimensional space. More...
ostream &	operator<< (ostream &out, const Polynomial_1d &poly)
void	read_probabilities_or_die (const std::string &filename, utility::vector1< double > *probs)
	Loads normalized, per-residue probabilities from filename, storing the result in probs. Assumes line i holds the probability of sampling residue i. There must be 1 line for each residue in the pose on which this data will be used. More...
void	print_probabilities (const utility::vector1< double > &probs, std::ostream &out)
	Writes probs to the specified ostream. More...
template<class InputIterator >
double	sum (InputIterator first, InputIterator last)
	Returns the sum of all elements on the range [first, last) More...
template<class InputIterator >
void	normalize (InputIterator first, InputIterator last)
	Normalizes elements on the range [first, last) More...
template<class RandomAccessIterator >
void	cumulative (RandomAccessIterator first, RandomAccessIterator last)
	Converts pdf to cdf. More...
template<class ForwardIterator >
void	product (ForwardIterator probs1_first, ForwardIterator probs1_last, ForwardIterator probs2_first, ForwardIterator probs2_last)
	Multiplies two probability vectors with one another. Probability vectors are assumed to have equal lengths. More...
template<typename T >
std::ostream &	operator<< (std::ostream &stream, Quaternion< T > const &q)
	stream << Quaternion output operator More...
template<typename T >
std::istream &	operator>> (std::istream &stream, Quaternion< T > &q)
	stream >> Quaternion input operator More...
template<typename T >
T	sec (T const &x)
	Secant. More...
template<typename T >
T	csc (T const &x)
	Cosecant. More...
template<typename T >
T	cot (T const &x)
	Cotangent. More...
template<typename T >
bool	in_sin_cos_range (T const &x, T const &tol=T(.001))
	Is a sine or cosine value within a specified tolerance of the valid [-1,1] range? More...
template<typename T >
T	sin_cos_range (T const &x, T const &tol=T(.001))
	Adjust a sine or cosine value to the valid [-1,1] range if within a specified tolerance or exit with an error. More...
template<typename T >
T	arccos (T const x)
	like std::acos but with range checking More...
double	urs_norm4 (double a, double b, double c, double d)
platform::Real	urs_R2ang (numeric::xyzMatrix< Real > R)
numeric::Real	median (utility::vector1< numeric::Real > const &values)
	Returns the median from a vector1 of Real values. More...
numeric::Real	mean (utility::vector1< numeric::Real > const &values)
Real &	access_Real_MathNTensor (MathNTensorBaseOP< Real > tensorbase, utility::vector1< Size > const &position)
	Utility function to access an entry in a MathNTensor of arbitrary dimensionality unknown at compile time, given a MathNTensorBaseOP. More...
Real const &	const_access_Real_MathNTensor (MathNTensorBaseCOP< Real > tensorbase, utility::vector1< Size > const &position)
	Utility function to access an entry in a MathNTensor of arbitrary dimensionality unknown at compile time, given a MathNTensorBaseCOP. More...
Size	get_Real_MathNTensor_dimension_size (MathNTensorBaseCOP< Real > tensorbase, Size const dimension_index)
	Given a MathNTensorBaseCOP, get the size along one dimension. More...
template<typename Number >
Number	clamp (Number value, Number lower_bound, Number upper_bound)
	Clamps to the closed interval [lower_bound, upper_bound]. Templated type must implement operator<. More...
double	log (double x, double base)
	Computes log(x) in the given base. More...
bool	equal_by_epsilon (numeric::Real value1, numeric::Real value2, numeric::Real epsilon)
	are two Real values are equal up to some epsilon More...
template<typename T >
T	max (utility::vector1< T > const &values)
template<typename T >
T	min (utility::vector1< T > const &values)
Real	boltzmann_accept_probability (Real const score_before, Real const score_after, Real const temperature)
	Calculates the acceptance probability of a given score-change at the given temperature, generally used in simulated annealing algorithms. Returns a value in the range (0-1). More...
template<typename T >
T	find_nearest_value (typename utility::vector1< T > const &input_list, T key, platform::Size min_index, platform::Size max_index)
	recursive binary search that finds the value closest to key. Call find_nearest_value(input_list,value) instead. It's the driver function for this function. This fails miserably (and silently!) on a non-sorted vector, so don't do that!. More...
template<typename T >
T	find_nearest_value (typename utility::vector1< T > const &input_list, T key)
	given a vector and an input value, return the value in the vector that is closest to the input This is a wrapper for find_nearest_value(input_list,key,min,max) and insures that you're sorted. More...
template<class F , class V >
std::ostream &	operator<< (std::ostream &out, VoxelArray< F, V > const &v)
template<typename T >
T	wrap_2pi (T const &angle)
	Wrap the given angle in the range [0, 2 * pi). More...
template<typename T >
T	wrap_pi (T const &angle)
	Wrap the given angle in the range [-pi, pi). More...
template<typename T >
T	wrap_360 (T const &angle)
	Wrap the given angle in the range [0, 360). More...
template<typename T >
T	wrap_180 (T const &angle)
	Wrap the given angle in the range [-180, 180). More...
template<typename T >
xyzVector< T >	operator* (xyzMatrix< T > const &m, xyzVector< T > const &v)
template<typename T >
xyzVector< T >	product (xyzMatrix< T > const &m, xyzVector< T > const &v)
	xyzMatrix * xyzVector product More...
template<typename T >
xyzVector< T > &	inplace_product (xyzMatrix< T > const &m, xyzVector< T > &v)
	xyzMatrix * xyzVector in-place product More...
template<typename T >
xyzVector< T >	transpose_product (xyzMatrix< T > const &m, xyzVector< T > const &v)
	xyzMatrix^T * xyzVector product More...
template<typename T >
xyzVector< T > &	inplace_transpose_product (xyzMatrix< T > const &m, xyzVector< T > &v)
	xyzMatrix^T * xyzVector in-place transpose product More...
template<typename T >
xyzMatrix< T >	outer_product (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector xyzVector outer product More...
template<typename T >
xyzMatrix< T >	inverse (xyzMatrix< T > const &a)
template<typename T >
xyzMatrix< T >	projection_matrix (xyzVector< T > const &v)
	geometric center More...
template<typename T >
void	dihedral_radians (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4, T &angle)
	Dihedral (torsion) angle in radians: angle value passed. More...
template<typename T >
T	dihedral_radians (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4)
	Dihedral (torsion) angle in radians: angle value returned. More...
template<typename T >
void	dihedral_degrees (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4, T &angle)
	Dihedral (torsion) angle in degrees: angle value passed. More...
template<typename T >
T	dihedral_degrees (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4)
	Dihedral (torsion) angle in degrees: angle value returned. More...
template<typename T >
void	dihedral (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4, T &angle)
	Dihedral (torsion) angle in degrees: angle value passed. More...
template<typename T >
T	dihedral (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4)
	Dihedral (torsion) angle in degrees: angle value returned. More...
template<typename T >
xyzMatrix< T >	rotation_matrix (xyzVector< T > const &axis, T const &theta)
	Rotation matrix for rotation about an axis by an angle in radians. More...
template<typename T >
xyzVector< T >	rotation_axis (xyzMatrix< T > const &R, T &theta)
	Transformation from rotation matrix to helical axis of rotation. More...
template<typename T >
xyzVector< T >	rotation_axis_angle (xyzMatrix< T > const &R)
	Transformation from rotation matrix to compact axis-angle representation. More...
template<typename T >
xyzVector< T >	eigenvalue_jacobi (xyzMatrix< T > const &a, T const &tol)
	Classic Jacobi algorithm for the eigenvalues of a real symmetric matrix. More...
template<typename T >
xyzVector< T >	eigenvector_jacobi (xyzMatrix< T > const &a, T const &tol, xyzMatrix< T > &J)
	Classic Jacobi algorithm for the eigenvalues and eigenvectors of a real symmetric matrix. More...
template<typename T >
void	jacobi_rotation (xyzMatrix< T > const &m, int const i, int const j, xyzMatrix< T > &r)
	Jacobi rotation. More...
template<typename T >
sphericalVector< T >	xyz_to_spherical (xyzVector< T > const &xyz)
template<typename T >
xyzVector< T >	spherical_to_xyz (sphericalVector< T > const &spherical)
template<typename T >
xyzVector< T >	closest_point_on_line (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &q)
	xyzMatrix * xyzVector More...
template<typename T >
xyzVector< T >	center_of_mass (utility::vector1< xyzVector< T > > const &coords)
	calculate center of mass for coordinates More...
template<typename U >
U	angle_of (xyzVector< U > const &a, xyzVector< U > const &b)
	Angle between two vectors (in radians on [ 0, pi ]) More...
template<typename U >
U	angle_of (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c)
	Angle formed by three consecutive points (in radians on [ 0, pi ]) More...
template<typename U >
U	cos_of (xyzVector< U > const &a, xyzVector< U > const &b)
	Cosine of angle between two vectors. More...
template<typename U >
U	cos_of (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c)
	Cosine of angle formed by three consecutive points. More...
template<typename U >
U	sin_of (xyzVector< U > const &a, xyzVector< U > const &b)
	Sine of angle between two vectors. More...
template<typename U >
U	sin_of (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c)
	Sine of angle formed by three consecutive points. More...
template<typename T >
void	angle_radians (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, T &angle)
	Plane angle in radians: angle value passed. More...
template<typename T >
T	angle_radians (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3)
	Plane angle in radians: angle value returned. More...
double	angle_radians_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3)
template<typename T >
T	angle_degrees (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3)
	Plane angle in degrees: angle value returned. More...
double	angle_degrees_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3)
template<typename T >
T	angle_radians (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4)
	Angle between two vectors in radians. More...
double	angle_radians_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4)
template<typename T >
T	angle_degrees (xyzVector< T > const &p1, xyzVector< T > const &p2, xyzVector< T > const &p3, xyzVector< T > const &p4)
	Angle between two vectors in radians. More...
double	angle_degrees_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4)
void	dihedral_radians_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4, double &angle)
double	dihedral_radians_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4)
void	dihedral_degrees_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4, double &angle)
double	dihedral_degrees_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4)
void	dihedral_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4, double &angle)
double	dihedral_double (xyzVector< double > const &p1, xyzVector< double > const &p2, xyzVector< double > const &p3, xyzVector< double > const &p4)
template<typename T >
xyzMatrix< T >	rotation_matrix (xyzVector< T > const &axis_angle)
template<typename T >
xyzMatrix< T >	rotation_matrix_radians (xyzVector< T > const &axis, T const &theta)
	Rotation matrix for rotation about an axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	rotation_matrix_degrees (xyzVector< T > const &axis, T const &theta)
	Rotation matrix for rotation about an axis by an angle in degrees. More...
template<typename T >
xyzMatrix< T >	x_rotation_matrix (T const &theta)
	Rotation matrix for rotation about the x axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	x_rotation_matrix_radians (T const &theta)
	Rotation matrix for rotation about the x axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	x_rotation_matrix_degrees (T const &theta)
	Rotation matrix for rotation about the x axis by an angle in degrees. More...
template<typename T >
xyzMatrix< T >	y_rotation_matrix (T const &theta)
	Rotation matrix for rotation about the y axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	y_rotation_matrix_radians (T const &theta)
	Rotation matrix for rotation about the y axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	y_rotation_matrix_degrees (T const &theta)
	Rotation matrix for rotation about the y axis by an angle in degrees. More...
template<typename T >
xyzMatrix< T >	z_rotation_matrix (T const &theta)
	Rotation matrix for rotation about the z axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	z_rotation_matrix_radians (T const &theta)
	Rotation matrix for rotation about the z axis by an angle in radians. More...
template<typename T >
xyzMatrix< T >	z_rotation_matrix_degrees (T const &theta)
	Rotation matrix for rotation about the z axis by an angle in degrees. More...
template<typename T >
xyzMatrix< T >	alignVectorSets (xyzVector< T > A1, xyzVector< T > B1, xyzVector< T > A2, xyzVector< T > B2)
	Helper function to find the rotation to optimally transform the vectors A1-B1 to vectors A2-B2. More...
template<typename T >
T	rotation_angle (xyzMatrix< T > const &R)
	Transformation from rotation matrix to magnitude of helical rotation. More...
template<typename T >
xyzVector< T >	comma_seperated_string_to_xyz (std::string triplet)
	convert a string of comma separated values "0.2,0.4,0.3" to an xyzVector More...
template<typename T >
ObjexxFCL::FArray2D< T >	vector_of_xyzvectors_to_FArray (utility::vector1< xyzVector< T > > const &input)
	convert a vector1 of xyzVectors to an FArray2D More...
template<typename T >
utility::vector1< xyzVector< T > >	FArray_to_vector_of_xyzvectors (ObjexxFCL::FArray2D< T > const &input)
	convert an FArray2D to a vector of xyzVectors More...
template<typename T >
numeric::xyzMatrix< T >	FArray_to_xyzmatrix (ObjexxFCL::FArray2D< T > const &input)
	convert a 3x3 FArray 2D to an xyzMatrix More...
template<typename T >
ObjexxFCL::FArray2D< T >	xyzmatrix_to_FArray (numeric::xyzMatrix< T > const &input)
	convert an xyzMatrix to a 3x3 FArray 2D More...
template<typename T >
void	angles_between_0_180 (xyzVector< T > &angles)
template<typename T >
xyzMatrix< T >	rotation_matrix_from_euler_angles_ZYZ (xyzVector< T > const &angles)
template<typename T >
xyzMatrix< T >	rotation_matrix_from_euler_angles_ZXZ (xyzVector< T > const &angles)
template<typename T >
xyzMatrix< T >	rotation_matrix_from_euler_angles_ZYX (xyzVector< T > const &angles)
template<typename T >
xyzVector< T >	euler_angles_from_rotation_matrix_ZYZ (xyzMatrix< T > const &rotM)
template<typename T >
xyzVector< T >	euler_angles_from_rotation_matrix_ZXZ (xyzMatrix< T > const &rotM)
template<typename T >
xyzVector< T >	euler_angles_from_rotation_matrix_ZYX (xyzMatrix< T > const &rotM)
template<typename T >
void	to_json (nlohmann::json &j, const xyzVector< T > &v)
template<typename T >
void	from_json (const nlohmann::json &j, xyzVector< T > &v)
template<typename T >
utility::json_spirit::Value	serialize (xyzVector< T > coords)
	Convert vector to a json_spirit Value. More...
template<typename T >
xyzVector< T >	deserialize (utility::json_spirit::mArray data)
template<typename T >
xyzMatrix< T >	operator+ (T const &t, xyzMatrix< T > const &m)
	T + xyzMatrix. More...
template<typename T >
xyzMatrix< T >	operator- (T const &t, xyzMatrix< T > const &m)
	T - xyzMatrix. More...
template<typename T >
xyzMatrix< T >	operator* (T const &t, xyzMatrix< T > const &m)
	T * xyzMatrix. More...
template<typename T >
bool	operator== (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix == xyzMatrix More...
template<typename T >
bool	operator!= (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix != xyzMatrix More...
template<typename T >
bool	operator< (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix < xyzMatrix More...
template<typename T >
bool	operator<= (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix <= xyzMatrix More...
template<typename T >
bool	operator>= (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix >= xyzMatrix More...
template<typename T >
bool	operator> (xyzMatrix< T > const &a, xyzMatrix< T > const &b)
	xyzMatrix > xyzMatrix More...
template<typename T >
bool	operator== (xyzMatrix< T > const &m, T const &t)
	xyzMatrix == T More...
template<typename T >
bool	operator!= (xyzMatrix< T > const &m, T const &t)
	xyzMatrix != T More...
template<typename T >
bool	operator< (xyzMatrix< T > const &m, T const &t)
	xyzMatrix < T More...
template<typename T >
bool	operator<= (xyzMatrix< T > const &m, T const &t)
	xyzMatrix <= T More...
template<typename T >
bool	operator>= (xyzMatrix< T > const &m, T const &t)
	xyzMatrix >= T More...
template<typename T >
bool	operator> (xyzMatrix< T > const &m, T const &t)
	xyzMatrix > T More...
template<typename T >
bool	operator== (T const &t, xyzMatrix< T > const &m)
	T == xyzMatrix. More...
template<typename T >
bool	operator!= (T const &t, xyzMatrix< T > const &m)
	T != xyzMatrix. More...
template<typename T >
bool	operator< (T const &t, xyzMatrix< T > const &m)
	T < xyzMatrix. More...
template<typename T >
bool	operator<= (T const &t, xyzMatrix< T > const &m)
	T <= xyzMatrix. More...
template<typename T >
bool	operator>= (T const &t, xyzMatrix< T > const &m)
	T >= xyzMatrix. More...
template<typename T >
bool	operator> (T const &t, xyzMatrix< T > const &m)
	T > xyzMatrix. More...
template<typename T >
std::ostream &	operator<< (std::ostream &stream, xyzMatrix< T > const &m)
	stream << xyzMatrix output operator More...
template<typename T >
std::istream &	read_row (std::istream &stream, T &x, T &y, T &z)
	Read an xyzMatrix row from a stream. More...
template<typename T >
std::istream &	operator>> (std::istream &stream, xyzMatrix< T > &m)
	stream >> xyzMatrix input operator More...
template<typename T , class OutputIterator >
void	expand_xforms (OutputIterator container, xyzTransform< T > const &G1, xyzTransform< T > const &G2, xyzTransform< T > const &, int N=5, Real r=9e9, xyzVector< T > const &test_point=xyzVector< T >(Real(1.0), Real(3.0), Real(10.0)))
template<typename T , class OutputIterator >
void	expand_xforms (OutputIterator container, xyzTransform< T > const &G1, xyzTransform< T > const &G2, int N=5, Real r=9e9, xyzVector< T > const &test_point=xyzVector< T >(Real(1.0), Real(3.0), Real(10.0)))
template<typename T >
std::ostream &	operator<< (std::ostream &stream, xyzTransform< T > const &m)
	stream << xyzTransform output operator More...
template<typename T >
std::istream &	operator>> (std::istream &stream, xyzTransform< T > &m)
	stream >> xyzTransform input operator More...
template<typename T >
xyzTriple< T >	operator+ (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple + xyzTriple More...
template<typename T >
xyzTriple< T >	operator+ (xyzTriple< T > const &v, T const &t)
	xyzTriple + T More...
template<typename T >
xyzTriple< T >	operator+ (T const &t, xyzTriple< T > const &v)
	T + xyzTriple. More...
template<typename T >
xyzTriple< T >	operator- (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple - xyzTriple More...
template<typename T >
xyzTriple< T >	operator- (xyzTriple< T > const &v, T const &t)
	xyzTriple - T More...
template<typename T >
xyzTriple< T >	operator- (T const &t, xyzTriple< T > const &v)
	T - xyzTriple. More...
template<typename T >
xyzTriple< T >	operator* (xyzTriple< T > const &v, T const &t)
	xyzTriple * T More...
template<typename T >
xyzTriple< T >	operator* (T const &t, xyzTriple< T > const &v)
	T * xyzTriple. More...
template<typename T >
xyzTriple< T >	operator/ (xyzTriple< T > const &v, T const &t)
	xyzTriple / T More...
template<typename T >
void	add (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &r)
	Add: xyzTriple + xyzTriple. More...
template<typename T >
void	add (xyzTriple< T > const &v, T const &t, xyzTriple< T > &r)
	Add: xyzTriple + T. More...
template<typename T >
void	add (T const &t, xyzTriple< T > const &v, xyzTriple< T > &r)
	Add: T + xyzTriple. More...
template<typename T >
void	subtract (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &r)
	Subtract: xyzTriple - xyzTriple. More...
template<typename T >
void	subtract (xyzTriple< T > const &v, T const &t, xyzTriple< T > &r)
	Subtract: xyzTriple - T. More...
template<typename T >
void	subtract (T const &t, xyzTriple< T > const &v, xyzTriple< T > &r)
	Subtract: T - xyzTriple. More...
template<typename T >
void	multiply (xyzTriple< T > const &v, T const &t, xyzTriple< T > &r)
	Multiply: xyzTriple * T. More...
template<typename T >
void	multiply (T const &t, xyzTriple< T > const &v, xyzTriple< T > &r)
	Multiply: T * xyzTriple. More...
template<typename T >
void	divide (xyzTriple< T > const &v, T const &t, xyzTriple< T > &r)
	Divide: xyzTriple / T. More...
template<typename T >
xyzTriple< T >	min (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple with min coordinates of two xyzTriples More...
template<typename T >
xyzTriple< T >	max (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple with max coordinates of two xyzTriples More...
template<typename T >
T	distance (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Distance. More...
template<typename T >
T	distance_squared (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Distance squared. More...
template<typename T >
T	dot (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Dot product. More...
template<typename T >
T	dot_product (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Dot product. More...
template<typename T >
T	inner_product (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Inner product ( == dot product ) More...
template<typename T >
xyzTriple< T >	cross (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Cross product. More...
template<typename T >
xyzTriple< T >	cross_product (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Cross product. More...
template<typename T >
void	cross (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename T >
void	cross_product (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename T >
xyzTriple< T >	midpoint (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Midpoint of 2 xyzTriples. More...
template<typename T >
void	midpoint (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &m)
	Midpoint of 2 xyzTriples: Return via argument (slightly faster) More...
template<typename T >
xyzTriple< T >	center (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Center of 2 xyzTriples. More...
template<typename T >
void	center (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > &m)
	Center of 2 xyzTriples: Return via argument (slightly faster) More...
template<typename T >
xyzTriple< T >	center (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c)
	Center of 3 xyzTriples. More...
template<typename T >
void	center (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c, xyzTriple< T > &m)
	Center of 3 xyzTriples: Return via argument (slightly faster) More...
template<typename T >
xyzTriple< T >	center (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c, xyzTriple< T > const &d)
	Center of 4 xyzTriples. More...
template<typename T >
void	center (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c, xyzTriple< T > const &d, xyzTriple< T > &m)
	Center of 4 xyzTriples: Return via argument (slightly faster) More...
template<typename T >
T	angle_of (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Angle between two vectors (in radians on [ 0, pi ]) More...
template<typename T >
T	angle_of (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c)
	Angle formed by three consecutive points (in radians on [ 0, pi ]) More...
template<typename T >
T	cos_of (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Cosine of angle between two vectors. More...
template<typename T >
T	cos_of (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c)
	Cosine of angle formed by three consecutive points. More...
template<typename T >
T	sin_of (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Sine of angle between two vectors. More...
template<typename T >
T	sin_of (xyzTriple< T > const &a, xyzTriple< T > const &b, xyzTriple< T > const &c)
	Sine of angle formed by three consecutive points. More...
template<typename T >
bool	operator== (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple == xyzTriple More...
template<typename T >
bool	operator!= (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple != xyzTriple More...
template<typename T >
bool	operator< (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple < xyzTriple More...
template<typename T >
bool	operator<= (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple <= xyzTriple More...
template<typename T >
bool	operator>= (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple >= xyzTriple More...
template<typename T >
bool	operator> (xyzTriple< T > const &a, xyzTriple< T > const &b)
	xyzTriple > xyzTriple More...
template<typename T >
bool	operator== (xyzTriple< T > const &v, T const &t)
	xyzTriple == T More...
template<typename T >
bool	operator!= (xyzTriple< T > const &v, T const &t)
	xyzTriple != T More...
template<typename T >
bool	operator< (xyzTriple< T > const &v, T const &t)
	xyzTriple < T More...
template<typename T >
bool	operator<= (xyzTriple< T > const &v, T const &t)
	xyzTriple <= T More...
template<typename T >
bool	operator>= (xyzTriple< T > const &v, T const &t)
	xyzTriple >= T More...
template<typename T >
bool	operator> (xyzTriple< T > const &v, T const &t)
	xyzTriple > T More...
template<typename T >
bool	operator== (T const &t, xyzTriple< T > const &v)
	T == xyzTriple. More...
template<typename T >
bool	operator!= (T const &t, xyzTriple< T > const &v)
	T != xyzTriple. More...
template<typename T >
bool	operator< (T const &t, xyzTriple< T > const &v)
	T < xyzTriple. More...
template<typename T >
bool	operator<= (T const &t, xyzTriple< T > const &v)
	T <= xyzTriple. More...
template<typename T >
bool	operator>= (T const &t, xyzTriple< T > const &v)
	T >= xyzTriple. More...
template<typename T >
bool	operator> (T const &t, xyzTriple< T > const &v)
	T > xyzTriple. More...
template<typename T >
bool	equal_length (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Equal length? More...
template<typename T >
bool	not_equal_length (xyzTriple< T > const &a, xyzTriple< T > const &b)
	Not equal length? More...
template<typename U >
U	dot (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Dot product. More...
template<typename U >
U	dot_product (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Dot product. More...
template<typename U >
U	inner_product (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Inner product ( == dot product ) More...
template<typename U >
bool	equal_length (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Equal length? More...
template<typename U >
xyzTriple< U >	cross (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Cross product. More...
template<typename U >
xyzTriple< U >	cross_product (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Cross product. More...
template<typename U >
void	cross (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename U >
void	cross_product (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename U >
xyzTriple< U >	midpoint (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Midpoint of 2 xyzTriples. More...
template<typename U >
void	midpoint (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &m)
	Midpoint of 2 xyzTriples: Return via argument (slightly faster) More...
template<typename U >
xyzTriple< U >	center (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Center of 2 xyzTriples. More...
template<typename U >
void	center (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &m)
	Center of 2 xyzTriples: Return via argument (slightly faster) More...
template<typename U >
xyzTriple< U >	center (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c)
	Center of 3 xyzTriples. More...
template<typename U >
void	center (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c, xyzTriple< U > &m)
	Center of 3 xyzTriples: Return via argument (slightly faster) More...
template<typename U >
xyzTriple< U >	center (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c, xyzTriple< U > const &d)
	Center of 4 xyzTriples. More...
template<typename U >
void	center (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c, xyzTriple< U > const &d, xyzTriple< U > &m)
	Center of 4 xyzTriples: Return via argument (slightly faster) More...
template<typename U >
U	angle_of (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Angle between two vectors (in radians on [ 0, pi ]) More...
template<typename U >
U	angle_of (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c)
	Angle formed by three consecutive points (in radians on [ 0, pi ]) More...
template<typename U >
U	cos_of (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Cosine of angle between two vectors. More...
template<typename U >
U	cos_of (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c)
	Cosine of angle formed by three consecutive points. More...
template<typename U >
U	sin_of (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Sine of angle between two vectors. More...
template<typename U >
U	sin_of (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > const &c)
	Sine of angle formed by three consecutive points. More...
template<typename U >
U	distance_squared (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Distance squared. More...
template<typename U >
bool	not_equal_length (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Not equal length? More...
template<typename U >
void	add (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &r)
	Add: xyzTriple + xyzTriple. More...
template<typename U >
void	add (xyzTriple< U > const &v, U const &t, xyzTriple< U > &r)
	Add: xyzTriple + Value. More...
template<typename U >
void	add (U const &t, xyzTriple< U > const &v, xyzTriple< U > &r)
	Add: Value + xyzTriple. More...
template<typename U >
void	subtract (xyzTriple< U > const &a, xyzTriple< U > const &b, xyzTriple< U > &r)
	Subtract: xyzTriple - xyzTriple. More...
template<typename U >
void	subtract (xyzTriple< U > const &v, U const &t, xyzTriple< U > &r)
	Subtract: xyzTriple - Value. More...
template<typename U >
void	subtract (U const &t, xyzTriple< U > const &v, xyzTriple< U > &r)
	Subtract: Value - xyzTriple. More...
template<typename U >
void	multiply (xyzTriple< U > const &v, U const &t, xyzTriple< U > &r)
	Multiply: xyzTriple * Value. More...
template<typename U >
void	multiply (U const &t, xyzTriple< U > const &v, xyzTriple< U > &r)
	Multiply: Value * xyzTriple. More...
template<typename U >
void	divide (xyzTriple< U > const &v, U const &t, xyzTriple< U > &r)
	Divide: xyzTriple / Value. More...
template<typename U >
xyzTriple< U >	min (xyzTriple< U > const &a, xyzTriple< U > const &b)
	xyzTriple with min coordinates of two xyzTriples More...
template<typename U >
xyzTriple< U >	max (xyzTriple< U > const &a, xyzTriple< U > const &b)
	xyzTriple with max coordinates of two xyzTriples More...
template<typename U >
U	distance (xyzTriple< U > const &a, xyzTriple< U > const &b)
	Distance. More...
template<typename T >
std::ostream &	operator<< (std::ostream &stream, xyzTriple< T > const &v)
	stream << xyzTriple output operator More...
template<typename T >
std::istream &	operator>> (std::istream &stream, xyzTriple< T > &v)
	stream >> xyzTriple input operator More...
template<typename T >
xyzVector< T >	operator+ (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector + xyzVector More...
template<typename T >
xyzVector< T >	operator+ (xyzVector< T > const &v, T const &t)
	xyzVector + T More...
template<typename T >
xyzVector< T >	operator+ (T const &t, xyzVector< T > const &v)
	T + xyzVector. More...
template<typename T >
xyzVector< T >	operator- (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector - xyzVector More...
template<typename T >
xyzVector< T >	operator- (xyzVector< T > const &v, T const &t)
	xyzVector - T More...
template<typename T >
xyzVector< T >	operator- (T const &t, xyzVector< T > const &v)
	T - xyzVector. More...
template<typename T >
xyzVector< T >	operator* (xyzVector< T > const &v, T const &t)
	xyzVector * T More...
template<typename T >
xyzVector< T >	operator* (T const &t, xyzVector< T > const &v)
	T * xyzVector. More...
template<typename T >
xyzVector< T >	operator/ (xyzVector< T > const &v, T const &t)
	xyzVector / T More...
template<typename T >
void	add (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &r)
	Add: xyzVector + xyzVector. More...
template<typename T >
void	add (xyzVector< T > const &v, T const &t, xyzVector< T > &r)
	Add: xyzVector + T. More...
template<typename T >
void	add (T const &t, xyzVector< T > const &v, xyzVector< T > &r)
	Add: T + xyzVector. More...
template<typename T >
void	subtract (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &r)
	Subtract: xyzVector - xyzVector. More...
template<typename T >
void	subtract (xyzVector< T > const &v, T const &t, xyzVector< T > &r)
	Subtract: xyzVector - T. More...
template<typename T >
void	subtract (T const &t, xyzVector< T > const &v, xyzVector< T > &r)
	Subtract: T - xyzVector. More...
template<typename T >
void	multiply (xyzVector< T > const &v, T const &t, xyzVector< T > &r)
	Multiply: xyzVector * T. More...
template<typename T >
void	multiply (T const &t, xyzVector< T > const &v, xyzVector< T > &r)
	Multiply: T * xyzVector. More...
template<typename T >
void	divide (xyzVector< T > const &v, T const &t, xyzVector< T > &r)
	Divide: xyzVector / T. More...
template<typename T >
xyzVector< T >	min (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector with min coordinates of two xyzVectors More...
template<typename T >
xyzVector< T >	max (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector with max coordinates of two xyzVectors More...
template<typename T >
T	dot (xyzVector< T > const &a, xyzVector< T > const &b)
	Distance. More...
template<typename T >
T	dot_product (xyzVector< T > const &a, xyzVector< T > const &b)
	Dot product. More...
template<typename T >
T	inner_product (xyzVector< T > const &a, xyzVector< T > const &b)
	Inner product ( == dot product ) More...
template<typename T >
xyzVector< T >	cross (xyzVector< T > const &a, xyzVector< T > const &b)
	Cross product. More...
template<typename T >
xyzVector< T >	cross_product (xyzVector< T > const &a, xyzVector< T > const &b)
	Cross product. More...
template<typename T >
void	cross (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename T >
void	cross_product (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename T >
xyzVector< T >	midpoint (xyzVector< T > const &a, xyzVector< T > const &b)
	Midpoint of 2 xyzVectors. More...
template<typename T >
void	midpoint (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &m)
	Midpoint of 2 xyzVectors: Return via argument (slightly faster) More...
template<typename T >
xyzVector< T >	center (xyzVector< T > const &a, xyzVector< T > const &b)
	Center of 2 xyzVectors. More...
template<typename T >
void	center (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > &m)
	Center of 2 xyzVectors: Return via argument (slightly faster) More...
template<typename T >
xyzVector< T >	center (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > const &c)
	Center of 3 xyzVectors. More...
template<typename T >
void	center (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > const &c, xyzVector< T > &m)
	Center of 3 xyzVectors: Return via argument (slightly faster) More...
template<typename T >
xyzVector< T >	center (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > const &c, xyzVector< T > const &d)
	Center of 4 xyzVectors. More...
template<typename T >
void	center (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > const &c, xyzVector< T > const &d, xyzVector< T > &m)
	Center of 4 xyzVectors: Return via argument (slightly faster) More...
template<typename T >
bool	operator== (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector == xyzVector More...
template<typename T >
bool	operator!= (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector != xyzVector More...
template<typename T >
bool	operator< (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector < xyzVector More...
template<typename T >
bool	operator<= (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector <= xyzVector More...
template<typename T >
bool	operator>= (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector >= xyzVector More...
template<typename T >
bool	operator> (xyzVector< T > const &a, xyzVector< T > const &b)
	xyzVector > xyzVector More...
template<typename T >
bool	operator== (xyzVector< T > const &v, T const &t)
	xyzVector == T More...
template<typename T >
bool	operator!= (xyzVector< T > const &v, T const &t)
	xyzVector != T More...
template<typename T >
bool	operator< (xyzVector< T > const &v, T const &t)
	xyzVector < T More...
template<typename T >
bool	operator<= (xyzVector< T > const &v, T const &t)
	xyzVector <= T More...
template<typename T >
bool	operator>= (xyzVector< T > const &v, T const &t)
	xyzVector >= T More...
template<typename T >
bool	operator> (xyzVector< T > const &v, T const &t)
	xyzVector > T More...
template<typename T >
bool	operator== (T const &t, xyzVector< T > const &v)
	T == xyzVector. More...
template<typename T >
bool	operator!= (T const &t, xyzVector< T > const &v)
	T != xyzVector. More...
template<typename T >
bool	operator< (T const &t, xyzVector< T > const &v)
	T < xyzVector. More...
template<typename T >
bool	operator<= (T const &t, xyzVector< T > const &v)
	T <= xyzVector. More...
template<typename T >
bool	operator>= (T const &t, xyzVector< T > const &v)
	T >= xyzVector. More...
template<typename T >
bool	operator> (T const &t, xyzVector< T > const &v)
	T > xyzVector. More...
template<typename T >
bool	equal_length (xyzVector< T > const &a, xyzVector< T > const &b)
	Equal length? More...
template<typename T >
bool	not_equal_length (xyzVector< T > const &a, xyzVector< T > const &b)
	Not equal length? More...
template<typename U >
void	subtract (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &r)
	Subtract: xyzVector - xyzVector. More...
template<typename U >
void	subtract (xyzVector< U > const &v, U const &t, xyzVector< U > &r)
	Subtract: xyzVector - Value. More...
template<typename U >
void	subtract (U const &t, xyzVector< U > const &v, xyzVector< U > &r)
	Subtract: Value - xyzVector. More...
template<typename U >
void	multiply (xyzVector< U > const &v, U const &t, xyzVector< U > &r)
	Multiply: xyzVector * Value. More...
template<typename U >
void	multiply (U const &t, xyzVector< U > const &v, xyzVector< U > &r)
	Multiply: Value * xyzVector. More...
template<typename T >
xyzVector< T >	update_operation (xyzVector< T > const &a, xyzVector< T > const &b)
template<typename T >
xyzVector< T >	update_5way_operation (xyzVector< T > const &a, xyzVector< T > const &b, xyzVector< T > const &c, xyzVector< T > const &d, xyzVector< T > const &e)
template<typename U >
xyzVector< U >	min (xyzVector< U > const &a, xyzVector< U > const &b)
	xyzVector with min coordinates of two xyzVectors More...
template<typename U >
xyzVector< U >	max (xyzVector< U > const &a, xyzVector< U > const &b)
	xyzVector with max coordinates of two xyzVectors More...
template<typename U >
xyzVector< U >	cross (xyzVector< U > const &a, xyzVector< U > const &b)
	Cross product. More...
template<typename U >
xyzVector< U >	cross_product (xyzVector< U > const &a, xyzVector< U > const &b)
	Cross product. More...
template<typename U >
void	cross (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename U >
void	cross_product (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &c)
	Cross product: Return via argument (slightly faster) More...
template<typename U >
xyzVector< U >	midpoint (xyzVector< U > const &a, xyzVector< U > const &b)
	Midpoint of 2 xyzVectors. More...
template<typename U >
void	midpoint (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &m)
	Midpoint of 2 xyzVectors: Return via argument (slightly faster) More...
template<typename U >
xyzVector< U >	center (xyzVector< U > const &a, xyzVector< U > const &b)
	Center of 2 xyzVectors. More...
template<typename U >
void	center (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &m)
	Center of 2 xyzVectors: Return via argument (slightly faster) More...
template<typename U >
xyzVector< U >	center (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c)
	Center of 3 xyzVectors. More...
template<typename U >
void	center (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c, xyzVector< U > &m)
	Center of 3 xyzVectors: Return via argument (slightly faster) More...
template<typename U >
xyzVector< U >	center (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c, xyzVector< U > const &d)
	Center of 4 xyzVectors. More...
template<typename U >
void	center (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > const &c, xyzVector< U > const &d, xyzVector< U > &m)
	Center of 4 xyzVectors: Return via argument (slightly faster) More...
template<typename U >
void	add (xyzVector< U > const &a, xyzVector< U > const &b, xyzVector< U > &r)
	Add: xyzVector + xyzVector. More...
template<typename U >
void	add (xyzVector< U > const &v, U const &t, xyzVector< U > &r)
	Add: xyzVector + Value. More...
template<typename U >
void	add (U const &t, xyzVector< U > const &v, xyzVector< U > &r)
	Add: Value + xyzVector. More...
template<typename U >
bool	equal_length (xyzVector< U > const &a, xyzVector< U > const &b)
	Equal length? More...
template<typename U >
bool	not_equal_length (xyzVector< U > const &a, xyzVector< U > const &b)
	Not equal length? More...
template<typename U >
U	dot (xyzVector< U > const &a, xyzVector< U > const &b)
	Dot product. More...
template<typename U >
U	inner_product (xyzVector< U > const &a, xyzVector< U > const &b)
	Inner product ( == dot product ) More...
template<typename U >
void	divide (xyzVector< U > const &v, U const &t, xyzVector< U > &r)
	Divide: xyzVector / Value. More...
template<typename T >
std::ostream &	operator<< (std::ostream &stream, xyzVector< T > const &v)
	stream << xyzVector output operator More...
template<typename T >
std::istream &	operator>> (std::istream &stream, xyzVector< T > &v)
	stream >> xyzVector input operator More...
template<typename T >
std::string	truncate_and_serialize_xyz_vector (xyzVector< T > vector, Real precision)
void	calc_zscore (std::map< Size, Real > const &input_v, std::map< Size, Real > &zscore_v, bool negating=false)
	Calculate a Z-score from a set of data. Real i_zscore = (input_v[i]-mean)/stdev;. More...

Detailed Description

Unit headers.

A collection of functions for working with probabilities.

Vector0's that can perform mathmatical functions.

Generic base class for the MathNTensor class. Since the MathNTensor class takes a type AND a dimensionality as template arguments, it's not possible to have a generic pointer to a MathNTensor of arbitrary dimensionality. The base class allows this.

File input/output for the MathNTensor class.

construction/destructor of 3-D Matrix's with some functions

Mathmatical functions for the MathMatrix class.

construction/destructor of Matrix's with some functions

Tricubic spline for smoothly interpolating a function in 3 dimensions.

Forward declaration for the SplineGenerator.

Base class for abstract N-dimensional PolycubicSpline.

Polycubic spline for smoothly interpolating a function in n dimensions.

Forward declarations of Interpolator.

Cubic spline for all your evil desires.

Forward declarations for the cubic spline class.

Bicubic spline for all your hearts' desires.

Forward declarations for the bicubic spline class.

read the header file!

A 2D histogram based upon a map structure.

A 1D histogram based upon a map structure.

Return the 2d area of a projection, need x and y (or z) coordinates as well as their respective element radius and probe radius, probe radius can be set to zero if only the projection of protein in vaccum is desired.

Boost headers.

Utility headers.

Core headers Utility headers C++ headers

Numeric headers Utility headers C++ headers

C++ headers

Very simple class for histograms based upon maps. You provide the key, which is templated, meaning that the key can be a string, real, size, enum. It will return a count, if you want it

Author

Steven Combs

Very simple class for histograms based upon maps. You provide the key, which is templated, meaning that the two keys can be strings, reals, sizes. It will return a count, if you want it

Author

Steven Combs

Also called Keys spline or polycubic 'convolution'. See: https://en.wikipedia.org/wiki/Bicubic_interpolation

Unlike prior Rosetta spline interpolation (see interpolation::polycubic_interpolation or B-spline implementation in core::scoring::electron_density::SplineInterp), this does not require pre-training of spline which can be both time-intensive & memory intensive. Instead, uses an interpolant based on nearest neighbor grid points (like polylinear interpolation) and next-nearest neighbor.

First derivative is continuous (but second deriv is not, in general).

If we need more accuracy & smoothness, there is a higher-order cubic spline that looks out one more neighbor (see Keys, "Cubic convolution interpolation for digital image processing", IEEE Transactions on Acoustics, Speech, and Signal Processing 1981).

If we need more speed, following is pretty inefficient to ensure generality (see notes). Also, there is apparently a faster version called osculatory interpolation that predated Keys & Catmull & Rom by 80 years; see Meijering & Unser, "A Note on Cubic Convolution Interpolation", IEEE Transactions on Image Processing 2003.

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler

Steven Combs

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

This is an implementation of an algorithm from Numerical Recipes. It relies heavily on the implementation of the cubic spline (from Numerical Recipes), the MathMatrix, and the MathVector. You MUST USE the MathVector and MathMatrix implementations to use this function. The spline is very customizable and allows you to define the border behaviors (start/end of spline values). If you use the e_Natural (enum) BorderFlag, the start/end (border) of the spline will be linear. This may not be ideal for scoring functions as you want the a smoothing effect at the start/end (border) values. Instead, you probably want to use the e_FirstDeriv (enum) BorderFlag with the first derivate (private member value firstbe_) set to 0. This will cause a smoothing out of the start/end (border) of spline. If you want the splie to be continuous, you should use the e_Periodic (enum) BorderFlag.

To "train" the spline, use must provide the spline with a MathMatrix (numeric::MathMatrix). Lets look at an example. x values y 1__2__ 3 .1 | 1 2 3 | v .3 | 4 5 6 | a .5 | 7 8 9 | l |__________| u e s

Given the above Matrix (MathMatrix) You would want your start (START[2] private member value start_) values to be START[] = {1,.1}. You would then want to assign the delta (DELTA[2], private member value delta_) values to DELTA[] = {1,.2}. These delta values is the change between your x values and your y values. For example, the change between x1 and x2 is 1. Therefore, the delta for the x-values will be 1. For y values, you have y.1, y.3 which is a change of .2, therefore the delta will be .2. You do not have to specify an end because the algorithm will stop when it reaches the last value in the matrix.

Finally, the LinCont determins that if the argument x or y is outside the range decide if the spline should be continued linearly.

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler

The below comments are for the Bicubic spline but apply for the cubic spline. This is an implementation of an algorithm from Numerical Recipes. It relies heavily on the implementation of the cubic spline (from Numerical Recipes), the MathMatrix, and the MathVector. You MUST USE the MathVector and MathMatrix implementations to use this function. The spline is very customizable and allows you to define the border behaviors (start/end of spline values). If you use the e_Natural (enum) BorderFlag, the start/end (border) of the spline will be linear. This may not be ideal for scoring functions as you want the a smoothing effect at the start/end (border) values. Instead, you probably want to use the e_FirstDeriv (enum) BorderFlag with the first derivate (private member value firstbe_) set to 0. This will cause a smoothing out of the start/end (border) of spline. If you want the splie to be continuous, you should use the e_Periodic (enum) BorderFlag.

To "train" the spline, use must provide the spline with a MathMatrix (numeric::MathMatrix). Lets look at an example. x values y 1__2__ 3 .1 | 1 2 3 | v .3 | 4 5 6 | a .5 | 7 8 9 | l |__________| u e s

Given the above Matrix (MathMatrix) You would want your start (START[2] private member value start_) values to be START[] = {1,.1}. You would then want to assign the delta (DELTA[2], private member value delta_) values to DELTA[] = {1,.2}. These delta values is the change between your x values and your y values. For example, the change between x1 and x2 is 1. Therefore, the delta for the x-values will be 1. For y values, you have y.1, y.3 which is a change of .2, therefore the delta will be .2. You do not have to specify an end because the algorithm will stop when it reaches the last value in the matrix.

Finally, the LinCont determins that if the argument x or y is outside the range decide if the spline should be continued linearly.

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler ported to Rosetta by Andrew Leaver-Fay generalized to N dimensions by Andrew Watkins

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler ported to Rosetta by Andrew Leaver-Fay generalized to n dimensions by Andrew Watkins

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References:

Numerical Recipes in c++ 2nd edition Ralf Mueller

Author

Steven Combs, Ralf Mueller, Jens Meiler ported to Rosetta by Andrew Leaver-Fay

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) The Matrix is constructed out of arrays and places values into rows/columns based on however many columns/rows you specify. Actual operations of the MathMatrix are implemented in numeric/MathMatrix_operations.hh. To access specific values (elements), you must use the operator (). For example: to access row 5, column 3 of a matrix, you would use matrix(5,3). *****NOTE**** The MathMatrix class is indexed at 0!!!!

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) The Matrix is construction is found in numeric/MathMatrix.hh. These are mathematical functions that can be used by the MathMatrix class. ***Note that these are outside of class, but having the operators take two arguments ensures that no one will use the functions unknowningly

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) *****NOTE**** The MathNTensor class is indexed at 0!

Check out MathNTensor_io.hh for file i/o functions.

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

ported to Rosetta by Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)

generalized to N dimensions by Andrew Watkins

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) – added default constructor, clone() operator.

To avoid cryptic 'hardwiring' of binary file specification into the code, look for details of # bins as n_bins entry in JSON file.

File should be of the form '.bin.gz', with associated '.json' ASCII file.

Author

Rhiju Das

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) *****NOTE**** The MathTensor class is indexed at 0!!!!

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

ported to Rosetta by Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) The MathVector is constructed just like utility::vector0, however this class does not inherit from utility::vector0. It is implemented this way to avoid confusion. Most functions from the std::vector / utility::vector0 ARE NOT included. This is a vector that performs mathematical functions, not a "storage" vector. Actual mathematical functions found in numeric/MathVector_operations. To access specific values you must use the operator (). For example: vector(5), will give you the value at index 5. This is done to distinguish from utility::vector!

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

This is an implementation of an algorithm that was taken from BCL (Jens Meiler) The Matrix is construction is found in numeric/MathVector.hh. These are mathematical functions that can be used by the MathVector class. ***Note that these are outside of class, but having the operators take two arguments ensures that no one will use the functions unknowningly

References:

Nils Woetzl Jens Meiler

Author

Steven Combs, Nils Woetzl, Jens Meiler

Currently supported RG types: standard - build in C++ random generator ran3 - old generator from previos version of rosetta

Typedef Documentation

AxisRotationSamplerCOP

typedef utility::pointer::shared_ptr< AxisRotationSampler const > numeric::AxisRotationSamplerCOP

AxisRotationSamplerOP

typedef utility::pointer::shared_ptr< AxisRotationSampler > numeric::AxisRotationSamplerOP

BodyPosition_double

typedef BodyPosition< double > numeric::BodyPosition_double

BodyPosition_float

typedef BodyPosition< float > numeric::BodyPosition_float

BodyPosition_longdouble

typedef BodyPosition< long double > numeric::BodyPosition_longdouble

CalculatorOP

typedef utility::pointer::shared_ptr<Calculator> numeric::CalculatorOP

ClusteringTreeNodeAP

typedef utility::pointer::weak_ptr<ClusteringTreeNode> numeric::ClusteringTreeNodeAP

ClusteringTreeNodeOP

typedef utility::pointer::shared_ptr<ClusteringTreeNode> numeric::ClusteringTreeNodeOP

Length

using numeric::Length = typedef Real

MathNTensorBaseCOP

template<class T >

using numeric::MathNTensorBaseCOP = typedef utility::pointer::shared_ptr< MathNTensorBase< T > const >

MathNTensorBaseOP

template<class T >

using numeric::MathNTensorBaseOP = typedef utility::pointer::shared_ptr< MathNTensorBase< T > >

MathNTensorCOP

template<class T , numeric::Size N>

using numeric::MathNTensorCOP = typedef utility::pointer::shared_ptr< MathNTensor< T,N > const >

MathNTensorOP

template<class T , numeric::Size N>

using numeric::MathNTensorOP = typedef utility::pointer::shared_ptr< MathNTensor< T,N > >

Polynomial_1dCOP

typedef utility::pointer::shared_ptr< Polynomial_1d const > numeric::Polynomial_1dCOP

Polynomial_1dOP

typedef utility::pointer::shared_ptr< Polynomial_1d > numeric::Polynomial_1dOP

Quaternion_double

typedef Quaternion< double > numeric::Quaternion_double

Quaternion_float

typedef Quaternion< float > numeric::Quaternion_float

Quaternion_longdouble

typedef Quaternion< long double > numeric::Quaternion_longdouble

Real

using numeric::Real = typedef platform::Real

RocCurveOP

typedef utility::pointer::shared_ptr<RocCurve> numeric::RocCurveOP

RocPointOP

typedef utility::pointer::shared_ptr<RocPoint> numeric::RocPointOP

Size

typedef platform::Size numeric::Size

SSize

typedef platform::SSize numeric::SSize

UniformRotationSamplerCOP

typedef utility::pointer::shared_ptr< UniformRotationSampler const > numeric::UniformRotationSamplerCOP

UniformRotationSamplerOP

typedef utility::pointer::shared_ptr< UniformRotationSampler > numeric::UniformRotationSamplerOP

Vector

using numeric::Vector = typedef xyzVector<Real>

Xform

typedef xyzTransform< double > numeric::Xform

Xformf

typedef xyzTransform< float > numeric::Xformf

xyzMatrix_bool

typedef xyzMatrix< bool > numeric::xyzMatrix_bool

xyzMatrix_char

typedef xyzMatrix< char > numeric::xyzMatrix_char

xyzMatrix_double

typedef xyzMatrix< double > numeric::xyzMatrix_double

xyzMatrix_float

typedef xyzMatrix< float > numeric::xyzMatrix_float

xyzMatrix_int

typedef xyzMatrix< int > numeric::xyzMatrix_int

xyzMatrix_long

typedef xyzMatrix< long int > numeric::xyzMatrix_long

xyzMatrix_long_double

typedef xyzMatrix< long double > numeric::xyzMatrix_long_double

xyzMatrix_real

typedef xyzMatrix< platform::Real > numeric::xyzMatrix_real

xyzMatrix_schar

typedef xyzMatrix< signed char > numeric::xyzMatrix_schar

xyzMatrix_short

typedef xyzMatrix< short int > numeric::xyzMatrix_short

xyzMatrix_Size

typedef xyzMatrix< platform::Size > numeric::xyzMatrix_Size

xyzMatrix_size

typedef xyzMatrix< platform::Size > numeric::xyzMatrix_size

xyzMatrix_size_t

typedef xyzMatrix< platform::Size > numeric::xyzMatrix_size_t

xyzMatrix_uchar

typedef xyzMatrix< unsigned char > numeric::xyzMatrix_uchar

xyzMatrix_uint

typedef xyzMatrix< unsigned int > numeric::xyzMatrix_uint

xyzMatrix_ulong

typedef xyzMatrix< unsigned long int > numeric::xyzMatrix_ulong

xyzMatrix_ushort

typedef xyzMatrix< unsigned short int > numeric::xyzMatrix_ushort

xyzTransform_double

typedef xyzTransform< double > numeric::xyzTransform_double

xyzTransform_float

typedef xyzTransform< float > numeric::xyzTransform_float

xyzTransform_Real

typedef xyzTransform< numeric::Real > numeric::xyzTransform_Real

xyzTriple_bool

typedef xyzTriple< bool > numeric::xyzTriple_bool

xyzTriple_char

typedef xyzTriple< char > numeric::xyzTriple_char

xyzTriple_double

typedef xyzTriple< double > numeric::xyzTriple_double

xyzTriple_float

typedef xyzTriple< float > numeric::xyzTriple_float

xyzTriple_int

typedef xyzTriple< int > numeric::xyzTriple_int

xyzTriple_long

typedef xyzTriple< long int > numeric::xyzTriple_long

xyzTriple_longdouble

typedef xyzTriple< long double > numeric::xyzTriple_longdouble

xyzTriple_schar

typedef xyzTriple< signed char > numeric::xyzTriple_schar

xyzTriple_short

typedef xyzTriple< short int > numeric::xyzTriple_short

xyzTriple_size

typedef xyzTriple< std::size_t > numeric::xyzTriple_size

xyzTriple_size_t

typedef xyzTriple< std::size_t > numeric::xyzTriple_size_t

xyzTriple_uchar

typedef xyzTriple< unsigned char > numeric::xyzTriple_uchar

xyzTriple_uint

typedef xyzTriple< unsigned int > numeric::xyzTriple_uint

xyzTriple_ulong

typedef xyzTriple< unsigned long int > numeric::xyzTriple_ulong

xyzTriple_ushort

typedef xyzTriple< unsigned short int > numeric::xyzTriple_ushort

xyzVector_bool

typedef xyzVector< bool > numeric::xyzVector_bool

xyzVector_char

typedef xyzVector< char > numeric::xyzVector_char

xyzVector_double

typedef xyzVector< double > numeric::xyzVector_double

xyzVector_float

typedef xyzVector< float > numeric::xyzVector_float

xyzVector_int

typedef xyzVector< int > numeric::xyzVector_int

xyzVector_long

typedef xyzVector< long int > numeric::xyzVector_long

xyzVector_long_double

typedef xyzVector< long double > numeric::xyzVector_long_double

xyzVector_real

typedef xyzVector< Real > numeric::xyzVector_real

xyzVector_schar

typedef xyzVector< signed char > numeric::xyzVector_schar

xyzVector_short

typedef xyzVector< short int > numeric::xyzVector_short

xyzVector_size

typedef xyzVector< std::size_t > numeric::xyzVector_size

xyzVector_size_t

typedef xyzVector< std::size_t > numeric::xyzVector_size_t

xyzVector_uchar

typedef xyzVector< unsigned char > numeric::xyzVector_uchar

xyzVector_uint

typedef xyzVector< unsigned int > numeric::xyzVector_uint

xyzVector_ulong

typedef xyzVector< unsigned long int > numeric::xyzVector_ulong

xyzVector_ushort

typedef xyzVector< unsigned short int > numeric::xyzVector_ushort

Enumeration Type Documentation

RocStatus

enum numeric::RocStatus

Enumerator
true_positive
true_negative
false_positive
false_negative

Function Documentation

abs_difference()

template<typename T >

T numeric::abs_difference ( T const &  a, T const &  b  )

inline

Absolute difference.

References a, compute_difference::b, max(), and min().

access_Real_MathNTensor()

Real & numeric::access_Real_MathNTensor	(	MathNTensorBaseOP< Real >	tensorbase,
		utility::vector1< Size > const &	position
	)

Utility function to access an entry in a MathNTensor of arbitrary dimensionality unknown at compile time, given a MathNTensorBaseOP.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References enumerate_junctions::default, utility::pointer::dynamic_pointer_cast(), create_a3b_hbs::i, runtime_assert, runtime_assert_string_msg, and utility_exit_with_message.

add() [1/12]

template<typename T >

void numeric::add	(	T const &	t,
		xyzTriple< T > const &	v,
		xyzTriple< T > &	r
	)

Add: T + xyzTriple.

add() [2/12]

template<typename T >

void numeric::add	(	T const &	t,
		xyzVector< T > const &	v,
		xyzVector< T > &	r
	)

Add: T + xyzVector.

add() [3/12]

template<typename U >

void numeric::add ( U const &  t, xyzTriple< U > const &  v, xyzTriple< U > &  r  )

inline

Add: Value + xyzTriple.

add() [4/12]

template<typename U >

void numeric::add ( U const &  t, xyzVector< U > const &  v, xyzVector< U > &  r  )

inline

Add: Value + xyzVector.

add() [5/12]

template<typename T >

void numeric::add	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	r
	)

Add: xyzTriple + xyzTriple.

Referenced by utility::json_spirit::Semantic_actions< Value_type, Iter_type >::add_to_current(), mutant_modeler.MutantModeler::get_high_res_command_lines(), insert_stage_tag(), job_manager.StatusWindow::refresh(), utility::split(), utility::split_to_list(), utility::split_to_set(), and pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor::test_labels().

add() [6/12]

template<typename T >

void numeric::add	(	xyzTriple< T > const &	v,
		T const &	t,
		xyzTriple< T > &	r
	)

Add: xyzTriple + T.

add() [7/12]

template<typename U >

void numeric::add ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  r  )

inline

Add: xyzTriple + xyzTriple.

add() [8/12]

template<typename U >

void numeric::add ( xyzTriple< U > const &  v, U const &  t, xyzTriple< U > &  r  )

inline

Add: xyzTriple + Value.

add() [9/12]

template<typename T >

void numeric::add	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	r
	)

Add: xyzVector + xyzVector.

add() [10/12]

template<typename T >

void numeric::add	(	xyzVector< T > const &	v,
		T const &	t,
		xyzVector< T > &	r
	)

Add: xyzVector + T.

add() [11/12]

template<typename U >

void numeric::add ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  r  )

inline

Add: xyzVector + xyzVector.

add() [12/12]

template<typename U >

void numeric::add ( xyzVector< U > const &  v, U const &  t, xyzVector< U > &  r  )

inline

Add: xyzVector + Value.

alignVectorSets()

template<typename T >

xyzMatrix< T > numeric::alignVectorSets ( xyzVector< T >  A1, xyzVector< T >  B1, xyzVector< T >  A2, xyzVector< T >  B2  )

inline

Helper function to find the rotation to optimally transform the vectors A1-B1 to vectors A2-B2.

References numeric::xyzMatrix< T >::identity(), inverse(), numeric::xyzVector< T >::is_zero(), numeric::xyzVector< T >::normalize(), docking::R, predPRE::R2, numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

Referenced by getxform(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), main(), and run().

angle_degrees() [1/2]

template<typename T >

T numeric::angle_degrees ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  p3  )

inline

Plane angle in degrees: angle value returned.

Note

Given three positions in a chain ( p1, p2, p3 ), calculates the plane angle in degrees between the vectors p2->p1 and p2->p3

Angle returned is on [ 0, 180 ]

References basic::options::OptionKeys::hotspot::angle, angle_radians(), numeric::conversions::degrees(), and p2.

Referenced by angle_degrees_double(), DetectSymmetry::apply(), SwapElementsMover2::apply(), find_neighbors_directional(), get_interface_residues(), CrystDesign::get_interface_residues(), get_neighbor_residues(), CrystDesign::get_neighbor_residues(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), main(), and run().

angle_degrees() [2/2]

template<typename T >

T numeric::angle_degrees ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  p3, xyzVector< T > const &  p4  )

inline

Angle between two vectors in radians.

Note

Given two vectors (p1->p2 & p3->p4), calculate the angle between them

Angle returned is on [ 0, pi ]

References basic::options::OptionKeys::hotspot::angle, angle_radians(), numeric::conversions::degrees(), and p2.

angle_degrees_double() [1/2]

double numeric::angle_degrees_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3  )

inline

References angle_degrees(), and p2.

angle_degrees_double() [2/2]

double numeric::angle_degrees_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4  )

inline

References angle_degrees(), and p2.

angle_of() [1/6]

template<typename T >

T numeric::angle_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Angle between two vectors (in radians on [ 0, pi ])

angle_of() [2/6]

template<typename T >

T numeric::angle_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c
	)

Angle formed by three consecutive points (in radians on [ 0, pi ])

angle_of() [3/6]

template<typename U >

U numeric::angle_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Angle between two vectors (in radians on [ 0, pi ])

angle_of() [4/6]

template<typename U >

U numeric::angle_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c  )

inline

Angle formed by three consecutive points (in radians on [ 0, pi ])

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c

angle_of() [5/6]

template<typename U >

U numeric::angle_of ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Angle between two vectors (in radians on [ 0, pi ])

References a, compute_difference::b, sin_cos_range(), and docking::U.

Referenced by BuriedUnsatPolarsFinder::acc_geom_check(), angle_of(), ZincMatchFilter::apply(), BuriedUnsatPolarsFinder::don_geom_check(), enclosing_angles(), zinc2_homodimer_setup::filter_metal_geom(), HbondZinc::hbond_constraint(), initialize_from_pdb(), main(), mg_hires_pdbstats_from_pose(), mg_pdbstats_from_pose(), search_other_atoms(), zinc1_homodimer_design::setup_rollmoving(), and apps::public1::scenarios::chemically_conjugated_docking::ubq_ras_rotation_angle().

angle_of() [6/6]

template<typename U >

U numeric::angle_of ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c  )

inline

Angle formed by three consecutive points (in radians on [ 0, pi ])

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c

References a, angle_of(), compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

angle_radians() [1/3]

template<typename T >

T numeric::angle_radians ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  p3  )

inline

Plane angle in radians: angle value returned.

Note

Given three positions in a chain ( p1, p2, p3 ), calculates the plane angle in radians between the vectors p2->p1 and p2->p3

Angle returned is on [ 0, pi ]

References basic::options::OptionKeys::hotspot::angle, angle_radians(), and p2.

angle_radians() [2/3]

template<typename T >

void numeric::angle_radians ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  p3, T &  angle  )

inline

Plane angle in radians: angle value passed.

Note

Given thre positions in a chain ( p1, p2, p3 ), calculates the plane angle in radians between the vectors p2->p1 and p2->p3

Angle returned is on [ 0, pi ]

References a, basic::options::OptionKeys::hotspot::angle, compute_difference::b, dot(), p2, and sin_cos_range().

Referenced by pseudoTrace::add_to_C(), pseudoTrace::add_to_N(), angle_degrees(), angle_degrees(), angle_radians(), angle_radians_double(), ch_o_pdbstats_from_pose(), PoseWrap::check_scattach_res(), files_for_openMM_test(), Arch::intra_slidedis_to_component_disp(), main(), my_main(), output_angles(), output_sugar_geometry_parameters(), pdb_stats(), peptide_plane_test(), BruteFunGroupTK::place_c(), TCDock::precompute_intra(), DisulfideBondEnergy::probability(), run(), write_AHD_to_db(), and write_BAH_to_db().

angle_radians() [3/3]

template<typename T >

T numeric::angle_radians ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  p3, xyzVector< T > const &  p4  )

inline

Angle between two vectors in radians.

Note

Given two vectors (p1->p2 & p3->p4), calculate the angle between them

Angle returned is on [ 0, pi ]

References a, basic::options::OptionKeys::hotspot::angle, compute_difference::b, dot(), p2, and sin_cos_range().

angle_radians_double() [1/2]

double numeric::angle_radians_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3  )

inline

References angle_radians(), and p2.

angle_radians_double() [2/2]

double numeric::angle_radians_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4  )

inline

References angle_radians(), and p2.

angles_between_0_180()

template<typename T >

void numeric::angles_between_0_180 ( xyzVector< T > &  angles )

inline

References a, oop_conformations::angles, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, modulo(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by euler_angles_from_rotation_matrix_ZXZ(), euler_angles_from_rotation_matrix_ZYX(), and euler_angles_from_rotation_matrix_ZYZ().

arccos()

template<typename T >

T numeric::arccos ( T const  x )

inline

like std::acos but with range checking

References sin_cos_range(), and x.

Referenced by numeric::deriv::angle_p1_deriv(), numeric::deriv::angle_p1_p2_p3_deriv(), numeric::deriv::angle_p2_deriv(), numeric::deriv::dihedral_deriv_second(), get_angles(), dbscan_cluster_rotamer::get_common_int_coords(), kmeans_common::get_common_int_coords(), dbscan_cluster_rotamer::get_common_int_coords_2(), kmeans_common::get_common_int_coords_2(), hbond_stats(), and dbscan_cluster_rotamer::main_old_kmeans().

boltzmann_accept_probability()

Real numeric::boltzmann_accept_probability ( Real const  score_before, Real const  score_after, Real const  temperature  )

inline

Calculates the acceptance probability of a given score-change at the given temperature, generally used in simulated annealing algorithms. Returns a value in the range (0-1).

References max(), min(), and local::temperature.

calc_zscore()

void numeric::calc_zscore	(	std::map< Size, Real > const &	input_v,
		std::map< Size, Real > &	zscore_v,
		bool	negating = false
	)

Calculate a Z-score from a set of data. Real i_zscore = (input_v[i]-mean)/stdev;.

Author

Ray Wang (wangy.nosp@m.r@uw.nosp@m..edu) Negating flips the zscore (i_zscore = -1*i_zscore)

References mean(), create_a3b_hbs::nres, myspace::stdev(), and sum().

ccd_angle()

void numeric::ccd_angle	(	utility::vector1< xyzVector< Real > > const &	F,
		utility::vector1< xyzVector< Real > > const &	M,
		xyzVector< Real > const &	axis_atom,
		xyzVector< Real > const &	theta_hat,
		Real &	alpha,
		Real &	S
	)

Parameters

<F>	the coordinates of the fixed target atoms
<M>	the coordinates of the moving positions to be overlapped with the target atoms
<theta_hat>	axis vector of the torsion angle
<alpha>	empty angle to be calculated
<S>	empty deviation to be calculated

The objective of an individual cyclic coordinate descent (CCD) move is to minimize the deviation between a set of points that should perfectly superimpose. The deviation squared (S) can be expressed as:

S = Sum(r^2 + f^2) - 2 Sum[r(f_vector dot r_hat)] cos theta - 2 Sum[r(f_vector dot s_hat)] sin theta

The derivative of S with respect to theta (the angle about the rotation axis):

dS/dtheta = 2 Sum[r(f_vector dot r_hat)] sin theta - 2 Sum[r(f_vector dot s_hat)] cos theta

Setting dS/dtheta to zero gives the minimal value of theta, which we call alpha:

tan alpha = Sum[r(f_vector dot s_hat] / Sum[r(f_vector dot r_hat]

If we define... a = Sum(r^2 + f^2) b = 2 Sum[r(f_vector dot r_hat)] c = 2 Sum[r(f_vector dot s_hat)] then S can be rewritten: S = a - b cos alpha - c sin alpha and we can express alpha as tan alpha = c / b

References aa, ObjexxFCL::abs(), compute_difference::alpha, cross(), numeric::conversions::degrees(), dot(), test.T009_Exceptions::e, ObjexxFCL::format::F(), create_a3b_hbs::i, numeric::xyzVector< T >::is_unit(), numeric::xyzVector< T >::length(), min(), numeric::xyzVector< T >::normalized(), and O.

center() [1/24]

template<typename T >

xyzTriple< T > numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Center of 2 xyzTriples.

Referenced by numeric::geometry::hashing::SixDCoordinateBinner::bin_center_point(), numeric::geometry::hashing::SixDOffsetTree::lookup(), and numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index().

center() [2/24]

template<typename T >

void numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	m
	)

Center of 2 xyzTriples: Return via argument (slightly faster)

center() [3/24]

template<typename T >

xyzTriple< T > numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c
	)

Center of 3 xyzTriples.

center() [4/24]

template<typename T >

void numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c,
		xyzTriple< T > &	m
	)

Center of 3 xyzTriples: Return via argument (slightly faster)

center() [5/24]

template<typename T >

xyzTriple< T > numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c,
		xyzTriple< T > const &	d
	)

Center of 4 xyzTriples.

center() [6/24]

template<typename T >

void numeric::center	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c,
		xyzTriple< T > const &	d,
		xyzTriple< T > &	m
	)

Center of 4 xyzTriples: Return via argument (slightly faster)

center() [7/24]

template<typename U >

xyzTriple<U> numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Center of 2 xyzTriples.

center() [8/24]

template<typename U >

void numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  m  )

inline

Center of 2 xyzTriples: Return via argument (slightly faster)

center() [9/24]

template<typename U >

xyzTriple<U> numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c  )

inline

Center of 3 xyzTriples.

center() [10/24]

template<typename U >

void numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c, xyzTriple< U > &  m  )

inline

Center of 3 xyzTriples: Return via argument (slightly faster)

center() [11/24]

template<typename U >

xyzTriple<U> numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c, xyzTriple< U > const &  d  )

inline

Center of 4 xyzTriples.

center() [12/24]

template<typename U >

void numeric::center ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c, xyzTriple< U > const &  d, xyzTriple< U > &  m  )

inline

Center of 4 xyzTriples: Return via argument (slightly faster)

center() [13/24]

template<typename T >

xyzVector< T > numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Center of 2 xyzVectors.

center() [14/24]

template<typename T >

void numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	m
	)

Center of 2 xyzVectors: Return via argument (slightly faster)

center() [15/24]

template<typename T >

xyzVector< T > numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > const &	c
	)

Center of 3 xyzVectors.

center() [16/24]

template<typename T >

void numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > const &	c,
		xyzVector< T > &	m
	)

Center of 3 xyzVectors: Return via argument (slightly faster)

center() [17/24]

template<typename T >

xyzVector< T > numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > const &	c,
		xyzVector< T > const &	d
	)

Center of 4 xyzVectors.

center() [18/24]

template<typename T >

void numeric::center	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > const &	c,
		xyzVector< T > const &	d,
		xyzVector< T > &	m
	)

Center of 4 xyzVectors: Return via argument (slightly faster)

center() [19/24]

template<typename U >

xyzVector<U> numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Center of 2 xyzVectors.

center() [20/24]

template<typename U >

void numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  m  )

inline

Center of 2 xyzVectors: Return via argument (slightly faster)

center() [21/24]

template<typename U >

xyzVector<U> numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c  )

inline

Center of 3 xyzVectors.

center() [22/24]

template<typename U >

void numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c, xyzVector< U > &  m  )

inline

Center of 3 xyzVectors: Return via argument (slightly faster)

center() [23/24]

template<typename U >

xyzVector<U> numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c, xyzVector< U > const &  d  )

inline

Center of 4 xyzVectors.

center() [24/24]

template<typename U >

void numeric::center ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c, xyzVector< U > const &  d, xyzVector< U > &  m  )

inline

Center of 4 xyzVectors: Return via argument (slightly faster)

center_of_mass()

template<typename T >

xyzVector< T > numeric::center_of_mass ( utility::vector1< xyzVector< T > > const &  coords )

inline

calculate center of mass for coordinates

Referenced by ligand_centroid(), numeric::geometry::residual_squared_of_points_to_plane(), and numeric::geometry::vector_normal_to_ring_plane_of_best_fit().

clamp()

template<typename Number >

Number numeric::clamp	(	Number	value,
		Number	lower_bound,
		Number	upper_bound
	)

Clamps to the closed interval [lower_bound, upper_bound]. Templated type must implement operator<.

References value.

closest_point_on_line()

template<typename T >

xyzVector< T > numeric::closest_point_on_line ( xyzVector< T > const &  p1, xyzVector< T > const &  p2, xyzVector< T > const &  q  )

inline

xyzMatrix * xyzVector

Note

Same as product( xyzMatrix, xyzVector )

return the point closest to point p3 that lies on the line defined by p1 and p2

comma_seperated_string_to_xyz()

template<typename T >

xyzVector<T> numeric::comma_seperated_string_to_xyz ( std::string  triplet )

inline

convert a string of comma separated values "0.2,0.4,0.3" to an xyzVector

References utility::from_string(), runtime_assert, split_string(), utility::string_split(), pyrosetta.distributed.cluster.exceptions::T, and basic::options::OptionKeys::in::file::xyz.

const_access_Real_MathNTensor()

Real const & numeric::const_access_Real_MathNTensor	(	MathNTensorBaseCOP< Real >	tensorbase,
		utility::vector1< Size > const &	position
	)

Utility function to access an entry in a MathNTensor of arbitrary dimensionality unknown at compile time, given a MathNTensorBaseCOP.

Utility function to get const access to an entry in a MathNTensor of arbitrary dimensionality unknown at compile time, given a MathNTensorBaseCOP.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References enumerate_junctions::default, utility::pointer::dynamic_pointer_cast(), create_a3b_hbs::i, runtime_assert, runtime_assert_string_msg, and utility_exit_with_message.

cos_of() [1/6]

template<typename T >

T numeric::cos_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Cosine of angle between two vectors.

cos_of() [2/6]

template<typename T >

T numeric::cos_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c
	)

Cosine of angle formed by three consecutive points.

cos_of() [3/6]

template<typename U >

U numeric::cos_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Cosine of angle between two vectors.

cos_of() [4/6]

template<typename U >

U numeric::cos_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c  )

inline

Cosine of angle formed by three consecutive points.

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c.

cos_of() [5/6]

template<typename U >

U numeric::cos_of ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Cosine of angle between two vectors.

References a, compute_difference::b, sin_cos_range(), and docking::U.

Referenced by cos_of(), and sin_of().

cos_of() [6/6]

template<typename U >

U numeric::cos_of ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c  )

inline

Cosine of angle formed by three consecutive points.

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c.

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and cos_of().

cot()

template<typename T >

T numeric::cot ( T const &  x )

inline

Cotangent.

References pyrosetta.distributed.cluster.exceptions::T, and x.

cross() [1/8]

template<typename T >

xyzTriple< T > numeric::cross	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Cross product.

Referenced by numeric::deriv::angle_p2_deriv(), ccd_angle(), numeric::deriv::dihedral_p1_cosine_deriv_first(), numeric::deriv::dihedral_p2_cosine_deriv_first(), dihedral_radians(), numeric::xyzTransform< T >::from_four_points(), numeric::deriv::helper(), numeric::deriv::p1_theta_deriv(), and sicfast().

cross() [2/8]

template<typename T >

void numeric::cross	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	c
	)

Cross product: Return via argument (slightly faster)

cross() [3/8]

template<typename U >

xyzTriple<U> numeric::cross ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Cross product.

cross() [4/8]

template<typename U >

void numeric::cross ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  c  )

inline

Cross product: Return via argument (slightly faster)

cross() [5/8]

template<typename T >

xyzVector< T > numeric::cross	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Cross product.

cross() [6/8]

template<typename T >

void numeric::cross	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	c
	)

Cross product: Return via argument (slightly faster)

cross() [7/8]

template<typename U >

xyzVector<U> numeric::cross ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Cross product.

cross() [8/8]

template<typename U >

void numeric::cross ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  c  )

inline

Cross product: Return via argument (slightly faster)

cross_product() [1/8]

template<typename T >

xyzTriple< T > numeric::cross_product	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Cross product.

cross_product() [2/8]

template<typename T >

void numeric::cross_product	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	c
	)

Cross product: Return via argument (slightly faster)

cross_product() [3/8]

template<typename U >

xyzTriple<U> numeric::cross_product ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Cross product.

cross_product() [4/8]

template<typename U >

void numeric::cross_product ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  c  )

inline

Cross product: Return via argument (slightly faster)

cross_product() [5/8]

template<typename T >

xyzVector< T > numeric::cross_product	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Cross product.

cross_product() [6/8]

template<typename T >

void numeric::cross_product	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	c
	)

Cross product: Return via argument (slightly faster)

cross_product() [7/8]

template<typename U >

xyzVector<U> numeric::cross_product ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Cross product.

cross_product() [8/8]

template<typename U >

void numeric::cross_product ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  c  )

inline

Cross product: Return via argument (slightly faster)

csc()

template<typename T >

T numeric::csc ( T const &  x )

inline

Cosecant.

References pyrosetta.distributed.cluster.exceptions::T, and x.

Referenced by numeric::BodyPosition< T >::BodyPosition().

cube()

template<typename T >

T numeric::cube ( T const &  x )

inline

cube( x ) == x^3

References x.

cubic_polynomial_deriv()

platform::Real numeric::cubic_polynomial_deriv	(	platform::Real const	x,
		CubicPolynomial const &	cp
	)

Evaluate derivative of cubic polynomial given x and polynomial coefficients.

References x.

cubic_polynomial_from_spline()

CubicPolynomial numeric::cubic_polynomial_from_spline	(	platform::Real	xlo,
		platform::Real	xhi,
		SplineParameters const &	sp
	)

Compute cubic polynomial coefficients from a set of SplineParameters.

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, basic::options::OptionKeys::cp::cp, test.T009_Exceptions::e, create_a3b_hbs::f, numeric::SplineParameters::y2hi, numeric::SplineParameters::y2lo, numeric::SplineParameters::yhi, and numeric::SplineParameters::ylo.

cumulative()

template<class RandomAccessIterator >

void numeric::cumulative	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Converts pdf to cdf.

References create_a3b_hbs::first, create_a3b_hbs::i, and normalize().

deep_copy() [1/3]

template<class T , numeric::Size N>

MathNTensorOP< T, N > numeric::deep_copy

(

MathNTensor< T, N > const &

source

)

References numeric::MathNTensor< T, N >::clone().

deep_copy() [2/3]

template MathNTensorBaseOP< Real > numeric::deep_copy

(

MathNTensorBase< Real > const &

)

Explicit template instantiation, apparently needed for PyRosetta.

deep_copy() [3/3]

template<class T >

MathNTensorBaseOP< T > numeric::deep_copy

(

MathNTensorBase< T > const &

source

)

References numeric::MathNTensorBase< T >::clone().

deserialize()

template<typename T >

xyzVector<T> numeric::deserialize ( utility::json_spirit::mArray  data )

inline

References data, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

dihedral() [1/2]

template<typename T >

T numeric::dihedral	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4
	)

Dihedral (torsion) angle in degrees: angle value returned.

Note

This is a Rosetta++ compatibility version that operates in degrees

References numeric::conversions::degrees(), dihedral_radians(), and p2.

dihedral() [2/2]

template<typename T >

void numeric::dihedral	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4,
		T &	angle
	)

Dihedral (torsion) angle in degrees: angle value passed.

Note

This is a Rosetta++ compatibility version that operates in degrees

References basic::options::OptionKeys::hotspot::angle, dihedral_radians(), p2, and numeric::conversions::to_degrees().

Referenced by dihedral_double(), dock(), fix_alpha_for_pack_phosphate(), main(), and register_options().

dihedral_degrees() [1/2]

template<typename T >

T numeric::dihedral_degrees	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4
	)

Dihedral (torsion) angle in degrees: angle value returned.

References numeric::conversions::degrees(), dihedral_radians(), and p2.

dihedral_degrees() [2/2]

template<typename T >

void numeric::dihedral_degrees	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4,
		T &	angle
	)

Dihedral (torsion) angle in degrees: angle value passed.

References basic::options::OptionKeys::hotspot::angle, dihedral_radians(), p2, and numeric::conversions::to_degrees().

Referenced by addcyclicconstraints(), align_carboxyl_m8(), align_native_state(), alncys(), ZincMatchFilter::apply(), calc_c3_rmsd(), ch_o_pdbstats_from_pose(), Tet4HMatchAligner::checkalign(), dihedral_degrees_double(), find_dsf(), fix_cyclic_termini(), generate_disulfide_conformations(), get_cys_rts(), Link::get_phi(), Link::get_psi(), get_rmsd(), get_rmsd_debug(), gpu_refold_test(), ik_his_clamp(), main(), my_main(), pdb_stats(), perturb_bb_and_relax(), pose2bin(), DisulfideBondEnergy::probability(), run(), run_diiron_glu(), run_sf4h(), set_disulf(), Link::set_phi(), Link::set_psi(), store_backbone(), storeposedata(), apps::public1::scenarios::chemically_conjugated_docking::ubq_ras_rotation_angle(), CovalentPeptidomimeticDockDesign::update_hydrogens(), and CovalentPeptidomimeticCreator::update_hydrogens().

dihedral_degrees_double() [1/2]

double numeric::dihedral_degrees_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4  )

inline

References dihedral_degrees(), and p2.

dihedral_degrees_double() [2/2]

void numeric::dihedral_degrees_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4, double &  angle  )

inline

References basic::options::OptionKeys::hotspot::angle, dihedral_degrees(), and p2.

dihedral_double() [1/2]

double numeric::dihedral_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4  )

inline

References dihedral(), and p2.

dihedral_double() [2/2]

void numeric::dihedral_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4, double &  angle  )

inline

References basic::options::OptionKeys::hotspot::angle, dihedral(), and p2.

dihedral_radians() [1/2]

template<typename T >

T numeric::dihedral_radians	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4
	)

Dihedral (torsion) angle in radians: angle value returned.

Note

Given four positions in a chain ( p1, p2, p3, p4 ), calculates the dihedral (torsion) angle in radians between the vectors p2->p1 and p3->p4 while sighting along the axis defined by the vector p2->p3 (positive indicates right handed twist)

Angle returned is on [ -pi, pi ]

Degenerate cases are handled and assigned a zero angle but assumed rare (wrt performance tuning)

For a reference on the determination of the dihedral angle formula see: http://www.math.fsu.edu/~quine/IntroMathBio_04/torsion_pdb/torsion_pdb.pdf

References basic::options::OptionKeys::hotspot::angle, dihedral_radians(), and p2.

dihedral_radians() [2/2]

template<typename T >

void numeric::dihedral_radians	(	xyzVector< T > const &	p1,
		xyzVector< T > const &	p2,
		xyzVector< T > const &	p3,
		xyzVector< T > const &	p4,
		T &	angle
	)

Dihedral (torsion) angle in radians: angle value passed.

Note

Given four positions in a chain ( p1, p2, p3, p4 ), calculates the dihedral (torsion) angle in radians between the vectors p2->p1 and p3->p4 while sighting along the axis defined by the vector p2->p3 (positive indicates right handed twist)

Angle returned is on [ -pi, pi ]

Degenerate cases are handled and assigned a zero angle but assumed rare (wrt performance tuning)

For a reference on the determination of the dihedral angle formula see: http://www.math.fsu.edu/~quine/IntroMathBio_04/torsion_pdb/torsion_pdb.pdf

References a, basic::options::OptionKeys::hotspot::angle, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, cross(), dot(), p2, x, and predPRE::y.

Referenced by dihedral(), dihedral_degrees(), numeric::deriv::dihedral_deriv_second(), dihedral_radians(), dihedral_radians_double(), gpu_refold_test(), main(), minimize_test(), print_internal_coord_test(), set_loop_conformation(), and write_chi_to_db().

dihedral_radians_double() [1/2]

double numeric::dihedral_radians_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4  )

inline

References dihedral_radians(), and p2.

dihedral_radians_double() [2/2]

void numeric::dihedral_radians_double ( xyzVector< double > const &  p1, xyzVector< double > const &  p2, xyzVector< double > const &  p3, xyzVector< double > const &  p4, double &  angle  )

inline

References basic::options::OptionKeys::hotspot::angle, dihedral_radians(), and p2.

distance() [1/3]

template<typename T >

T numeric::distance ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

distance between two MathVectors A->B

References measure_params::norm().

Referenced by numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >::all_matches_below_threshold(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >::closest_match(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >::closest_match_subset(), numeric::deriv::distance_f1_f2_deriv(), numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >::first_match(), main(), and numeric::random::uniform_vector_sphere().

distance() [2/3]

template<typename T >

T numeric::distance	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Distance.

distance() [3/3]

template<typename U >

U numeric::distance ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Distance.

distance_squared() [1/2]

template<typename T >

T numeric::distance_squared	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Distance squared.

Referenced by CountContact::apply(), InterfaceStrandFinderMover::bb_score(), ExposedStrandMover::bb_score(), HDmakerMover::bb_score(), best_beta_backbones::bump_check(), ClashCheck::clash_check(), MatchSet::clash_check(), clash_check_bb(), ClashCheck::clash_check_naive(), MatchSet::clash_check_naive(), clashcheck(), clashcheckhalf(), count_int_CBs_clashes(), ddg(), dock(), PoseWrap::dump_pdb(), pyrosetta.toolbox.atom_pair_energy::etable_atom_pair_energies(), Bola::get_target_distance(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), main(), place_sf4(), repack_iface(), run(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), test(), and PoseWrap::update_designable_packable().

distance_squared() [2/2]

template<typename U >

U numeric::distance_squared ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Distance squared.

divide() [1/4]

template<typename T >

void numeric::divide	(	xyzTriple< T > const &	v,
		T const &	t,
		xyzTriple< T > &	r
	)

Divide: xyzTriple / T.

divide() [2/4]

template<typename U >

void numeric::divide ( xyzTriple< U > const &  v, U const &  t, xyzTriple< U > &  r  )

inline

Divide: xyzTriple / Value.

divide() [3/4]

template<typename T >

void numeric::divide	(	xyzVector< T > const &	v,
		T const &	t,
		xyzVector< T > &	r
	)

Divide: xyzVector / T.

divide() [4/4]

template<typename U >

void numeric::divide ( xyzVector< U > const &  v, U const &  t, xyzVector< U > &  r  )

inline

Divide: xyzVector / Value.

do_abs()

double numeric::do_abs

(

double

a

)

References a, and ObjexxFCL::abs().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_add_symbol()

void numeric::do_add_symbol	(	CalculatorParser &	cp,
		std::string	name,
		double	value
	)

References value.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_cos()

double numeric::do_cos

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_exp()

double numeric::do_exp

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_ln()

double numeric::do_ln

(

double

a

)

References a, and log().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_log()

double numeric::do_log	(	double	a,
		double	b
	)

References a, compute_difference::b, and log().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_log10()

double numeric::do_log10

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_log2()

double numeric::do_log2

(

double

a

)

References a, and log().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_max()

double numeric::do_max

(

std::vector< double >

a

)

References a, and max().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_mean()

double numeric::do_mean

(

std::vector< double >

a

)

References a, and mean().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_median()

double numeric::do_median

(

std::vector< double >

a

)

References a, and median().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_min()

double numeric::do_min

(

std::vector< double >

a

)

References a, and min().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_pow()

double numeric::do_pow	(	double	a,
		double	b
	)

References a, compute_difference::b, and ObjexxFCL::pow().

Referenced by numeric::CalculatorParser::CalculatorParser().

do_sin()

double numeric::do_sin

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_sqrt()

double numeric::do_sqrt

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

do_tan()

double numeric::do_tan

(

double

a

)

References a.

Referenced by numeric::CalculatorParser::CalculatorParser().

dot() [1/4]

template<typename T >

T numeric::dot	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Dot product.

Referenced by numeric::deriv::angle_p1_deriv(), numeric::deriv::angle_p1_p2_p3_deriv(), numeric::deriv::angle_p2_deriv(), angle_radians(), ccd_angle(), numeric::deriv::dihedral_p1_cosine_deriv_first(), numeric::deriv::dihedral_p2_cosine_deriv_first(), dihedral_radians(), numeric::xyzTransform< T >::intersect3D_2Planes(), numeric::deriv::p1_theta_deriv(), sicfast(), numeric::HomogeneousTransform< T >::to_local_coordinate(), and numeric::deriv::x_and_dtheta_dx().

dot() [2/4]

template<typename U >

U numeric::dot ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Dot product.

dot() [3/4]

template<typename T >

T numeric::dot	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Distance.

Distance squared

Dot product

dot() [4/4]

template<typename U >

U numeric::dot ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Dot product.

dot_product() [1/3]

template<typename T >

T numeric::dot_product	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Dot product.

dot_product() [2/3]

template<typename U >

U numeric::dot_product ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Dot product.

dot_product() [3/3]

template<typename T >

T numeric::dot_product	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Dot product.

References a, and compute_difference::b.

eigenvalue_jacobi()

template<typename T >

xyzVector< T > numeric::eigenvalue_jacobi	(	xyzMatrix< T > const &	a,
		T const &	tol
	)

Classic Jacobi algorithm for the eigenvalues of a real symmetric matrix.

Note

Use eigenvector_jacobi if eigenvectors are also desired

eigenvector_jacobi()

template<typename T >

xyzVector< T > numeric::eigenvector_jacobi	(	xyzMatrix< T > const &	a,
		T const &	tol,
		xyzMatrix< T > &	J
	)

Classic Jacobi algorithm for the eigenvalues and eigenvectors of a real symmetric matrix.

Note

Use eigenvalue_jacobi if eigenvectors are not desired

Referenced by numeric::model_quality::findUU(), get_euler_axes(), get_reflection_axis(), pca_align_BROKEN(), and principal_components_and_eigenvalues().

eq_tol()

template<typename T >

bool numeric::eq_tol ( T const &  x, T const &  y, T const &  r_tol, T const &  a_tol  )

inline

Equal within specified relative and absolute tolerances?

References ObjexxFCL::abs(), max(), min(), pyrosetta.distributed.cluster.exceptions::T, x, and predPRE::y.

Referenced by numeric::interpolation::bilinearly_interpolated(), and numeric::interpolation::Histogram< X, Y >::set_params().

equal_by_epsilon()

bool numeric::equal_by_epsilon ( numeric::Real  value1, numeric::Real  value2, numeric::Real  epsilon  )

inline

are two Real values are equal up to some epsilon

implemented only for Reals, to prevent unsigned hassle (Barak 30/6/2009)

equal_length() [1/4]

template<typename T >

bool numeric::equal_length	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Equal length?

equal_length() [2/4]

template<typename U >

bool numeric::equal_length ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Equal length?

equal_length() [3/4]

template<typename T >

bool numeric::equal_length	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Equal length?

equal_length() [4/4]

template<typename U >

bool numeric::equal_length ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Equal length?

euler_angles_from_rotation_matrix_ZXZ()

template<typename T >

xyzVector<T> numeric::euler_angles_from_rotation_matrix_ZXZ ( xyzMatrix< T > const &  rotM )

inline

References ObjexxFCL::abs(), angles_between_0_180(), test.T009_Exceptions::e, numeric::NumericTraits< T >::pi(), numeric::NumericTraits< T >::pi_over_180(), and sin_cos_range().

euler_angles_from_rotation_matrix_ZYX()

template<typename T >

xyzVector<T> numeric::euler_angles_from_rotation_matrix_ZYX ( xyzMatrix< T > const &  rotM )

inline

References ObjexxFCL::abs(), angles_between_0_180(), test.T009_Exceptions::e, numeric::NumericTraits< T >::pi_over_180(), numeric::NumericTraits< T >::pi_over_2(), and sin_cos_range().

euler_angles_from_rotation_matrix_ZYZ()

template<typename T >

xyzVector<T> numeric::euler_angles_from_rotation_matrix_ZYZ ( xyzMatrix< T > const &  rotM )

inline

References ObjexxFCL::abs(), angles_between_0_180(), test.T009_Exceptions::e, numeric::NumericTraits< T >::pi(), numeric::NumericTraits< T >::pi_over_180(), and sin_cos_range().

eval_cubic_polynomial()

platform::Real numeric::eval_cubic_polynomial ( platform::Real const  x, CubicPolynomial const &  cp  )

inline

Evaluate cubic polynomial at value x given polynomial coefficients.

References x.

expand_xforms() [1/2]

template<typename T , class OutputIterator >

void numeric::expand_xforms	(	OutputIterator	container,
		xyzTransform< T > const &	G1,
		xyzTransform< T > const &	G2,
		int	N = 5,
		Real	r = 9e9,
		xyzVector< T > const &	test_point = xyzVector<T>(Real(1.0),Real(3.0),Real(10.0))
	)

References expand_xforms(), N, and create_a3b_hbs::r.

expand_xforms() [2/2]

template<typename T , class OutputIterator >

void numeric::expand_xforms	(	OutputIterator	container,
		xyzTransform< T > const &	G1,
		xyzTransform< T > const &	G2,
		xyzTransform< T > const &	,
		int	N = 5,
		Real	r = 9e9,
		xyzVector< T > const &	test_point = xyzVector<T>(Real(1.0),Real(3.0),Real(10.0))
	)

References create_a3b_hbs::i, test.T110_numeric::I, N, create_a3b_hbs::r, and x.

Referenced by TCDock::dump_pdb(), and expand_xforms().

factorial()

template<typename T >

T numeric::factorial

(

T const &

N

)

Calculate the value of N!.

Dangerous for large values of N. Uses a recursive algorithm – might not be efficient and can't be inlined.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References N.

FArray_to_vector_of_xyzvectors()

template<typename T >

utility::vector1< xyzVector<T> > numeric::FArray_to_vector_of_xyzvectors ( ObjexxFCL::FArray2D< T > const &  input )

inline

convert an FArray2D to a vector of xyzVectors

References gaussian-sampling::input, enumerate_junctions::int, bin_torsions::output, x, predPRE::y, and predPRE::z.

Referenced by numeric::model_quality::findUU().

FArray_to_xyzmatrix()

template<typename T >

numeric::xyzMatrix<T> numeric::FArray_to_xyzmatrix ( ObjexxFCL::FArray2D< T > const &  input )

inline

convert a 3x3 FArray 2D to an xyzMatrix

References gaussian-sampling::input, and numeric::xyzMatrix< T >::rows().

Referenced by numeric::model_quality::findUU().

fast_remainder()

template<typename T >

T numeric::fast_remainder ( T const &  x, T const &  y  )

inline

Remainder of x with respect to division by y that is of smallest magnitude.

Note

Emulates the C99 remainder function except for rounding halfway values to even multiples

Returns zero if y is zero

Return value has magnitude <= | y / 2 |

References x, and predPRE::y.

find_nearest_value() [1/2]

template<typename T >

T numeric::find_nearest_value	(	typename utility::vector1< T > const &	input_list,
		T	key
	)

given a vector and an input value, return the value in the vector that is closest to the input This is a wrapper for find_nearest_value(input_list,key,min,max) and insures that you're sorted.

References subloop_histogram::key.

find_nearest_value() [2/2]

template<typename T >

T numeric::find_nearest_value	(	typename utility::vector1< T > const &	input_list,
		T	key,
		platform::Size	min_index,
		platform::Size	max_index
	)

recursive binary search that finds the value closest to key. Call find_nearest_value(input_list,value) instead. It's the driver function for this function. This fails miserably (and silently!) on a non-sorted vector, so don't do that!.

References ObjexxFCL::abs(), subloop_histogram::key, basic::options::OptionKeys::max_distance, and min_index().

first_principal_component()

template<typename T >

xyzVector< T > numeric::first_principal_component ( utility::vector1< xyzVector< T > > const &  coords )

inline

return the first principal component of the given set of points

References principal_components().

from_json()

template<typename T >

void numeric::from_json	(	const nlohmann::json &	j,
		xyzVector< T > &	v
	)

References create_a3b_hbs::j, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

gcd()

template<typename T >

T numeric::gcd ( T const &  m, T const &  n  )

inline

Greatest common divisor.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, max(), min(), mod(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and pyrosetta.distributed.cluster.exceptions::T.

Referenced by count_analytically_cyclic(), and count_analytically_improper_rotational().

ge_tol()

template<typename T >

bool numeric::ge_tol ( T const &  x, T const &  y, T const &  r_tol, T const &  a_tol  )

inline

Greater than or equal within specified relative and absolute tolerances?

References ObjexxFCL::abs(), max(), min(), pyrosetta.distributed.cluster.exceptions::T, x, and predPRE::y.

get_cluster_data()

template<class T >

void numeric::get_cluster_data	(	utility::vector1< T > &	data_in,
		ClusteringTreeNodeOP	cluster,
		utility::vector1< T > &	data_out
	)

References basic::options::OptionKeys::optE::data_in, basic::options::OptionKeys::optE::data_out, and create_a3b_hbs::i.

Referenced by main().

get_Real_MathNTensor_dimension_size()

Size numeric::get_Real_MathNTensor_dimension_size	(	MathNTensorBaseCOP< Real >	tensorbase,
		Size const	dimension_index
	)

Given a MathNTensorBaseCOP, get the size along one dimension.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References enumerate_junctions::default, utility::pointer::dynamic_pointer_cast(), runtime_assert, runtime_assert_string_msg, and utility_exit_with_message.

gt_tol()

template<typename T >

bool numeric::gt_tol ( T const &  x, T const &  y, T const &  r_tol, T const &  a_tol  )

inline

Greater than within specified relative and absolute tolerances?

References ObjexxFCL::abs(), max(), min(), pyrosetta.distributed.cluster.exceptions::T, x, and predPRE::y.

hsv_to_rgb() [1/2]

numeric::xyzVector< platform::Real > numeric::hsv_to_rgb

(

numeric::xyzVector< platform::Real >

hsv_triplet

)

convert an HSV color to RGB

References enumerate_junctions::default, create_a3b_hbs::f, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, enumerate_junctions::q, predPRE::t, value, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

hsv_to_rgb() [2/2]

numeric::xyzVector< platform::Real > numeric::hsv_to_rgb	(	platform::Real	h,
		platform::Real	s,
		platform::Real	v
	)

convert an HSV color to RGB

References h, docking::s, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

in_sin_cos_range()

template<typename T >

bool numeric::in_sin_cos_range ( T const &  x, T const &  tol = T( .001 )  )

inline

Is a sine or cosine value within a specified tolerance of the valid [-1,1] range?

References pyrosetta.distributed.cluster.exceptions::T, loops_kic::tol, and x.

inner_product() [1/4]

template<typename T >

T numeric::inner_product	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Inner product ( == dot product )

Referenced by hd(), and numeric::MathVector< T >::square_norm().

inner_product() [2/4]

template<typename U >

U numeric::inner_product ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Inner product ( == dot product )

inner_product() [3/4]

template<typename T >

T numeric::inner_product	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Inner product ( == dot product )

inner_product() [4/4]

template<typename U >

U numeric::inner_product ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Inner product ( == dot product )

inplace_product()

template<typename T >

xyzVector< T >& numeric::inplace_product	(	xyzMatrix< T > const &	m,
		xyzVector< T > &	v
	)

xyzMatrix * xyzVector in-place product

Note

Input xyzVector is modified

Referenced by numeric::BodyPosition< T >::invert(), numeric::BodyPosition< T >::operator()(), and numeric::BodyPosition< T >::transform().

inplace_transpose_product()

template<typename T >

xyzVector< T >& numeric::inplace_transpose_product	(	xyzMatrix< T > const &	m,
		xyzVector< T > &	v
	)

xyzMatrix^T * xyzVector in-place transpose product

Note

Input xyzVector is modified

Referenced by numeric::BodyPosition< T >::inverse_transform().

inverse()

template<typename T >

xyzMatrix< T > numeric::inverse

(

xyzMatrix< T > const &

a

)

Referenced by alignVectorSets(), CrystFFTDock::apply(), CrystFFTDock::do_convolution(), generate_from_fiber(), get_primary_point_group(), CrystFFTDock::get_transform_distance(), numeric::linear_algebra::minimum_bounding_ellipse(), numeric::UniformRotationSampler::remove_redundant(), CrystFFTDock::resample_maps_and_get_self(), Spacegroup::set_parameters(), and slice_ellipsoid_envelope().

jacobi_rotation()

template<typename T >

void numeric::jacobi_rotation	(	xyzMatrix< T > const &	m,
		int const	i,
		int const	j,
		xyzMatrix< T > &	r
	)

Jacobi rotation.

Note

Compute the orthogonal transformation used to zero out a pair of off-diagonal elements

References ObjexxFCL::abs(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::r, docking::s, and predPRE::t.

le_tol()

template<typename T >

bool numeric::le_tol ( T const &  x, T const &  y, T const &  r_tol, T const &  a_tol  )

inline

Less than or equal within specified relative and absolute tolerances?

References ObjexxFCL::abs(), max(), min(), pyrosetta.distributed.cluster.exceptions::T, x, and predPRE::y.

linear_interpolate()

template<class Value >

double numeric::linear_interpolate	(	Value	start,
		Value	stop,
		unsigned	curr_stage,
		unsigned	num_stages
	)

Linearly interpolates a quantity from start to stop over (num_stages + 1) stages.

References basic::options::OptionKeys::cutoutdomain::start.

log()

double numeric::log ( double  x, double  base  )

inline

Computes log(x) in the given base.

References test.T005_Bindings::base, and x.

Referenced by CountContact::apply(), PairDistance::apply(), ScTrials::apply(), calc_sequence_score(), calculate_binding_energy(), capri15_relax(), compute_bb_motif_score(), numeric::random::WeightedReservoirSampler< T >::consider_sample(), correct_rama(), dinucleotide_test(), do_ln(), do_log(), do_log2(), do_the_match(), each_aa_test(), DisulfideBondEnergy::evaluate(), numeric::random::RandomGenerator::gaussian(), pyrosetta.distributed.utility.log.ProgressLogger::increment(), numeric::statistics::kl_divergence(), pyrosetta.distributed.utility.log::log_method(), main(), mathntensor_from_dist(), motif_column_deviation(), DisulfideBondEnergy::rebuildAndDetectDisulfideBond(), core::pack::annealer::FixbbSimAnnealer::run(), score_rnp(), sidechain_sample(), sigmoid_train(), DisulfideBondEnergy::tabulate(), and numeric::statistics::w().

lt_tol()

template<typename T >

bool numeric::lt_tol ( T const &  x, T const &  y, T const &  r_tol, T const &  a_tol  )

inline

Less than within specified relative and absolute tolerances?

References ObjexxFCL::abs(), max(), min(), pyrosetta.distributed.cluster.exceptions::T, x, and predPRE::y.

MakeVector() [1/3]

template<typename T >

MathVector< T > numeric::MakeVector

(

T const &

X

)

Referenced by numeric::interpolation::spline::BicubicSpline::F(), and numeric::interpolation::spline::BicubicSpline::FdF().

MakeVector() [2/3]

template<typename T >

MathVector< T > numeric::MakeVector ( T const &  X, T const &  Y  )

inline

Returns

construct MathVectors from two elements

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::Y.

MakeVector() [3/3]

template<typename T >

MathVector< T > numeric::MakeVector ( T const &  X, T const &  Y, T const &  Z  )

inline

Returns

construct MathVectors from three elements

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::Y.

max() [1/18]

double numeric::max ( double const  a, double const  b  )

inline

max( double, double )

References a, and compute_difference::b.

max() [2/18]

float numeric::max ( float const  a, float const  b  )

inline

max( float, float )

References a, and compute_difference::b.

max() [3/18]

int numeric::max ( int const  a, int const  b  )

inline

max( int, int )

References a, and compute_difference::b.

max() [4/18]

long double numeric::max ( long double const  a, long double const  b  )

inline

max( long double, long double )

References a, and compute_difference::b.

max() [5/18]

long int numeric::max ( long int const  a, long int const  b  )

inline

max( long int, long int )

References a, and compute_difference::b.

max() [6/18]

short int numeric::max ( short int const  a, short int const  b  )

inline

max( short int, short int )

References a, and compute_difference::b.

Referenced by abs_difference(), align_sf4(), align_zns(), alignaxis(), numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), numeric::CompleteLinkClusterer::comparator(), convex_hull(), do_max(), dock(), doit(), PoseWrap::dump_pdb(), eq_tol(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), find_farthest(), gcd(), ge_tol(), generate_combined_model(), get_nearest_loop_to_helix(), get_second_2_helices(), gt_tol(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::init(), MatchSet::init_clash_check(), ClashCheck::init_clash_check(), le_tol(), lt_tol(), max(), numeric::linear_algebra::minimum_bounding_ellipse(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), place_zns(), run(), run_tyr_his(), numeric::kinematic_closure::sbisect(), numeric::interpolation::Histogram< X, Y >::set_params(), sicfast(), numeric::kinematic_closure::solve_sturm(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), and numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit_lax().

max() [7/18]

template<typename T >

T const& numeric::max ( T const &  a, T const &  b, T const &  c  )

inline

max( a, b, c )

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

max() [8/18]

template<typename T >

T const& numeric::max ( T const &  a, T const &  b, T const &  c, T const &  d  )

inline

max( a, b, c, d )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and max().

max() [9/18]

template<typename T >

T const& numeric::max ( T const &  a, T const &  b, T const &  c, T const &  d, T const &  e  )

inline

max( a, b, c, d, e )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, max(), and max().

max() [10/18]

template<typename T >

T const& numeric::max ( T const &  a, T const &  b, T const &  c, T const &  d, T const &  e, T const &  f  )

inline

max( a, b, c, d, e, f )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, create_a3b_hbs::f, max(), and max().

max() [11/18]

unsigned int numeric::max ( unsigned int const  a, unsigned int const  b  )

inline

max( unsigned int, unsigned int )

References a, and compute_difference::b.

max() [12/18]

unsigned long int numeric::max ( unsigned long int const  a, unsigned long int const  b  )

inline

max( unsigned long int, unsigned long int )

References a, and compute_difference::b.

max() [13/18]

unsigned short int numeric::max ( unsigned short int const  a, unsigned short int const  b  )

inline

max( unsigned short int, unsigned short int )

References a, and compute_difference::b.

max() [14/18]

template<typename T >

T numeric::max

(

utility::vector1< T > const &

values

)

References create_a3b_hbs::ii, max(), and test.T040_Types::values.

max() [15/18]

template<typename T >

xyzTriple< T > numeric::max	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple with max coordinates of two xyzTriples

max() [16/18]

template<typename U >

xyzTriple<U> numeric::max ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

xyzTriple with max coordinates of two xyzTriples

max() [17/18]

template<typename T >

xyzVector< T > numeric::max	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector with max coordinates of two xyzVectors

max() [18/18]

template<typename U >

xyzVector<U> numeric::max ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

xyzVector with max coordinates of two xyzVectors

mean()

numeric::Real numeric::mean

(

utility::vector1< numeric::Real > const &

values

)

References value, and test.T040_Types::values.

Referenced by calc_zscore(), and do_mean().

median()

numeric::Real numeric::median

(

utility::vector1< numeric::Real > const &

values

)

Returns the median from a vector1 of Real values.

References test.T040_Types::values.

Referenced by do_median(), and main().

midpoint() [1/8]

template<typename T >

xyzTriple< T > numeric::midpoint	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Midpoint of 2 xyzTriples.

Referenced by HDmakerMover::apply(), HDmakerMover::find_midpoint(), fit_helix_in_map(), zinc_stats::ZincStatisticGenerator::recursively_model_rotamer_chis(), and zinc2_homodimer_setup::rollmove_to_inverse_C2_symmetry().

midpoint() [2/8]

template<typename T >

void numeric::midpoint	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	m
	)

Midpoint of 2 xyzTriples: Return via argument (slightly faster)

midpoint() [3/8]

template<typename U >

xyzTriple<U> numeric::midpoint ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Midpoint of 2 xyzTriples.

midpoint() [4/8]

template<typename U >

void numeric::midpoint ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  m  )

inline

Midpoint of 2 xyzTriples: Return via argument (slightly faster)

midpoint() [5/8]

template<typename T >

xyzVector< T > numeric::midpoint	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Midpoint of 2 xyzVectors.

midpoint() [6/8]

template<typename T >

void numeric::midpoint	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	m
	)

Midpoint of 2 xyzVectors: Return via argument (slightly faster)

midpoint() [7/8]

template<typename U >

xyzVector<U> numeric::midpoint ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Midpoint of 2 xyzVectors.

midpoint() [8/8]

template<typename U >

void numeric::midpoint ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  m  )

inline

Midpoint of 2 xyzVectors: Return via argument (slightly faster)

min() [1/18]

double numeric::min ( double const  a, double const  b  )

inline

min( double, double )

References a, and compute_difference::b.

min() [2/18]

float numeric::min ( float const  a, float const  b  )

inline

min( float, float )

References a, and compute_difference::b.

min() [3/18]

int numeric::min ( int const  a, int const  b  )

inline

min( int, int )

References a, and compute_difference::b.

min() [4/18]

long double numeric::min ( long double const  a, long double const  b  )

inline

min( long double, long double )

References a, and compute_difference::b.

min() [5/18]

long int numeric::min ( long int const  a, long int const  b  )

inline

min( long int, long int )

References a, and compute_difference::b.

min() [6/18]

short int numeric::min ( short int const  a, short int const  b  )

inline

min( short int, short int )

References a, and compute_difference::b.

Referenced by abs_difference(), add_symm_zns(), align_sf4(), align_zns(), alignaxis(), MatchSet::c2_linker_check_dist(), calculate_helical_parameters_helper(), numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), convex_hull(), do_min(), dock(), doit(), eq_tol(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), find_closest(), gcd(), ge_tol(), generate_combined_model(), get_second_2_helices(), gt_tol(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::init(), MatchSet::init_clash_check(), ClashCheck::init_clash_check(), le_tol(), lt_tol(), min(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), place_zns(), Bola::random_close_phipsi_from_rama(), rg2d(), DisulfEpos::rms(), run_tyr_his(), numeric::kinematic_closure::sbisect(), numeric::interpolation::Histogram< X, Y >::set_params(), sicfast(), numeric::kinematic_closure::solve_sturm(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), and numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit_lax().

min() [7/18]

template<typename T >

T const& numeric::min ( T const &  a, T const &  b, T const &  c  )

inline

min( a, b, c )

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

min() [8/18]

template<typename T >

T const& numeric::min ( T const &  a, T const &  b, T const &  c, T const &  d  )

inline

min( a, b, c, d )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and min().

min() [9/18]

template<typename T >

T const& numeric::min ( T const &  a, T const &  b, T const &  c, T const &  d, T const &  e  )

inline

min( a, b, c, d, e )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, min(), and min().

min() [10/18]

template<typename T >

T const& numeric::min ( T const &  a, T const &  b, T const &  c, T const &  d, T const &  e, T const &  f  )

inline

min( a, b, c, d, e, f )

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, create_a3b_hbs::f, min(), and min().

min() [11/18]

unsigned int numeric::min ( unsigned int const  a, unsigned int const  b  )

inline

min( unsigned int, unsigned int )

References a, and compute_difference::b.

min() [12/18]

unsigned long int numeric::min ( unsigned long int const  a, unsigned long int const  b  )

inline

min( unsigned long int, unsigned long int )

References a, and compute_difference::b.

min() [13/18]

unsigned short int numeric::min ( unsigned short int const  a, unsigned short int const  b  )

inline

min( unsigned short int, unsigned short int )

References a, and compute_difference::b.

min() [14/18]

template<typename T >

T numeric::min

(

utility::vector1< T > const &

values

)

References create_a3b_hbs::ii, min(), and test.T040_Types::values.

min() [15/18]

template<typename T >

xyzTriple< T > numeric::min	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple with min coordinates of two xyzTriples

min() [16/18]

template<typename U >

xyzTriple<U> numeric::min ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

xyzTriple with min coordinates of two xyzTriples

min() [17/18]

template<typename T >

xyzVector< T > numeric::min	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector with min coordinates of two xyzVectors

min() [18/18]

template<typename U >

xyzVector<U> numeric::min ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

xyzVector with min coordinates of two xyzVectors

mod()

template<typename T >

T numeric::mod ( T const &  x, T const &  y  )

inline

x(mod y) computational modulo returning magnitude < | y | and sign of x

Note

When used with negative integer arguments this assumes integer division rounds towards zero (de facto and future official standard)

References x, and predPRE::y.

Referenced by bin_angle(), gcd(), numeric::interpolation::InterpolatedPotential< N >::get_indices(), JDmover::periodic_range(), numeric::RemainderSelector< T, bool >::remainder(), and numeric::RemainderSelector< T, true >::remainder().

modulo()

template<typename T >

T numeric::modulo ( T const &  x, T const &  y  )

inline

x(mod y) mathematical modulo returning magnitude < | y | and sign of y

References x, and predPRE::y.

Referenced by angles_between_0_180(), numeric::interpolation::periodic_range::full::bilinearly_interpolated(), numeric::interpolation::periodic_range::half::bilinearly_interpolated(), numeric::interpolation::periodic_range::full::bin(), numeric::interpolation::periodic_range::half::bin(), numeric::interpolation::Histogram< X, Y >::bin_number(), numeric::interpolation::periodic_range::full::interpolated(), numeric::interpolation::periodic_range::half::interpolated(), nonnegative_principal_angle(), nonnegative_principal_angle_degrees(), and nonnegative_principal_angle_radians().

multiply() [1/8]

template<typename T >

void numeric::multiply	(	T const &	t,
		xyzTriple< T > const &	v,
		xyzTriple< T > &	r
	)

Multiply: T * xyzTriple.

multiply() [2/8]

template<typename T >

void numeric::multiply	(	T const &	t,
		xyzVector< T > const &	v,
		xyzVector< T > &	r
	)

Multiply: T * xyzVector.

multiply() [3/8]

template<typename U >

void numeric::multiply ( U const &  t, xyzTriple< U > const &  v, xyzTriple< U > &  r  )

inline

Multiply: Value * xyzTriple.

multiply() [4/8]

template<typename U >

void numeric::multiply ( U const &  t, xyzVector< U > const &  v, xyzVector< U > &  r  )

inline

Multiply: Value * xyzVector.

multiply() [5/8]

template<typename T >

void numeric::multiply	(	xyzTriple< T > const &	v,
		T const &	t,
		xyzTriple< T > &	r
	)

Multiply: xyzTriple * T.

multiply() [6/8]

template<typename U >

void numeric::multiply ( xyzTriple< U > const &  v, U const &  t, xyzTriple< U > &  r  )

inline

Multiply: xyzTriple * Value.

multiply() [7/8]

template<typename T >

void numeric::multiply	(	xyzVector< T > const &	v,
		T const &	t,
		xyzVector< T > &	r
	)

Multiply: xyzVector * T.

multiply() [8/8]

template<typename U >

void numeric::multiply ( xyzVector< U > const &  v, U const &  t, xyzVector< U > &  r  )

inline

Multiply: xyzVector * Value.

nearest()

template<typename R , typename T >

R numeric::nearest ( T const &  x )

inline

nearest< R >( x ): Nearest R

References docking::R, pyrosetta.distributed.cluster.exceptions::T, and x.

Referenced by numeric::kdtree::nearest_neighbor(), and numeric::kdtree::nearest_neighbors().

nearest_angle()

template<typename T >

T numeric::nearest_angle ( T const &  angle, T const &  base_angle  )

inline

Nearest periodic value of angle to a base angle in radians.

References basic::options::OptionKeys::hotspot::angle, nearest_ssize(), and numeric::NumericTraits< T >::pi_2().

nearest_angle_degrees()

template<typename T >

T numeric::nearest_angle_degrees ( T const &  angle, T const &  base_angle  )

inline

Nearest periodic value of angle to a base angle in degrees.

References basic::options::OptionKeys::hotspot::angle, nearest_ssize(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by compare_torsion_rmsd().

nearest_angle_radians()

template<typename T >

T numeric::nearest_angle_radians ( T const &  angle, T const &  base_angle  )

inline

Nearest periodic value of angle to a base angle in radians.

References basic::options::OptionKeys::hotspot::angle, nearest_ssize(), and numeric::NumericTraits< T >::pi_2().

Referenced by dump_pose_diff().

nearest_int()

template<typename T >

int numeric::nearest_int ( T const &  x )

inline

nearest_int( x ): Nearest int

References sign(), pyrosetta.distributed.cluster.exceptions::T, and x.

nearest_size()

template<typename T >

std::size_t numeric::nearest_size ( T const &  x )

inline

nearest_size( x ): Nearest std::size_t

References sign(), pyrosetta.distributed.cluster.exceptions::T, and x.

nearest_ssize()

template<typename T >

SSize numeric::nearest_ssize ( T const &  x )

inline

nearest_ssize( x ): Nearest SSize

References sign(), pyrosetta.distributed.cluster.exceptions::T, and x.

Referenced by numeric::interpolation::periodic_range::half::bin(), numeric::FastRemainderSelector< T, bool >::fast_remainder(), numeric::FastRemainderSelector< T, true >::fast_remainder(), nearest_angle(), nearest_angle_degrees(), nearest_angle_radians(), numeric::RemainderSelector< T, bool >::remainder(), and numeric::RemainderSelector< T, true >::remainder().

nint()

template<typename T >

int numeric::nint ( T const &  x )

inline

nint( x ): Nearest int

References sign(), pyrosetta.distributed.cluster.exceptions::T, and x.

nonnegative_principal_angle()

template<typename T >

T numeric::nonnegative_principal_angle ( T const &  angle )

inline

Positive principal value of angle in radians on [ 0, 2*pi )

References basic::options::OptionKeys::hotspot::angle, and modulo().

nonnegative_principal_angle_degrees()

template<typename T >

T numeric::nonnegative_principal_angle_degrees ( T const &  angle )

inline

Positive principal value of angle in degrees on [ 0, 360 )

References basic::options::OptionKeys::hotspot::angle, modulo(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by get_omgphipsi_bins(), get_symm_corrected_angle(), main(), and symmetrize_map().

nonnegative_principal_angle_radians()

template<typename T >

T numeric::nonnegative_principal_angle_radians ( T const &  angle )

inline

Positive principal value of angle in radians on [ 0, 2*pi )

References basic::options::OptionKeys::hotspot::angle, and modulo().

normalize()

template<class InputIterator >

void numeric::normalize	(	InputIterator	first,
		InputIterator	last
	)

Normalizes elements on the range [first, last)

References create_a3b_hbs::first, and sum().

Referenced by cumulative(), and product().

not_equal_length() [1/4]

template<typename T >

bool numeric::not_equal_length	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Not equal length?

not_equal_length() [2/4]

template<typename U >

bool numeric::not_equal_length ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Not equal length?

not_equal_length() [3/4]

template<typename T >

bool numeric::not_equal_length	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

Not equal length?

not_equal_length() [4/4]

template<typename U >

bool numeric::not_equal_length ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Not equal length?

References a, and compute_difference::b.

operator!=() [1/16]

template<typename T >

bool numeric::operator!=	(	BodyPosition< T > const &	p1,
		BodyPosition< T > const &	p2
	)

BodyPosition != BodyPosition.

operator!=() [2/16]

template<typename T >

bool numeric::operator!= ( const MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

compare to matrices for inequality

Parameters

MATRIX_LHS	lhs matrix
MATRIX_RHS	rhs matrix

Returns

!( MATRIX_LHS == MATRIX_RHS)

operator!=() [3/16]

template<typename T >

bool numeric::operator!= ( const MathMatrix< T > &  MATRIX_LHS, const T &  VALUE_RHS  )

inline

compare if all items in matrix are not equal to a given VALUE

Parameters

MATRIX_LHS	matrix with values
VALUE_RHS	value that is compared against

Returns

false if matrix is empty are all elements in matrix are equal to given VALUE

References numeric::MathMatrix< T >::begin(), and numeric::MathMatrix< T >::end().

operator!=() [4/16]

template<typename T >

bool numeric::operator!= ( const T &  VALUE_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

compare if all items in matrix are not equal to a given VALUE

Parameters

VALUE_LHS	value that is compared against
MATRIX_RHS	matrix with values

Returns

false if matrix is empty are all elements in matrix are equal to given VALUE

operator!=() [5/16]

template<typename T >

bool numeric::operator!= ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector != X (Comparison with T value)

operator!=() [6/16]

template<typename T >

bool numeric::operator!= ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator != (Comparison) MathVectors

operator!=() [7/16]

template<typename T >

bool numeric::operator!=	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T != xyzMatrix.

Value != xyzMatrix.

operator!=() [8/16]

template<typename T >

bool numeric::operator!=	(	T const &	t,
		xyzTriple< T > const &	v
	)

T != xyzTriple.

Value != xyzTriple.

operator!=() [9/16]

template<typename T >

bool numeric::operator!=	(	T const &	t,
		xyzVector< T > const &	v
	)

T != xyzVector.

Value != xyzVector.

operator!=() [10/16]

template<typename T >

bool numeric::operator!= ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator X != MathVector(Comparison with T value)

operator!=() [11/16]

template<typename T >

bool numeric::operator!=	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix != xyzMatrix

operator!=() [12/16]

template<typename T >

bool numeric::operator!=	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix != T

xyzMatrix != Value

operator!=() [13/16]

template<typename T >

bool numeric::operator!=	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple != xyzTriple

operator!=() [14/16]

template<typename T >

bool numeric::operator!=	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple != T

xyzTriple != Value

operator!=() [15/16]

template<typename T >

bool numeric::operator!=	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector != xyzVector

operator!=() [16/16]

template<typename T >

bool numeric::operator!=	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector != T

xyzVector != Value

operator*() [1/13]

template<typename T >

MathMatrix< T> numeric::operator* ( const MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

multiply two matrixs of equal size by building the inner product yielding the scalar product

Parameters

MATRIX_LHS	lhs matrix
MATRIX_RHS	rhs matrix

Returns

scalar representing root of inner product of the two ranges

References numeric::MathMatrix< T >::get_number_cols(), numeric::MathMatrix< T >::get_number_rows(), create_a3b_hbs::i, create_a3b_hbs::j, and create_a3b_hbs::k.

operator*() [2/13]

template<typename T >

MathVector< T> numeric::operator* ( const MathMatrix< T > &  MATRIX_LHS, const MathVector< T > &  VECTOR_RHS  )

inline

multiply matrix with vector

Parameters

MATRIX_LHS	lhs matrix
VECTOR	vector to be multiplied

Returns

resulting vector

References numeric::MathMatrix< T >::get_number_cols(), numeric::MathMatrix< T >::get_number_rows(), create_a3b_hbs::i, and create_a3b_hbs::j.

operator*() [3/13]

template<typename T >

MathMatrix< T> numeric::operator* ( const MathMatrix< T > &  MATRIX_LHS, const T &  SCALAR_RHS  )

inline

multiply matrix with scalar

Parameters

MATRIX_LHS	lhs matrix
SCALAR_RHS	rhs value to be multiplied

Returns

matrix that has the values multiplied with the scalar

operator*() [4/13]

template<typename T >

MathMatrix< T> numeric::operator* ( const T &  SCALAR_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

multiply scalar with matrix

Parameters

SCALAR_LHS	lhs value to be multiplied
MATRIX_RHS	rhs matrix

Returns

matrix that has the values multiplied with the scalar

operator*() [5/13]

template<typename T >

MathVector< T > numeric::operator* ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector * MathVector

operator*() [6/13]

template<typename T >

T numeric::operator* ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator MathVector * MathVector

References numeric::MathVector< T >::begin(), and numeric::MathVector< T >::end().

operator*() [7/13]

template<typename T >

xyzMatrix< T > numeric::operator*	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T * xyzMatrix.

Value * xyzMatrix.

operator*() [8/13]

template<typename T >

xyzTriple< T > numeric::operator*	(	T const &	t,
		xyzTriple< T > const &	v
	)

T * xyzTriple.

Value * xyzTriple.

operator*() [9/13]

template<typename T >

xyzVector< T > numeric::operator*	(	T const &	t,
		xyzVector< T > const &	v
	)

T * xyzVector.

Value * xyzVector.

operator*() [10/13]

template<typename T >

MathVector< T > numeric::operator* ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator MathVector * MathVector

operator*() [11/13]

template<typename T >

xyzVector< T > numeric::operator*	(	xyzMatrix< T > const &	m,
		xyzVector< T > const &	v
	)

operator*() [12/13]

template<typename T >

xyzTriple< T > numeric::operator*	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple * T

xyzTriple * Value

operator*() [13/13]

template<typename T >

xyzVector< T > numeric::operator*	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector * T

xyzVector * Value

operator*=()

template<typename T >

MathMatrix< T>& numeric::operator*= ( MathMatrix< T > &  MATRIX_LHS, const T &  SCALAR  )

inline

multiply matrix with scalar

Parameters

MATRIX_LHS	matrix to multiply to
SCALAR	scalar to be multiplied

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator+() [1/14]

template<typename T >

MathMatrix< T> numeric::operator+ ( const MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

sum two matrixs of equal size

Parameters

MATRIX_LHS	lhs matrix
MATRIX_RHS	rhs matrix

Returns

matrix with all individual summed elements of lhs and rhs matrix

operator+() [2/14]

template<typename T >

MathMatrix< T> numeric::operator+ ( const MathMatrix< T > &  MATRIX_LHS, const T &  VALUE_RHS  )

inline

add value to matrix

Parameters

MATRIX_LHS	lhs matrix
VALUE_RHS	rhs value to be added

Returns

matrix that has the value added to each value of the lhs given matrix

operator+() [3/14]

template<typename T >

MathMatrix< T> numeric::operator+ ( const T &  VALUE_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

add matrix to value

Parameters

VALUE_LHS	lhs value to be added
MATRIX_RHS	rhs matrix

Returns

matrix that has the value added to each value of the lhs given matrix

operator+() [4/14]

template<typename T >

MathVector< T > numeric::operator+ ( MathVector< T > const &  VECTOR )

inline

Returns

operator +MathVectors

operator+() [5/14]

template<typename T >

MathVector< T > numeric::operator+ ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector + MathVector

operator+() [6/14]

template<typename T >

MathVector< T > numeric::operator+ ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator MathVector + MathVector

operator+() [7/14]

template<typename T >

xyzMatrix< T > numeric::operator+	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T + xyzMatrix.

Value + xyzMatrix.

operator+() [8/14]

template<typename T >

xyzTriple< T > numeric::operator+	(	T const &	t,
		xyzTriple< T > const &	v
	)

T + xyzTriple.

Value + xyzTriple.

operator+() [9/14]

template<typename T >

xyzVector< T > numeric::operator+	(	T const &	t,
		xyzVector< T > const &	v
	)

T + xyzVector.

Value + xyzVector.

operator+() [10/14]

template<typename T >

MathVector< T > numeric::operator+ ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator MathVector + MathVector

operator+() [11/14]

template<typename T >

xyzTriple< T > numeric::operator+	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple + xyzTriple

operator+() [12/14]

template<typename T >

xyzTriple< T > numeric::operator+	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple + T

xyzTriple + Value

operator+() [13/14]

template<typename T >

xyzVector< T > numeric::operator+	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector + xyzVector

operator+() [14/14]

template<typename T >

xyzVector< T > numeric::operator+	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector + T

xyzVector + Value

operator+=() [1/2]

template<typename T >

MathMatrix< T>& numeric::operator+= ( MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

add one matrix to another

Parameters

MATRIX_LHS	matrix to add to
MATRIX_RHS	matrix to add

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator+=() [2/2]

template<typename T >

MathMatrix< T>& numeric::operator+= ( MathMatrix< T > &  MATRIX_LHS, const T &  VALUE  )

inline

add scalar to matrix

Parameters

MATRIX_LHS	matrix to add to
VALUE	scalar to be added

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator-() [1/14]

template<typename T >

MathMatrix< T> numeric::operator- ( const MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

subtract two matrixs of equal size

Parameters

MATRIX_LHS	lhs matrix
MATRIX_RHS	rhs matrix

Returns

matrix with all individual subtracted elements of rhs from lhs matrix

operator-() [2/14]

template<typename T >

MathMatrix< T> numeric::operator- ( const MathMatrix< T > &  MATRIX_LHS, const T &  VALUE_RHS  )

inline

subtract value from matrix

Parameters

MATRIX_LHS	lhs matrix
VALUE_RHS	rhs value to be subtracted

Returns

matrix that has the value subtracted from each value of the lhs given matrix

operator-() [3/14]

template<typename T >

MathMatrix< T> numeric::operator- ( const T &  VALUE_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

subtract matrix from value

Parameters

VALUE_LHS	rhs value to be subtracted
MATRIX_RHS	lhs matrix

Returns

matrix that has the values in the matrix subtracted from the value

References numeric::MathMatrix< T >::size().

operator-() [4/14]

template<typename T >

MathVector< T > numeric::operator- ( MathVector< T > const &  VECTOR )

inline

Returns

operator -MathVectors

References pyrosetta.distributed.cluster.exceptions::T.

operator-() [5/14]

template<typename T >

MathVector< T > numeric::operator- ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector - MathVector

operator-() [6/14]

template<typename T >

MathVector< T > numeric::operator- ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator MathVector - MathVector

operator-() [7/14]

template<typename T >

xyzMatrix< T > numeric::operator-	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T - xyzMatrix.

Value - xyzMatrix.

operator-() [8/14]

template<typename T >

xyzTriple< T > numeric::operator-	(	T const &	t,
		xyzTriple< T > const &	v
	)

T - xyzTriple.

Value - xyzTriple.

operator-() [9/14]

template<typename T >

xyzVector< T > numeric::operator-	(	T const &	t,
		xyzVector< T > const &	v
	)

T - xyzVector.

Value - xyzVector.

operator-() [10/14]

template<typename T >

MathVector< T > numeric::operator- ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator MathVector - MathVector

operator-() [11/14]

template<typename T >

xyzTriple< T > numeric::operator-	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple - xyzTriple

operator-() [12/14]

template<typename T >

xyzTriple< T > numeric::operator-	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple - T

xyzTriple - Value

operator-() [13/14]

template<typename T >

xyzVector< T > numeric::operator-	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector - xyzVector

operator-() [14/14]

template<typename T >

xyzVector< T > numeric::operator-	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector - T

xyzVector - Value

operator-=() [1/2]

template<typename T >

MathMatrix< T>& numeric::operator-= ( MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

subtract one matrix from another

Parameters

MATRIX_LHS	matrix to subtract from
MATRIX_RHS	matrix to subtract

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator-=() [2/2]

template<typename T >

MathMatrix< T>& numeric::operator-= ( MathMatrix< T > &  MATRIX_LHS, const T &  VALUE  )

inline

subtract scalar from matrix

Parameters

MATRIX_LHS	matrix to subtract from
VALUE	scalar to be added

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator/() [1/7]

template<typename T >

MathMatrix< T> numeric::operator/ ( const MathMatrix< T > &  MATRIX_LHS, const T &  SCALAR_RHS  )

inline

divide matrix with scalar

Parameters

MATRIX_LHS	lhs matrix
SCALAR_RHS	rhs value to be divided by

Returns

matrix that has the values divided by the scalar

operator/() [2/7]

template<typename T >

MathMatrix< T> numeric::operator/ ( const T &  SCALAR_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

divide scalar by matrix

Parameters

SCALAR_LHS	lhs value to be divided
MATRIX_RHS	rhs matrix to be used to divide the scalar

Returns

matrix that has the values of scalar divided by each according value of the matrix

References numeric::MathMatrix< T >::size().

operator/() [3/7]

template<typename T >

MathVector< T > numeric::operator/ ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector / MathVector

operator/() [4/7]

template<typename T >

MathVector< T > numeric::operator/ ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator MathVector / MathVector ; divides each element by according argument element

operator/() [5/7]

template<typename T >

MathVector< T > numeric::operator/ ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator MathVector / MathVector = Value * Inverse( MathVector)

operator/() [6/7]

template<typename T >

xyzTriple< T > numeric::operator/	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple / T

xyzTriple / Value

operator/() [7/7]

template<typename T >

xyzVector< T > numeric::operator/	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector / T

xyzVector / Value

operator/=() [1/2]

template<typename T >

MathMatrix< T>& numeric::operator/= ( MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &    )

inline

divide one matrix by another

Parameters

MATRIX_LHS	matrix to divided
MATRIX_RHS	matrix to divide by

Returns

the changed lhs matrix

operator/=() [2/2]

template<typename T >

MathMatrix< T>& numeric::operator/= ( MathMatrix< T > &  MATRIX_LHS, const T &  SCALAR  )

inline

divide matrix by scalar

Parameters

MATRIX_LHS	matrix to divide
SCALAR	scalar to divide by

Returns

the changed lhs matrix

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and basic::options::OptionKeys::mp::transform::transform.

operator<() [1/9]

template<typename T >

bool numeric::operator<	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T < xyzMatrix.

Value < xyzMatrix.

operator<() [2/9]

template<typename T >

bool numeric::operator<	(	T const &	t,
		xyzTriple< T > const &	v
	)

T < xyzTriple.

Value < xyzTriple.

operator<() [3/9]

template<typename T >

bool numeric::operator<	(	T const &	t,
		xyzVector< T > const &	v
	)

T < xyzVector.

Value < xyzVector.

operator<() [4/9]

template<typename T >

bool numeric::operator<	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix < xyzMatrix

operator<() [5/9]

template<typename T >

bool numeric::operator<	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix < T

xyzMatrix < Value

operator<() [6/9]

template<typename T >

bool numeric::operator<	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple < xyzTriple

xyzTriple < xyzTriple: Lexicographic order

operator<() [7/9]

template<typename T >

bool numeric::operator<	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple < T

xyzTriple < Value

operator<() [8/9]

template<typename T >

bool numeric::operator<	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector < xyzVector

operator<() [9/9]

template<typename T >

bool numeric::operator<	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector < T

xyzVector < Value

operator<<() [1/12]

std::ostream & numeric::operator<<	(	ostream &	out,
		const Polynomial_1d &	poly
	)

References erraser_single_res_analysis::out.

operator<<() [2/12]

std::ostream & numeric::operator<<	(	std::ostream &	os,
		MultiDimensionalHistogram const &	mdhist
	)

References numeric::MultiDimensionalHistogram::counts(), numeric::MultiDimensionalHistogram::dim_labels(), numeric::MultiDimensionalHistogram::end(), create_a3b_hbs::i, numeric::MultiDimensionalHistogram::label(), numeric::MultiDimensionalHistogram::num_bins(), numeric::MultiDimensionalHistogram::num_dimensions(), subloop_histogram::size, and numeric::MultiDimensionalHistogram::start().

operator<<() [3/12]

template<class F , class V >

std::ostream& numeric::operator<<	(	std::ostream &	out,
		VoxelArray< F, V > const &	v
	)

References erraser_single_res_analysis::out, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

operator<<() [4/12]

template<typename T >

std::ostream& numeric::operator<< ( std::ostream &  output, const IntervalSet< T > &  interval  )

inline

References create_a3b_hbs::i, basic::options::OptionKeys::ms::checkpoint::interval, and bin_torsions::output.

operator<<() [5/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		BodyPosition< T > const &	p
	)

stream << BodyPosition output operator

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, docking::R, basic::options::OptionKeys::ufv::right, predPRE::t, ObjexxFCL::uppercase(), w, and basic::options::OptionKeys::mp::visualize::width.

operator<<() [6/12]

std::ostream& numeric::operator<< ( std::ostream &  stream, HomogeneousTransform< double > const &  ht  )

inline

References numeric::HomogeneousTransform< T >::show().

operator<<() [7/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		HomogeneousTransform< T > const &	ht
	)

operator<<() [8/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		Quaternion< T > const &	q
	)

stream << Quaternion output operator

References enumerate_junctions::q, basic::options::OptionKeys::ufv::right, ObjexxFCL::uppercase(), w, and basic::options::OptionKeys::mp::visualize::width.

operator<<() [9/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		xyzMatrix< T > const &	m
	)

stream << xyzMatrix output operator

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::ufv::right, ObjexxFCL::uppercase(), w, and basic::options::OptionKeys::mp::visualize::width.

operator<<() [10/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		xyzTransform< T > const &	m
	)

stream << xyzTransform output operator

References basic::options::OptionKeys::hotspot::angle, numeric::conversions::degrees(), ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, rotation_axis(), pyrosetta.distributed.cluster.exceptions::T, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

operator<<() [11/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		xyzTriple< T > const &	v
	)

stream << xyzTriple output operator

References basic::options::OptionKeys::ufv::right, ObjexxFCL::uppercase(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, w, and basic::options::OptionKeys::mp::visualize::width.

operator<<() [12/12]

template<typename T >

std::ostream& numeric::operator<<	(	std::ostream &	stream,
		xyzVector< T > const &	v
	)

stream << xyzVector output operator

References basic::options::OptionKeys::ufv::right, ObjexxFCL::uppercase(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, w, and basic::options::OptionKeys::mp::visualize::width.

operator<=() [1/9]

template<typename T >

bool numeric::operator<=	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T <= xyzMatrix.

Value <= xyzMatrix.

operator<=() [2/9]

template<typename T >

bool numeric::operator<=	(	T const &	t,
		xyzTriple< T > const &	v
	)

T <= xyzTriple.

Value <= xyzTriple.

operator<=() [3/9]

template<typename T >

bool numeric::operator<=	(	T const &	t,
		xyzVector< T > const &	v
	)

T <= xyzVector.

Value <= xyzVector.

operator<=() [4/9]

template<typename T >

bool numeric::operator<=	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix <= xyzMatrix

operator<=() [5/9]

template<typename T >

bool numeric::operator<=	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix <= T

xyzMatrix <= Value

operator<=() [6/9]

template<typename T >

bool numeric::operator<=	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple <= xyzTriple

operator<=() [7/9]

template<typename T >

bool numeric::operator<=	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple <= T

xyzTriple <= Value

operator<=() [8/9]

template<typename T >

bool numeric::operator<=	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector <= xyzVector

operator<=() [9/9]

template<typename T >

bool numeric::operator<=	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector <= T

xyzVector <= Value

operator==() [1/16]

template<typename T >

bool numeric::operator==	(	BodyPosition< T > const &	p1,
		BodyPosition< T > const &	p2
	)

BodyPosition == BodyPosition.

operator==() [2/16]

template<typename T >

bool numeric::operator== ( const MathMatrix< T > &  MATRIX_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

compare to matricess for equality

Parameters

MATRIX_LHS	lhs matrix
MATRIX_RHS	rhs matrix

Returns

true is they are equal in size and all pairs of items are equal

References numeric::MathMatrix< T >::begin(), numeric::MathMatrix< T >::end(), and ObjexxFCL::equal().

operator==() [3/16]

template<typename T >

bool numeric::operator== ( const MathMatrix< T > &  MATRIX_LHS, const T &  VALUE_RHS  )

inline

compare if all items in matrix are equal to a given VALUE

Parameters

MATRIX_LHS	matrix with values
VALUE_RHS	value that is compared against

Returns

true if matrix is empty are all elements in matrix are equal to given VALUE

References numeric::MathMatrix< T >::begin(), and numeric::MathMatrix< T >::end().

operator==() [4/16]

template<typename T >

bool numeric::operator== ( const T &  VALUE_LHS, const MathMatrix< T > &  MATRIX_RHS  )

inline

compare if all items in matrix are equal to a given VALUE

Parameters

VALUE_LHS	value that is compared against
MATRIX_RHS	matrix with values

Returns

true if matrix is empty are all elements in matrix are equal to given VALUE

operator==() [5/16]

template<typename T >

bool numeric::operator== ( MathVector< T > const &  VECTOR, T const &  X  )

inline

Returns

operator MathVector == X (Comparison with T value) MathVectors

References numeric::MathVector< T >::begin(), numeric::MathVector< T >::end(), and ptr().

operator==() [6/16]

template<typename T >

bool numeric::operator== ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

operator == (Comparison) MathVectors

References numeric::MathVector< T >::begin(), numeric::MathVector< T >::end(), and numeric::MathVector< T >::size().

operator==() [7/16]

template<typename T >

bool numeric::operator==	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T == xyzMatrix.

Value == xyzMatrix.

operator==() [8/16]

template<typename T >

bool numeric::operator==	(	T const &	t,
		xyzTriple< T > const &	v
	)

T == xyzTriple.

Value == xyzTriple.

operator==() [9/16]

template<typename T >

bool numeric::operator==	(	T const &	t,
		xyzVector< T > const &	v
	)

T == xyzVector.

Value == xyzVector.

operator==() [10/16]

template<typename T >

bool numeric::operator== ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

operator X == MathVector(Comparison with T value)

operator==() [11/16]

template<typename T >

bool numeric::operator==	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix == xyzMatrix

operator==() [12/16]

template<typename T >

bool numeric::operator==	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix == T

xyzMatrix == Value

operator==() [13/16]

template<typename T >

bool numeric::operator==	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple == xyzTriple

operator==() [14/16]

template<typename T >

bool numeric::operator==	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple == T

xyzTriple == Value

operator==() [15/16]

template<typename T >

bool numeric::operator==	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector == xyzVector

operator==() [16/16]

template<typename T >

bool numeric::operator==	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector == T

xyzVector == Value

operator>() [1/9]

template<typename T >

bool numeric::operator>	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T > xyzMatrix.

Value > xyzMatrix.

operator>() [2/9]

template<typename T >

bool numeric::operator>	(	T const &	t,
		xyzTriple< T > const &	v
	)

T > xyzTriple.

Value > xyzTriple.

operator>() [3/9]

template<typename T >

bool numeric::operator>	(	T const &	t,
		xyzVector< T > const &	v
	)

T > xyzVector.

Value > xyzVector.

operator>() [4/9]

template<typename T >

bool numeric::operator>	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix > xyzMatrix

operator>() [5/9]

template<typename T >

bool numeric::operator>	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix > T

xyzMatrix > Value

operator>() [6/9]

template<typename T >

bool numeric::operator>	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple > xyzTriple

operator>() [7/9]

template<typename T >

bool numeric::operator>	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple > T

xyzTriple > Value

operator>() [8/9]

template<typename T >

bool numeric::operator>	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector > xyzVector

operator>() [9/9]

template<typename T >

bool numeric::operator>	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector > T

xyzVector > Value

operator>=() [1/9]

template<typename T >

bool numeric::operator>=	(	T const &	t,
		xyzMatrix< T > const &	m
	)

T >= xyzMatrix.

Value >= xyzMatrix.

operator>=() [2/9]

template<typename T >

bool numeric::operator>=	(	T const &	t,
		xyzTriple< T > const &	v
	)

T >= xyzTriple.

Value >= xyzTriple.

operator>=() [3/9]

template<typename T >

bool numeric::operator>=	(	T const &	t,
		xyzVector< T > const &	v
	)

T >= xyzVector.

Value >= xyzVector.

operator>=() [4/9]

template<typename T >

bool numeric::operator>=	(	xyzMatrix< T > const &	a,
		xyzMatrix< T > const &	b
	)

xyzMatrix >= xyzMatrix

operator>=() [5/9]

template<typename T >

bool numeric::operator>=	(	xyzMatrix< T > const &	m,
		T const &	t
	)

xyzMatrix >= T

xyzMatrix >= Value

operator>=() [6/9]

template<typename T >

bool numeric::operator>=	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

xyzTriple >= xyzTriple

operator>=() [7/9]

template<typename T >

bool numeric::operator>=	(	xyzTriple< T > const &	v,
		T const &	t
	)

xyzTriple >= T

xyzTriple >= Value

operator>=() [8/9]

template<typename T >

bool numeric::operator>=	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector >= xyzVector

operator>=() [9/9]

template<typename T >

bool numeric::operator>=	(	xyzVector< T > const &	v,
		T const &	t
	)

xyzVector >= T

xyzVector >= Value

operator>>() [1/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		BodyPosition< T > &	p
	)

stream >> BodyPosition input operator

Note

Reads row-ordered matrix elements from one or multiple lines

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, docking::R, read_row(), and predPRE::t.

operator>>() [2/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		Quaternion< T > &	q
	)

stream >> Quaternion input operator

Note

Supports whitespace-separated values with optional commas between values as long as whitespace is also present

Quaternion can optionally be enclosed in parentheses () or square brackets []

String or char values containing whitespace or commas or enclosed in quotes are not supported

References enumerate_junctions::q.

operator>>() [3/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		xyzMatrix< T > &	m
	)

stream >> xyzMatrix input operator

Note

Reads row-ordered matrix elements from one or multiple lines

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, and read_row().

operator>>() [4/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		xyzTransform< T > &	m
	)

stream >> xyzTransform input operator

Note

Reads row-ordered matrix elements from one or multiple lines

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

operator>>() [5/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		xyzTriple< T > &	v
	)

stream >> xyzTriple input operator

Note

Supports whitespace-separated values with optional commas between values as long as whitespace is also present

Vector can optionally be enclosed in parentheses () or square brackets []

String or char values containing whitespace or commas or enclosed in quotes are not supported

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

operator>>() [6/6]

template<typename T >

std::istream& numeric::operator>>	(	std::istream &	stream,
		xyzVector< T > &	v
	)

stream >> xyzVector input operator

Note

Supports whitespace-separated values with optional commas between values as long as whitespace is also present

Vector can optionally be enclosed in parentheses () or square brackets []

String or char values containing whitespace or commas or enclosed in quotes are not supported

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

operator^()

template<typename T >

MathVector< T > numeric::operator^ ( T const &  X, MathVector< T > const &  VECTOR  )

inline

Returns

MathVector operator Value ^ MathVector

References numeric::MathVector< T >::begin(), numeric::MathVector< T >::end(), and ObjexxFCL::pow().

outer_product()

template<typename T >

xyzMatrix< T > numeric::outer_product	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b
	)

xyzVector xyzVector outer product

Referenced by Tensor::add(), line_cone_intersection(), and pca_align_BROKEN().

principal_angle()

template<typename T >

T numeric::principal_angle ( T const &  angle )

inline

Principal value of angle in radians on ( -pi, pi ].

References basic::options::OptionKeys::hotspot::angle, and remainder().

Referenced by morph_by_internal_coords().

principal_angle_degrees()

template<typename T >

T numeric::principal_angle_degrees ( T const &  angle )

inline

Principal value of angle in degrees on ( -180, 180 ].

References basic::options::OptionKeys::hotspot::angle, remainder(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by adjust_pose_chi(), angle_diff(), B3AADihedralGrabber::apply(), copy_rotamerized_torsions(), count_bins(), fix_alpha_for_pack_phosphate(), get_omgphipsi_bins(), hack_create_torsion_value_string(), has_cis_bonds(), and sidechain_sample().

principal_angle_radians()

template<typename T >

T numeric::principal_angle_radians ( T const &  angle )

inline

Principal value of angle in radians on ( -pi, pi ].

References basic::options::OptionKeys::hotspot::angle, and remainder().

principal_component_eigenvalues()

template<typename T >

xyzVector< T > numeric::principal_component_eigenvalues ( utility::vector1< xyzVector< T > > const &  coords )

inline

return a vector containing the eigenvalues corresponding to the first 3 principal components of the given set of points.

References principal_components_and_eigenvalues().

principal_components()

template<typename T >

xyzMatrix< T > numeric::principal_components ( utility::vector1< xyzVector< T > > const &  coords )

inline

return a matrix containing the first 3 principal components of the given set of points. Matrix columns are principal components, first column is first component, etc.

References principal_components_and_eigenvalues().

Referenced by first_principal_component().

principal_components_and_eigenvalues()

template<typename T >

std::pair<xyzMatrix<T>, xyzVector<T> > numeric::principal_components_and_eigenvalues ( utility::vector1< xyzVector< T > > const &  coords )

inline

return a pair containing a matrix of the first 3 principal components and a vector of the corresponding eigenvalues of the given set of points.

References numeric::xyzMatrix< T >::col(), numeric::xyzMatrix< T >::col_x(), numeric::xyzMatrix< T >::col_y(), numeric::xyzMatrix< T >::col_z(), eigenvector_jacobi(), create_a3b_hbs::first, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by principal_component_eigenvalues(), and principal_components().

principal_components_and_eigenvalues_ndimensions()

std::pair<utility::vector1< utility::vector1< Real > >, utility::vector1< Real > > numeric::principal_components_and_eigenvalues_ndimensions ( utility::vector1< utility::vector1< Real > > const &  coords, bool const  shift_center  )

inline

Return a pair containing a matrix (vector of vectors) of all of the principal components and a vector of the corresponding eigenvalues of the given set of points in n-dimensional space.

Note that this does not assume that the input vectors are 3-dimensional. If shift_center=false, the mean vector is not subtracted by this function. (Failure to subtract mean vector prior to function call will produce odd results, however.)

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, runtime_assert_string_msg, and subloop_histogram::size.

Referenced by main(), and shift_center_and_PCA().

print_probabilities()

void numeric::print_probabilities	(	const utility::vector1< double > &	probs,
		std::ostream &	out
	)

Writes probs to the specified ostream.

References create_a3b_hbs::i.

product() [1/2]

template<class ForwardIterator >

void numeric::product	(	ForwardIterator	probs1_first,
		ForwardIterator	probs1_last,
		ForwardIterator	probs2_first,
		ForwardIterator	probs2_last
	)

Multiplies two probability vectors with one another. Probability vectors are assumed to have equal lengths.

References create_a3b_hbs::i, create_a3b_hbs::j, and normalize().

Referenced by cartesian_product(), numeric::interpolation::InterpolatedPotential< N >::dimension(), main(), detail::multiply(), numeric::HomogeneousTransform< T >::operator*(), place_water_acceptor(), place_water_donor(), and numeric::BodyPosition< T >::transformed().

product() [2/2]

template<typename T >

xyzVector< T > numeric::product	(	xyzMatrix< T > const &	m,
		xyzVector< T > const &	v
	)

xyzMatrix * xyzVector product

Note

Same as xyzMatrix * xyzVector

proj_angl() [1/3]

template<typename T >

T numeric::proj_angl ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B  )

inline

Returns

projection angle between two MathVectors 0->A and 0->B

References proj_angl().

proj_angl() [2/3]

template<typename T >

T numeric::proj_angl ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B, MathVector< T > const &  VECTOR_C  )

inline

Returns

projection angle between three MathVectors A->B and A->C

References proj_angl().

proj_angl() [3/3]

template<typename T >

T numeric::proj_angl ( MathVector< T > const &  VECTOR_A, MathVector< T > const &  VECTOR_B, MathVector< T > const &  VECTOR_C, MathVector< T > const &  VECTOR_D  )

inline

Returns

projection angle between four MathVectors A->B and C->D

References test.T400_Refinement::ab, basic::options::OptionKeys::hotspot::angle, max(), min(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by proj_angl().

projection_matrix()

template<typename T >

xyzMatrix< T > numeric::projection_matrix

(

xyzVector< T > const &

v

)

geometric center

Note

compute the geometric center of a list of points

Projection matrix onto the line through a vector

Referenced by align_carboxyl_diiron(), ik_his4(), ik_his_clamp(), intersecting_bpy_axes(), main(), proj(), projperp(), run(), run_diiron_glu(), and test_MAT_VEC().

quat2R()

template<typename T >

void numeric::quat2R ( Quaternion< T > const &  Q, xyzMatrix< T > &  R  )

inline

Interconvert Quaternion <=> Rotation Matrix.

References docking::Q, docking::R, xx, test.T110_numeric::xy, test.T110_numeric::xz, yy, test.T110_numeric::yz, and test.T110_numeric::zz.

Referenced by numeric::AxisRotationSampler::AxisRotationSampler().

R2quat()

template<typename T >

void numeric::R2quat ( xyzMatrix< T > const &  R, Quaternion< T > &  Q  )

inline

Interconvert Quaternion <=> Rotation Matrix.

References docking::Q, docking::R, and pyrosetta.distributed.cluster.converters::S.

read_probabilities_or_die()

void numeric::read_probabilities_or_die	(	const std::string &	filename,
		utility::vector1< double > *	probs
	)

Loads normalized, per-residue probabilities from filename, storing the result in probs. Assumes line i holds the probability of sampling residue i. There must be 1 line for each residue in the pose on which this data will be used.

References lactamize::filename, basic::options::OptionKeys::in::in, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and utility_exit_with_message.

read_row() [1/2]

template<typename T >

std::istream& numeric::read_row	(	std::istream &	stream,
		T &	x,
		T &	y,
		T &	z
	)

Read an xyzMatrix row from a stream.

Note

Supports whitespace-separated values with optional commas between values as long as whitespace is also present

Rows can optionally be enclosed in parentheses () or square brackets []

String or char values containing whitespace or commas or enclosed in quotes are not supported

References x, predPRE::y, and predPRE::z.

read_row() [2/2]

template<typename T >

std::istream& numeric::read_row	(	std::istream &	stream,
		T &	x,
		T &	y,
		T &	z,
		T &	t
	)

Read an BodyPosition row from a stream.

Note

Supports whitespace-separated values with optional commas between values as long as whitespace is also present

Rows can optionally be enclosed in parentheses () or square brackets []

String or char values containing whitespace or commas or enclosed in quotes are not supported

References predPRE::t, x, predPRE::y, and predPRE::z.

Referenced by operator>>().

read_tensor_from_file() [1/2]

template<class T , numeric::Size N>

void numeric::read_tensor_from_file	(	std::string const &	filename,
		MathNTensor< T, N > &	tensor
	)

References lactamize::filename, basic::options::OptionKeys::ddg::json, and read_tensor_from_file().

read_tensor_from_file() [2/2]

template<class T , numeric::Size N>

void numeric::read_tensor_from_file	(	std::string const &	filename_input,
		MathNTensor< T, N > &	tensor,
		utility::json_spirit::mObject &	json
	)

References utility::io::izstream::close(), utility::io::oc::cout, data, file_exists(), lactamize::filename, utility::json_spirit::get_mArray(), utility::json_spirit::Value_impl< Config >::get_obj(), utility::json_spirit::get_string_or_empty(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, basic::options::OptionKeys::ddg::json, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, utility::io::izstream::read(), utility::replace_in(), runtime_assert, loops_kic::success, pyrosetta.distributed.cluster.exceptions::T, utility_exit_with_message, value, and write_tensor_to_file_without_json().

Referenced by read_tensor_from_file(), and read_tensor_test().

remainder()

template<typename T >

T numeric::remainder ( T const &  x, T const &  y  )

inline

Remainder of x with respect to division by y that is of smallest magnitude.

Note

Emulates the C99 remainder function but also supports integer arguments

Returns zero if y is zero

Return value has magnitude <= | y / 2 |

If | n - ( x / y ) | == .5 the nearest even n is used

References x, and predPRE::y.

Referenced by zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::flush(), detail::get_round_direction(), detail::grisu_gen_digits(), id2torsion(), my_main(), detail::fixed_handler::on_digit(), detail::fixed_handler::on_start(), principal_angle(), principal_angle_degrees(), principal_angle_radians(), detail::dragonbox::remove_trailing_zeros(), zlib_stream::basic_unzip_streambuf< Elem, std::char_traits< Elem >, std::allocator< Elem >, unsigned char, std::allocator< unsigned char > >::underflow(), and zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::zip_to_stream().

remainder_conversion()

template<typename T , typename S >

T numeric::remainder_conversion ( T const &  t, S &  s  )

inline

Remainder and result of conversion to a different type.

References docking::s, pyrosetta.distributed.cluster.converters::S, and predPRE::t.

rgb_to_hsv() [1/2]

numeric::xyzVector< platform::Real > numeric::rgb_to_hsv

(

numeric::xyzVector< platform::Real >

rgb_triplet

)

convert and RGB color to HSV

References blue, green, numeric::xyzVector< T >::maximum_value(), numeric::xyzVector< T >::minimum_value(), red, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

rgb_to_hsv() [2/2]

numeric::xyzVector< platform::Real > numeric::rgb_to_hsv	(	platform::Real	r,
		platform::Real	g,
		platform::Real	b
	)

convert an RGB color to HSV

References compute_difference::b, g(), and create_a3b_hbs::r.

rotation_angle()

template<typename T >

T numeric::rotation_angle ( xyzMatrix< T > const &  R )

inline

Transformation from rotation matrix to magnitude of helical rotation.

Note

Input matrix must be orthogonal

Orientation of axis chosen so that the angle of rotation is non-negative [0,pi]

References ObjexxFCL::abs(), numeric::NumericTraits< T >::pi(), docking::R, sin_cos_range(), and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by numeric::EulerAngles< T >::angular_distance_between().

rotation_axis()

template<typename T >

xyzVector< T > numeric::rotation_axis	(	xyzMatrix< T > const &	R,
		T &	theta
	)

Transformation from rotation matrix to helical axis of rotation.

Note

Input matrix must be orthogonal

Angle of rotation is also returned

Orientation of axis chosen so that the angle of rotation is non-negative [0,pi]

Referenced by MatchSet::cross(), dock(), MyRT::from_rot(), main(), operator<<(), numeric::random::random_rotation_angle(), and rotation_axis_angle().

rotation_axis_angle()

template<typename T >

xyzVector< T > numeric::rotation_axis_angle

(

xyzMatrix< T > const &

R

)

Transformation from rotation matrix to compact axis-angle representation.

Note

Input matrix must be orthogonal

Orientation of axis chosen so that the angle of rotation is non-negative [0,pi]

References docking::R, rotation_axis(), and vec().

rotation_matrix() [1/2]

template<typename T >

xyzMatrix< T > numeric::rotation_matrix	(	xyzVector< T > const &	axis,
		T const &	theta
	)

Rotation matrix for rotation about an axis by an angle in radians.

Referenced by numeric::xyzTransform< T >::align(), SymRBMover::apply(), bk_test(), numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition(), HubDenovo::cen_fold(), change_docking_pose(), MatchSet::cross(), isctfast(), main(), rb_entropy_test(), numeric::xyzTransform< T >::rot(), rotation_matrix(), rotation_matrix_degrees(), rotation_matrix_radians(), zinc1_homodimer_design::setup_rollmoving(), sicfast(), slice_ellipsoid_envelope(), test_MAT_VEC(), and transform_pose().

rotation_matrix() [2/2]

template<typename T >

xyzMatrix< T > numeric::rotation_matrix ( xyzVector< T > const &  axis_angle )

inline

References axis_angle(), and rotation_matrix().

rotation_matrix_degrees()

template<typename T >

xyzMatrix< T > numeric::rotation_matrix_degrees ( xyzVector< T > const &  axis, T const &  theta  )

inline

Rotation matrix for rotation about an axis by an angle in degrees.

References numeric::conversions::radians(), and rotation_matrix().

Referenced by TCDock::__dock_base__(), align_carboxyl_diiron(), align_carboxyl_diiron_OLD(), Tet4HMatchAligner::align_rot(), Hit::apply(), ArchP4_42::ArchP4_42(), ArchP4g_42d::ArchP4g_42d(), ArchP4m_42d::ArchP4m_42d(), ArchP6_32::ArchP6_32(), ArchP6m_32d::ArchP6m_32d(), change_floating_sc_geometry(), ClashCheck::clash_check_trimer(), MatchSet::cross(), cxdock_design(), design_hits(), dock(), doit(), dostuff(), TCDock::dump_pdb(), TCDock::dump_top_hits(), find_dsf(), numeric::random::gaussian_random_xform(), TCDock::get_best_sub1_contact_delta_rotations(), TCDock::get_cmp1(), TCDock::get_cmp2(), iface_check_c3(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), Arch::init(), intersecting_bpy_axes(), intersecting_disulfide_axes(), is_near_C2Z_iface(), main(), make_dock_olig(), make_two_trimers(), TCDock::min_termini_dis(), TCDock::min_termini_proj(), TCDock::precompute_intra(), numeric::xyzTransform< T >::rot_deg(), rot_pose(), run(), TCDock::run(), run_diiron_glu(), run_m8(), set_disulf(), Arch::slide_axis(), TCDock::swap_axis(), TCDock::swap_axis_rotation(), test_chi_xform(), testone(), visualize(), Arch::xform1(), and Arch::xform2().

rotation_matrix_from_euler_angles_ZXZ()

template<typename T >

xyzMatrix<T> numeric::rotation_matrix_from_euler_angles_ZXZ ( xyzVector< T > const &  angles )

inline

References oop_conformations::angles.

rotation_matrix_from_euler_angles_ZYX()

template<typename T >

xyzMatrix<T> numeric::rotation_matrix_from_euler_angles_ZYX ( xyzVector< T > const &  angles )

inline

References oop_conformations::angles.

rotation_matrix_from_euler_angles_ZYZ()

template<typename T >

xyzMatrix<T> numeric::rotation_matrix_from_euler_angles_ZYZ ( xyzVector< T > const &  angles )

inline

References oop_conformations::angles.

rotation_matrix_radians()

template<typename T >

xyzMatrix< T > numeric::rotation_matrix_radians ( xyzVector< T > const &  axis, T const &  theta  )

inline

Rotation matrix for rotation about an axis by an angle in radians.

References rotation_matrix().

Referenced by make_helix(), and map_morph().

scalar_product()

template<typename T >

T numeric::scalar_product	(	MathVector< T > const &	VECTOR_A,
		MathVector< T > const &	VECTOR_B
	)

Returns

scalar product of two MathVectors

sec()

template<typename T >

T numeric::sec ( T const &  x )

inline

Secant.

References pyrosetta.distributed.cluster.exceptions::T, and x.

Referenced by get_sequence_and_secstruct_from_dssp(), get_t033_ss(), map_sec(), and set_secstruct_from_psipred_ss2().

serialize()

template<typename T >

utility::json_spirit::Value numeric::serialize ( xyzVector< T >  coords )

inline

Convert vector to a json_spirit Value.

Note

Format is a list in the form [x,y,z]

References utility::tools::make_vector(), x, numeric::xyzVector< T >::x(), predPRE::y, numeric::xyzVector< T >::y(), predPRE::z, and numeric::xyzVector< T >::z().

sign()

template<typename T >

int numeric::sign ( T const &  x )

inline

sign( x )

References pyrosetta.distributed.cluster.exceptions::T, and x.

Referenced by HubDenovo::cen_fold(), numeric::NearestSelector< R, T, true >::nearest(), nearest_int(), nearest_size(), nearest_ssize(), nint(), and urs_R2ang().

sign_transfered()

template<typename S , typename T >

T numeric::sign_transfered ( S const &  sigma, T const &  x  )

inline

Sign transfered value.

References ObjexxFCL::abs(), pyrosetta.distributed.cluster.converters::S, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, and x.

Referenced by numeric::model_quality::rms_fit(), numeric::model_quality::rmsfitca2(), and numeric::model_quality::rmsfitca3().

sin_cos_range()

template<typename T >

T numeric::sin_cos_range ( T const &  x, T const &  tol = T( .001 )  )

inline

Adjust a sine or cosine value to the valid [-1,1] range if within a specified tolerance or exit with an error.

Note

The = on the first <= and >= else if conditions were added to work-around optimization register passing bugs where x can be passed by a register with a float value of +/-1.0f but where x has a full register precision value slightly different from +/-1.0f/ The first else if cases were failing but with the = added these if conditions will succeed. The alternative fix of declaring "volatile float const x" is slower for most calls. DON'T REMOVE THESE = EVEN THOUGH THEY APPEAR TO BE SUPERFLUOUS!!!

References utility::io::oc::cerr, utility::io::oc::cout, CREATE_EXCEPTION, pyrosetta.distributed.cluster.exceptions::T, loops_kic::tol, utility_exit, and x.

Referenced by angle_of(), angle_radians(), arccos(), cos_of(), euler_angles_from_rotation_matrix_ZXZ(), euler_angles_from_rotation_matrix_ZYX(), euler_angles_from_rotation_matrix_ZYZ(), numeric::HomogeneousTransform< T >::euler_angles_rad(), numeric::xyzTransform< T >::euler_angles_rad(), numeric::EulerAngles< T >::from_rotation_matrix(), random_unit_vector(), rotation_angle(), numeric::xyzTransform< T >::rotation_cosine(), and numeric::xyzTransform< T >::rotation_sine().

sin_of() [1/6]

template<typename T >

T numeric::sin_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b
	)

Sine of angle between two vectors.

sin_of() [2/6]

template<typename T >

T numeric::sin_of	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > const &	c
	)

Sine of angle formed by three consecutive points.

sin_of() [3/6]

template<typename U >

U numeric::sin_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b  )

inline

Sine of angle between two vectors.

sin_of() [4/6]

template<typename U >

U numeric::sin_of ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > const &  c  )

inline

Sine of angle formed by three consecutive points.

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c

sin_of() [5/6]

template<typename U >

U numeric::sin_of ( xyzVector< U > const &  a, xyzVector< U > const &  b  )

inline

Sine of angle between two vectors.

References a, compute_difference::b, cos_of(), square(), and docking::U.

Referenced by sin_of().

sin_of() [6/6]

template<typename U >

U numeric::sin_of ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > const &  c  )

inline

Sine of angle formed by three consecutive points.

Note

For points a, b, c, the angle is the angle between the vectors a - b and c - b in other words, the positive angle about b from a to c

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and sin_of().

spherical_to_xyz()

template<typename T >

xyzVector< T > numeric::spherical_to_xyz ( sphericalVector< T > const &  spherical )

inline

References numeric::sphericalVector< T >::phi(), numeric::constants::f::pi_over_180, numeric::sphericalVector< T >::radius(), numeric::sphericalVector< T >::theta(), and basic::options::OptionKeys::in::file::xyz.

square()

template<typename T >

T numeric::square ( T const &  x )

inline

square( x ) == x^2

References x.

Referenced by CapriTotalEnergy::finalize_total_energy(), find_neighbors(), MatchSet::init_clash_check(), ClashCheck::init_clash_check(), numeric::model_quality::maxsub(), run_pep_prep(), CapriTotalEnergy::score_experimental_constraints(), Spacegroup::set_parameters(), sin_of(), numeric::fourier::SHT::so3_correlate(), and numeric::fourier::SHT::sph_standardize().

subtract() [1/12]

template<typename T >

void numeric::subtract	(	T const &	t,
		xyzTriple< T > const &	v,
		xyzTriple< T > &	r
	)

Subtract: T - xyzTriple.

subtract() [2/12]

template<typename T >

void numeric::subtract	(	T const &	t,
		xyzVector< T > const &	v,
		xyzVector< T > &	r
	)

Subtract: T - xyzVector.

subtract() [3/12]

template<typename U >

void numeric::subtract ( U const &  t, xyzTriple< U > const &  v, xyzTriple< U > &  r  )

inline

Subtract: Value - xyzTriple.

subtract() [4/12]

template<typename U >

void numeric::subtract ( U const &  t, xyzVector< U > const &  v, xyzVector< U > &  r  )

inline

Subtract: Value - xyzVector.

subtract() [5/12]

template<typename T >

void numeric::subtract	(	xyzTriple< T > const &	a,
		xyzTriple< T > const &	b,
		xyzTriple< T > &	r
	)

Subtract: xyzTriple - xyzTriple.

Referenced by util::get_surrounding_res().

subtract() [6/12]

template<typename T >

void numeric::subtract	(	xyzTriple< T > const &	v,
		T const &	t,
		xyzTriple< T > &	r
	)

Subtract: xyzTriple - T.

subtract() [7/12]

template<typename U >

void numeric::subtract ( xyzTriple< U > const &  a, xyzTriple< U > const &  b, xyzTriple< U > &  r  )

inline

Subtract: xyzTriple - xyzTriple.

subtract() [8/12]

template<typename U >

void numeric::subtract ( xyzTriple< U > const &  v, U const &  t, xyzTriple< U > &  r  )

inline

Subtract: xyzTriple - Value.

subtract() [9/12]

template<typename T >

void numeric::subtract	(	xyzVector< T > const &	a,
		xyzVector< T > const &	b,
		xyzVector< T > &	r
	)

Subtract: xyzVector - xyzVector.

subtract() [10/12]

template<typename T >

void numeric::subtract	(	xyzVector< T > const &	v,
		T const &	t,
		xyzVector< T > &	r
	)

Subtract: xyzVector - T.

subtract() [11/12]

template<typename U >

void numeric::subtract ( xyzVector< U > const &  a, xyzVector< U > const &  b, xyzVector< U > &  r  )

inline

Subtract: xyzVector - xyzVector.

subtract() [12/12]

template<typename U >

void numeric::subtract ( xyzVector< U > const &  v, U const &  t, xyzVector< U > &  r  )

inline

Subtract: xyzVector - Value.

sum()

template<class InputIterator >

double numeric::sum	(	InputIterator	first,
		InputIterator	last
	)

Returns the sum of all elements on the range [first, last)

References create_a3b_hbs::first.

Referenced by calc_zscore(), numeric::nls::lm_lmdif(), numeric::nls::lm_lmpar(), numeric::nls::lm_qrfac(), numeric::nls::lm_qrsolv(), main(), and normalize().

to_json()

template<typename T >

void numeric::to_json	(	nlohmann::json &	j,
		const xyzVector< T > &	v
	)

References create_a3b_hbs::j, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

transpose_product()

template<typename T >

xyzVector< T > numeric::transpose_product	(	xyzMatrix< T > const &	m,
		xyzVector< T > const &	v
	)

xyzMatrix^T * xyzVector product

Referenced by numeric::BodyPosition< T >::inverse_transformed(), and numeric::BodyPosition< T >::inverse_translation().

truncate_and_serialize_xyz_vector()

template<typename T >

std::string numeric::truncate_and_serialize_xyz_vector	(	xyzVector< T >	vector,
		Real	precision
	)

References basic::options::OptionKeys::optE::fixed.

update_5way_operation()

template<typename T >

xyzVector<T> numeric::update_5way_operation ( xyzVector< T > const &  a, xyzVector< T > const &  b, xyzVector< T > const &  c, xyzVector< T > const &  d, xyzVector< T > const &  e  )

inline

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, numeric::xyzVector< T >::x_, numeric::xyzVector< T >::y_, and numeric::xyzVector< T >::z_.

update_operation()

template<typename T >

xyzVector<T> numeric::update_operation ( xyzVector< T > const &  a, xyzVector< T > const &  b  )

inline

References a, and compute_difference::b.

urs_norm4()

double numeric::urs_norm4 ( double  a, double  b, double  c, double  d  )

inline

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

Referenced by urs_R2ang().

urs_R2ang()

platform::Real numeric::urs_R2ang ( numeric::xyzMatrix< Real >  R )

inline

References basic::options::OptionKeys::hotspot::angle, numeric::conversions::degrees(), create_a3b_hbs::r, docking::R, sign(), and urs_norm4().

Referenced by CrystFFTDock::get_transform_distance(), and numeric::UniformRotationSampler::remove_redundant().

vector_of_xyzvectors_to_FArray()

template<typename T >

ObjexxFCL::FArray2D<T> numeric::vector_of_xyzvectors_to_FArray ( utility::vector1< xyzVector< T > > const &  input )

inline

convert a vector1 of xyzVectors to an FArray2D

References gaussian-sampling::input, enumerate_junctions::int, bin_torsions::output, x, predPRE::y, and predPRE::z.

wrap_180()

template<typename T >

T numeric::wrap_180 ( T const &  angle )

inline

Wrap the given angle in the range [-180, 180).

No conversion to degrees is implied.

References basic::options::OptionKeys::hotspot::angle.

wrap_2pi()

template<typename T >

T numeric::wrap_2pi ( T const &  angle )

inline

Wrap the given angle in the range [0, 2 * pi).

No conversion to radians is implied.

References basic::options::OptionKeys::hotspot::angle.

Referenced by numeric::kinematic_closure::radians::torsion().

wrap_360()

template<typename T >

T numeric::wrap_360 ( T const &  angle )

inline

Wrap the given angle in the range [0, 360).

No conversion to degrees is implied.

References basic::options::OptionKeys::hotspot::angle.

wrap_pi()

template<typename T >

T numeric::wrap_pi ( T const &  angle )

inline

Wrap the given angle in the range [-pi, pi).

No conversion to radians is implied.

References basic::options::OptionKeys::hotspot::angle, and numeric::NumericTraits< T >::pi().

write_tensor_to_file() [1/2]

template<class T , numeric::Size N>

bool numeric::write_tensor_to_file	(	std::string const &	filename,
		MathNTensor< T, N > const &	tensor
	)

References lactamize::filename, utility::tools::make_vector(), numeric::MathNTensor< T, N >::n_bins(), utility_exit_with_message, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, value, and write_tensor_to_file().

write_tensor_to_file() [2/2]

template<class T , numeric::Size N>

bool numeric::write_tensor_to_file	(	std::string const &	filename,
		MathNTensor< T, N > const &	tensor,
		utility::json_spirit::Value const &	json_input
	)

References utility::io::ozstream::close(), lactamize::filename, utility::io::ozstream::good(), basic::options::OptionKeys::ddg::json, erraser_single_res_analysis::out, utility::replace_in(), loops_kic::success, utility_exit_with_message, detail::write(), and write_tensor_to_file_without_json().

Referenced by my_main(), and write_tensor_to_file().

write_tensor_to_file_without_json()

template<class T , numeric::Size N>

bool numeric::write_tensor_to_file_without_json	(	std::string const &	filename,
		MathNTensor< T, N > const &	tensor
	)

References utility::io::ozstream::close(), numeric::MathNTensor< T, N >::data(), lactamize::filename, utility::io::ozstream::good(), erraser_single_res_analysis::out, numeric::MathNTensor< T, N >::size(), pyrosetta.distributed.cluster.exceptions::T, and utility::io::ozstream::write().

Referenced by read_tensor_from_file(), and write_tensor_to_file().

x_rotation_matrix()

template<typename T >

xyzMatrix< T > numeric::x_rotation_matrix ( T const &  theta )

inline

Rotation matrix for rotation about the x axis by an angle in radians.

References numeric::xyzMatrix< T >::rows(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by x_rotation_matrix_degrees(), and x_rotation_matrix_radians().

x_rotation_matrix_degrees()

template<typename T >

xyzMatrix< T > numeric::x_rotation_matrix_degrees ( T const &  theta )

inline

Rotation matrix for rotation about the x axis by an angle in degrees.

References numeric::conversions::radians(), and x_rotation_matrix().

Referenced by MyRotMover::apply(), DetectSymmetry::apply(), compute_chi(), dostuff(), get_rmsd(), get_rmsd_debug(), main(), move_jump(), move_pose(), place_water_acceptor(), place_water_donor(), numeric::random::random_rotation_angle(), DisulfideBondEnergy::rebuildAndDetectDisulfideBond(), rotatePoint(), numeric::HomogeneousTransform< T >::set_xaxis_rotation_deg(), and DisulfideBondEnergy::tabulate().

x_rotation_matrix_radians()

template<typename T >

xyzMatrix< T > numeric::x_rotation_matrix_radians ( T const &  theta )

inline

Rotation matrix for rotation about the x axis by an angle in radians.

References x_rotation_matrix().

Referenced by main(), and numeric::HomogeneousTransform< T >::set_xaxis_rotation_rad().

xyz_to_spherical()

template<typename T >

sphericalVector< T > numeric::xyz_to_spherical

(

xyzVector< T > const &

xyz

)

References numeric::sphericalVector< T >::phi(), numeric::constants::f::pi_over_180, numeric::sphericalVector< T >::radius(), numeric::sphericalVector< T >::theta(), and basic::options::OptionKeys::in::file::xyz.

xyzmatrix_to_FArray()

template<typename T >

ObjexxFCL::FArray2D<T> numeric::xyzmatrix_to_FArray ( numeric::xyzMatrix< T > const &  input )

inline

convert an xyzMatrix to a 3x3 FArray 2D

References gaussian-sampling::input, and bin_torsions::output.

y_rotation_matrix()

template<typename T >

xyzMatrix< T > numeric::y_rotation_matrix ( T const &  theta )

inline

Rotation matrix for rotation about the y axis by an angle in radians.

References numeric::xyzMatrix< T >::rows(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by y_rotation_matrix_degrees(), and y_rotation_matrix_radians().

y_rotation_matrix_degrees()

template<typename T >

xyzMatrix< T > numeric::y_rotation_matrix_degrees ( T const &  theta )

inline

Rotation matrix for rotation about the y axis by an angle in degrees.

References numeric::conversions::radians(), and y_rotation_matrix().

Referenced by MyRotMover::apply(), DetectSymmetry::apply(), SwapElementsMover2::apply(), dock(), main(), numeric::random::random_rotation_angle(), and numeric::HomogeneousTransform< T >::set_yaxis_rotation_deg().

y_rotation_matrix_radians()

template<typename T >

xyzMatrix< T > numeric::y_rotation_matrix_radians ( T const &  theta )

inline

Rotation matrix for rotation about the y axis by an angle in radians.

References y_rotation_matrix().

Referenced by main(), and numeric::HomogeneousTransform< T >::set_yaxis_rotation_rad().

z_rotation_matrix()

template<typename T >

xyzMatrix< T > numeric::z_rotation_matrix ( T const &  theta )

inline

Rotation matrix for rotation about the z axis by an angle in radians.

References numeric::xyzMatrix< T >::rows(), and pyrosetta.distributed.cluster.exceptions::T.

Referenced by dock(), zinc1_homodimer_design::setup_rollmoving(), z_rotation_matrix_degrees(), and z_rotation_matrix_radians().

z_rotation_matrix_degrees()

template<typename T >

xyzMatrix< T > numeric::z_rotation_matrix_degrees ( T const &  theta )

inline

Rotation matrix for rotation about the z axis by an angle in degrees.

References numeric::conversions::radians(), and z_rotation_matrix().

Referenced by MyRotMover::apply(), DetectSymmetry::apply(), SwapElementsMover2::apply(), dock(), get_rmsd(), get_rmsd_debug(), main(), place_water_acceptor(), numeric::random::random_rotation_angle(), and numeric::HomogeneousTransform< T >::set_zaxis_rotation_deg().

z_rotation_matrix_radians()

template<typename T >

xyzMatrix< T > numeric::z_rotation_matrix_radians ( T const &  theta )

inline

Rotation matrix for rotation about the z axis by an angle in radians.

References z_rotation_matrix().

Referenced by compute_chi(), main(), DisulfideBondEnergy::rebuildAndDetectDisulfideBond(), numeric::HomogeneousTransform< T >::set_zaxis_rotation_rad(), and DisulfideBondEnergy::tabulate().