Namespaces
	radians

Classes
struct	p

Typedefs
typedef Eigen::Matrix< Real, 8, 8 >	Matrix8

typedef Eigen::Matrix< Real, 16, 16 >	Matrix16

typedef Eigen::Matrix< Real, Eigen::Dynamic, 1, 0, 16, 1 >	Vector16

using	SolverType = linear_algebra::GeneralizedEigenSolver< Matrix16 >

typedef utility::fixedsizearray1< Real, 3 >	PseudoVector

typedef utility::fixedsizearray1 < PseudoVector, 3 >	PseudoMatrix

typedef struct numeric::kinematic_closure::p	poly

typedef utility::vector1 < numeric::Size >	IndexList

typedef utility::fixedsizearray1 < numeric::Real, 3 >	Coordinate

typedef utility::vector1 < Coordinate >	CoordinateList

typedef utility::vector1 < numeric::Real >	ParameterList

typedef utility::vector1 < ParameterList >	ParameterMatrix

Functions
void	triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 3 > &calpha, utility::fixedsizearray1< Real, 3 > &salpha)

void	triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 4 > &calpha, utility::fixedsizearray1< Real, 4 > &salpha)

void	sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 3 > &cosine, utility::fixedsizearray1< Real, 3 > &sine)

void	sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 4 > &cosine, utility::fixedsizearray1< Real, 4 > &sine)

void	triaxialCoefficients (const utility::fixedsizearray1< Real, 3 > &vb, const utility::fixedsizearray1< Real, 3 > &xi, const utility::fixedsizearray1< Real, 3 > &eta, const utility::fixedsizearray1< Real, 3 > &delta, const utility::fixedsizearray1< Real, 3 > &theta, const utility::vector1< int > &order, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &A, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &B, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &C, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &D, utility::fixedsizearray1< Real, 3 > &cal, utility::fixedsizearray1< Real, 3 > &sal, int &f)

void	cross (const utility::fixedsizearray1< Real, 3 > &L, const utility::fixedsizearray1< Real, 3 > &r0, utility::fixedsizearray1< Real, 3 > &r)

void	frame (const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &R, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &U)

Real	eucDistance (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b)

Real	scpn (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)

Real	bondangle (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)

Real	torsion (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c, const utility::fixedsizearray1< Real, 3 > &d)

void	chainParams (const int &n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, Real &vbond, Real &xi, Real &eta, Real &delta, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)

void	chainXYZ (const int &n, const utility::vector1< Real > &b_len1, const utility::vector1< Real > &b_ang1, const utility::vector1< Real > &t_ang1, const bool space, const utility::fixedsizearray1< Real, 3 > &R0, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &Q, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)

void	chainXYZ (const int &n, const utility::vector1< Real > &b_len, const utility::vector1< Real > &b_ang, const utility::vector1< Real > &t_ang, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)

void	chainTORS (const int &n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, utility::vector1< Real > &t_ang, utility::vector1< Real > &b_ang, utility::vector1< Real > &b_len, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)

void	rotateX (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rx)

void	rotateY (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Ry)

void	rotateZ (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rz)

void	bridgeObjects (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, const utility::vector1< Real > &dt, const utility::vector1< Real > &da, const utility::vector1< Real > &db, const utility::vector1< int > &pivots, const utility::vector1< int > &order, utility::vector1< utility::vector1< Real > > &t_ang, utility::vector1< utility::vector1< Real > > &b_ang, utility::vector1< utility::vector1< Real > > &b_len, int &nsol)
	Solve the triaxial loop closure problem for a system of atoms. More...

void	test_bridgeObjects ()

void	test_rotateX ()

void	test_chainTORS ()

void	test_chainXYZ ()

void	test_chainParams ()

void	test_torsion ()

void	test_bondangle ()

void	test_scpn ()

void	test_eucDistance ()

void	test_frame ()

void	test_cross ()

void	test_triaxialCoefficients ()

void	test_sincos ()

void	test_triangle ()

void	chainXYZ (const int &n, const utility::vector1< numeric::Real > &b_len, const utility::vector1< numeric::Real > &b_ang, const utility::vector1< numeric::Real > &t_ang, const bool space, const utility::vector1< numeric::Real > &R0, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &Q, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &atoms)

void	bridgeObjects_nonredundant (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &stub1, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &stub2, const utility::vector1< numeric::Real > &torsions_chain1, const utility::vector1< numeric::Real > &torsions_chain2, const utility::vector1< numeric::Real > &angles, const utility::vector1< numeric::Real > &bonds, utility::vector1< utility::vector1< Real > > &pivot_torsions, int &nsol)
	Nonredundant version of the bridgeObject function stub1 are the coordinates of the first pivot and 2 atoms preceeding it; stub2 are the coordinates of the third pivot and 2 atoms after it; torsions_chain1 are the torsions from pivot1 to pivot2, which has a length of (pivot2 - pivot1 - 2); torsions_chain2 are the torsions from pivot2 to pivot3, which has a length of (pivot3 - pivot2 - 2); angles are the bond angles from pivot1 to pivot3, which has a length of (pivot3 - pivot1 + 1); bonds are the bond lengths from pivot1 to pivot3, which has a length of (pivot3 - pivot1); pivot_torsions are the solutions of pivot tosions whose dimension is nsol * 6 where nsol is the number of solutions. More...

Eigen::IOFormat	scipy (8, 0,", ",",\n","[","]","[","]")

void	point_value2 (const utility::fixedsizearray1< Real, 3 > &A, const utility::vector1< Real > &t, utility::vector1< Real > &C)
	dixon functions /// More...

void	point_value4 (const utility::vector1< Real > &A, const utility::vector1< Real > &t, utility::vector1< Real > &C)

void	point_value6 (const utility::vector1< Real > &B, const utility::vector1< Real > &t, utility::vector1< Real > &C)

void	point_value8 (const utility::vector1< Real > &A, const utility::vector1< Real > &t, utility::vector1< Real > &C)

void	point_value16 (const utility::vector1< Real > &A, const utility::vector1< Real > &t, utility::vector1< Real > &C)

void	polyProduct2x2 (const utility::fixedsizearray1< Real, 3 > &A, const utility::fixedsizearray1< Real, 3 > &B, utility::vector1< Real > &C)

void	polyProduct4x2 (const utility::vector1< Real > &A, const utility::fixedsizearray1< Real, 3 > &B, utility::vector1< Real > &C)

void	polyProduct4x4 (const utility::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	polyProduct4sq (const utility::vector1< Real > &A, utility::vector1< Real > &C)

void	polyProduct6x6 (const utility::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	polyProduct12x4 (const utility::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	polyProduct8x8 (const utility::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	polyProduct8sq (const utility::vector1< Real > &A, utility::vector1< Real > &C)

void	vectorDiff (const utility::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	dixonResultant (const utility::vector1< utility::vector1< Real > > &A, const utility::vector1< utility::vector1< Real > > &B, const utility::vector1< utility::vector1< Real > > &C, const utility::vector1< utility::vector1< Real > > &D, utility::vector1< utility::vector1< utility::vector1< Real > > > &R)

void	build_dixon_matrices (PseudoMatrix const &A, PseudoMatrix const &B, PseudoMatrix const &C, PseudoMatrix const &D, Matrix8 &R0, Matrix8 &R1, Matrix8 &R2)

void	build_sin_and_cos (utility::vector1< PseudoVector > const &u, utility::vector1< PseudoVector > &sin, utility::vector1< PseudoVector > &cos)

void	dixon_eig (PseudoMatrix const &A, PseudoMatrix const &B, PseudoMatrix const &C, PseudoMatrix const &D, vector1< int > const &, utility::vector1< utility::fixedsizearray1< Real, 3 > > &cos, utility::vector1< utility::fixedsizearray1< Real, 3 > > &sin, utility::vector1< utility::fixedsizearray1< Real, 3 > > &u, int &num_solutions)

void	dixon_sturm (const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &A, const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &B, const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &C, const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &D, const utility::vector1< int > &order, utility::vector1< utility::fixedsizearray1< Real, 3 > > &cos, utility::vector1< utility::fixedsizearray1< Real, 3 > > &sin, utility::vector1< utility::fixedsizearray1< Real, 3 > > &tau, int &nsol)

void	test_point_value2 ()

void	test_polyProduct6x6 ()

void	test_polyProduct4sq ()

void	test_polyProduct4x4 ()

void	test_polyProduct4x2 ()

void	test_polyProduct2x2 ()

void	test_dixon ()

void	dixon_eig (const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &A, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &B, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &C, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &D, const utility::vector1< int > &order, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &cos, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &sin, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &tau, int &nsol)

bool	vectorsEqual (const utility::vector1< Real > &A, const utility::vector1< Real > &B)

template<class Iterable >
void	printVector (const Iterable &V)
	helper functions /// More...

template<class MatrixLike >
void	printMatrix (const MatrixLike &M)
	prints the matrix More...

template<class MatrixLike >
void	printTranspose (const MatrixLike &M)

template<Size rows>
void	multMatrix (const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, rows >, rows > &A, const utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &B, utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &C)

template<Size rows>
void	multTransMatrix (const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, rows >, rows > &A, const utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &B, utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &C)

void	initialize_sturm (double tol_secant, int max_iter_sturm, int *max_iter_secant)

double	hyper_tan (double a, double x)

int	modp (poly u, poly v, poly *r)

int	buildsturm (int ord, poly *sseq)

int	numroots (int np, poly sseq, int atneg, int *atpos)

double	evalpoly (int ord, double *coef, double x)

int	numchanges (int np, poly *sseq, double a)

int	modrf (int ord, double coef, double a, double b, double val)

void	sbisect (int np, poly sseq, double min, double max, int atmin, int atmax, double roots)

void	solve_sturm (const int &p_order, int &n_root, const utility::vector1< double > &poly_coeffs, utility::vector1< double > &roots)

Real	dot (Coordinate const &a, Coordinate const &b)

Coordinate	cross (Coordinate const &a, Coordinate const &b)

Coordinate	norm (Coordinate const &a)

std::ostream &	operator<< (std::ostream &out, ParameterList const &x)

std::ostream &	operator<< (std::ostream &out, ParameterMatrix const &xx)

Coordinate	operator+ (Coordinate const &a, Coordinate const &b)

Coordinate	operator- (Coordinate const &a, Coordinate const &b)

Coordinate	operator* (Coordinate const &a, Real const &k)

Coordinate	operator* (Real const &k, Coordinate const &a)

Coordinate	operator/ (Coordinate const &a, Real const &k)

Coordinate	operator/ (Real const &k, Coordinate const &a)

template<class T >
Coordinate &	operator<< (Coordinate &a, xyzVector< T > const &b)

template<class T >
xyzVector< T > &	operator<< (xyzVector< T > &a, Coordinate const &b)

Variables
string	skipl = "\n\n"

double	RELERROR

int	MAXIT

int	MAX_ITER_SECANT

Typedef Documentation

typedef utility::fixedsizearray1<numeric::Real,3> numeric::kinematic_closure::Coordinate

typedef utility::vector1<Coordinate> numeric::kinematic_closure::CoordinateList

typedef utility::vector1<numeric::Size> numeric::kinematic_closure::IndexList

typedef Eigen::Matrix<Real, 16, 16> numeric::kinematic_closure::Matrix16

typedef Eigen::Matrix<Real, 8, 8> numeric::kinematic_closure::Matrix8

typedef utility::vector1<numeric::Real> numeric::kinematic_closure::ParameterList

typedef utility::vector1<ParameterList> numeric::kinematic_closure::ParameterMatrix

typedef struct numeric::kinematic_closure::p numeric::kinematic_closure::poly

typedef utility::fixedsizearray1<PseudoVector,3> numeric::kinematic_closure::PseudoMatrix

typedef utility::fixedsizearray1<Real,3> numeric::kinematic_closure::PseudoVector

using numeric::kinematic_closure::SolverType = typedef linear_algebra::GeneralizedEigenSolver<Matrix16>

typedef Eigen::Matrix<Real, Eigen::Dynamic, 1, 0, 16, 1> numeric::kinematic_closure::Vector16

Function Documentation

numeric::Real numeric::kinematic_closure::bondangle	(	const utility::fixedsizearray1< Real, 3 > &	a,
		const utility::fixedsizearray1< Real, 3 > &	b,
		const utility::fixedsizearray1< Real, 3 > &	c
	)

References eucDistance(), rad2deg, and scpn().

Referenced by chainParams(), chainTORS(), and test_bondangle().

void numeric::kinematic_closure::bridgeObjects	(	const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	atoms,
		const utility::vector1< Real > &	dt,
		const utility::vector1< Real > &	da,
		const utility::vector1< Real > &	db,
		const utility::vector1< int > &	pivots,
		const utility::vector1< int > &	order,
		utility::vector1< utility::vector1< Real > > &	t_ang,
		utility::vector1< utility::vector1< Real > > &	b_ang,
		utility::vector1< utility::vector1< Real > > &	b_len,
		int &	nsol
	)

Solve the triaxial loop closure problem for a system of atoms.

Parameters

[in]	atoms	- matrix of cartesian coordiantes of N-CA-C atoms indexed as atoms[atom][dimension]
[in]	dt	- desired torsions for each atom
[in]	da	- desired bond angle for each atom
[in]	db	- desired bond length for each atom
[in]	pivots	- 3 indices (base 1) of atoms to be used as loop closure pivots
[in]	order	- length 3 vector giving order to solve for the tau parameters (use 1,2,3 if unsure)
[out]	t_ang	- matrix giving torsion angles for each atom for each solution, indexed as t_ang[solution][atom]
[out]	b_ang	- matrix giving bond angles for each atom for each solution, indexed as b_ang[solution][atom]
[out]	b_len	- matrix giving bond lengths for each atom for each solution, indexed as b_len[solution][atom]
[out]	nsol	- number of solutions found

Global Read:

Global Write:

Returns

Remarks: dt, da, and db are cast to Real precision when placed in t_ang1,2, b_ang1,2 and b_len1,2. Solution is carried out in Real precision. Solutions are cast back to Reals when placed into t_ang.

References:

Author: Evangelos A. Coutsias; Daniel J. Mandell

References ObjexxFCL::format::A(), erraser_analysis::atoms, C, chainParams(), chainXYZ(), basic::options::OptionKeys::out::path::db, deg2rad, dixon_eig(), demo.D060_Folding::f, basic::options::OptionKeys::frags::j, test.G201_Module_Structure::l1, test.G200_Module_Region::loop, multMatrix(), multTransMatrix(), rotateX(), rotateZ(), torsion(), and triaxialCoefficients().

Referenced by bridgeObjects_nonredundant(), and test_bridgeObjects().

void numeric::kinematic_closure::bridgeObjects_nonredundant	(	const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	stub1,
		const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	stub2,
		const utility::vector1< numeric::Real > &	torsions_chain1,
		const utility::vector1< numeric::Real > &	torsions_chain2,
		const utility::vector1< numeric::Real > &	angles,
		const utility::vector1< numeric::Real > &	bonds,
		utility::vector1< utility::vector1< Real > > &	pivot_torsions,
		int &	nsol
	)

Nonredundant version of the bridgeObject function stub1 are the coordinates of the first pivot and 2 atoms preceeding it; stub2 are the coordinates of the third pivot and 2 atoms after it; torsions_chain1 are the torsions from pivot1 to pivot2, which has a length of (pivot2 - pivot1 - 2); torsions_chain2 are the torsions from pivot2 to pivot3, which has a length of (pivot3 - pivot2 - 2); angles are the bond angles from pivot1 to pivot3, which has a length of (pivot3 - pivot1 + 1); bonds are the bond lengths from pivot1 to pivot3, which has a length of (pivot3 - pivot1); pivot_torsions are the solutions of pivot tosions whose dimension is nsol * 6 where nsol is the number of solutions.

References erraser_analysis::atoms, bridgeObjects(), basic::options::OptionKeys::out::path::db, and basic::options::OptionKeys::frags::j.

void numeric::kinematic_closure::build_dixon_matrices	(	PseudoMatrix const &	A,
		PseudoMatrix const &	B,
		PseudoMatrix const &	C,
		PseudoMatrix const &	D,
		Matrix8 &	R0,
		Matrix8 &	R1,
		Matrix8 &	R2
	)

Referenced by dixon_eig().

void numeric::kinematic_closure::build_sin_and_cos	(	utility::vector1< PseudoVector > const &	u,
		utility::vector1< PseudoVector > &	sin,
		utility::vector1< PseudoVector > &	cos
	)

References basic::options::OptionKeys::frags::j.

Referenced by dixon_eig().

int numeric::kinematic_closure::buildsturm	(	int	ord,
		poly *	sseq
	)

inline

References numeric::kinematic_closure::p::coef, demo.D060_Folding::f, modp(), and numeric::kinematic_closure::p::ord.

Referenced by solve_sturm().

void numeric::kinematic_closure::chainParams	(	const int &	n,
		const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	atoms,
		Real &	vbond,
		Real &	xi,
		Real &	eta,
		Real &	delta,
		utility::fixedsizearray1< Real, 3 > &	R0,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	Q
	)

References erraser_analysis::atoms, bondangle(), eucDistance(), frame(), and torsion().

Referenced by bridgeObjects(), and test_chainParams().

void numeric::kinematic_closure::chainTORS	(	const int &	n,
		const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	atoms,
		utility::vector1< Real > &	t_ang,
		utility::vector1< Real > &	b_ang,
		utility::vector1< Real > &	b_len,
		utility::fixedsizearray1< Real, 3 > &	R0,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	Q
	)

References erraser_analysis::atoms, bondangle(), eucDistance(), frame(), basic::options::OptionKeys::frags::j, and torsion().

Referenced by test_chainTORS().

void numeric::kinematic_closure::chainXYZ	(	const int &	n,
		const utility::vector1< numeric::Real > &	b_len,
		const utility::vector1< numeric::Real > &	b_ang,
		const utility::vector1< numeric::Real > &	t_ang,
		const bool	space,
		const utility::vector1< numeric::Real > &	R0,
		const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	Q,
		utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &	atoms
	)

void numeric::kinematic_closure::chainXYZ	(	const int &	n,
		const utility::vector1< Real > &	b_len1,
		const utility::vector1< Real > &	b_ang1,
		const utility::vector1< Real > &	t_ang1,
		const bool	space,
		const utility::fixedsizearray1< Real, 3 > &	R0,
		const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	Q,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	atoms
	)

References erraser_analysis::atoms, deg2rad, basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::s, and test.T850_SubClassing::v.

Referenced by bridgeObjects(), chainXYZ(), and test_chainXYZ().

void numeric::kinematic_closure::chainXYZ	(	const int &	n,
		const utility::vector1< Real > &	b_len,
		const utility::vector1< Real > &	b_ang,
		const utility::vector1< Real > &	t_ang,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	atoms
	)

References erraser_analysis::atoms, and chainXYZ().

Coordinate numeric::kinematic_closure::cross	(	Coordinate const &	a,
		Coordinate const &	b
	)

References pyrosetta.tests.__main__::result.

void numeric::kinematic_closure::cross	(	const utility::fixedsizearray1< Real, 3 > &	L,
		const utility::fixedsizearray1< Real, 3 > &	r0,
		utility::fixedsizearray1< Real, 3 > &	r
	)

Referenced by frame(), test_cross(), and torsion().

void numeric::kinematic_closure::dixon_eig	(	const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	A,
		const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	B,
		const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	C,
		const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	D,
		const utility::vector1< int > &	order,
		utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &	cos,
		utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &	sin,
		utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &	tau,
		int &	nsol
	)

void numeric::kinematic_closure::dixon_eig	(	PseudoMatrix const &	A,
		PseudoMatrix const &	B,
		PseudoMatrix const &	C,
		PseudoMatrix const &	D,
		vector1< int > const &	,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	cos,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	sin,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	u,
		int &	num_solutions
	)

References ObjexxFCL::abs(), build_dixon_matrices(), build_sin_and_cos(), test.T009_Exceptions::e, test.T110_numeric::I, numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::num_real_solutions(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvalues(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvectors(), and test.T110_numeric::V.

Referenced by numeric::kinematic_closure::radians::bridge_objects(), and bridgeObjects().

void numeric::kinematic_closure::dixon_sturm	(	const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	A,
		const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	B,
		const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	C,
		const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	D,
		const utility::vector1< int > &	order,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	cos,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	sin,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	tau,
		int &	nsol
	)

void numeric::kinematic_closure::dixonResultant	(	const utility::vector1< utility::vector1< Real > > &	A,
		const utility::vector1< utility::vector1< Real > > &	B,
		const utility::vector1< utility::vector1< Real > > &	C,
		const utility::vector1< utility::vector1< Real > > &	D,
		utility::vector1< utility::vector1< utility::vector1< Real > > > &	R
	)

References C, DIXON_RESULTANT_SIZE, and DIXON_SIZE.

Real numeric::kinematic_closure::dot	(	Coordinate const &	a,
		Coordinate const &	b
	)

Real numeric::kinematic_closure::eucDistance	(	const utility::fixedsizearray1< Real, 3 > &	a,
		const utility::fixedsizearray1< Real, 3 > &	b
	)

References ObjexxFCL::pow().

Referenced by bondangle(), chainParams(), chainTORS(), and test_eucDistance().

double numeric::kinematic_closure::evalpoly	(	int	ord,
		double *	coef,
		double	x
	)

inline

References demo.D060_Folding::f.

Referenced by numchanges().

void numeric::kinematic_closure::frame	(	const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	R,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	U
	)

References cross().

Referenced by chainParams(), chainTORS(), DockFragmentsMover::cluster_frags(), make_1mer_frags(), make_frags(), run(), DockFragmentsMover::run(), and test_frame().

double numeric::kinematic_closure::hyper_tan	(	double	a,
		double	x
	)

inline

References numeric::crick_equations::x().

void numeric::kinematic_closure::initialize_sturm	(	double *	tol_secant,
		int *	max_iter_sturm,
		int *	max_iter_secant
	)

inline

References MAX_ITER_SECANT, MAXIT, and RELERROR.

Referenced by dixon_sturm().

int numeric::kinematic_closure::modp	(	poly *	u,
		poly *	v,
		poly *	r
	)

inline

References numeric::kinematic_closure::p::coef, basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::frags::j, numeric::kinematic_closure::p::ord, and SMALL_ENOUGH.

Referenced by buildsturm().

int numeric::kinematic_closure::modrf	(	int	ord,
		double *	coef,
		double	a,
		double	b,
		double *	val
	)

inline

References basic::options::OptionKeys::score::fiber_diffraction::b, MAX_ITER_SECANT, RELERROR, and numeric::crick_equations::x().

Referenced by sbisect().

template<Size rows>

void numeric::kinematic_closure::multMatrix	(	const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, rows >, rows > &	A,
		const utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &	B,
		utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &	C
	)

References C, and basic::options::OptionKeys::frags::j.

Referenced by numeric::kinematic_closure::radians::bridge_objects(), and bridgeObjects().

template<Size rows>

void numeric::kinematic_closure::multTransMatrix	(	const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, rows >, rows > &	A,
		const utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &	B,
		utility::vector1< utility::fixedsizearray1< numeric::Real, rows > > &	C
	)

References C, and basic::options::OptionKeys::frags::j.

Referenced by numeric::kinematic_closure::radians::bridge_objects(), and bridgeObjects().

Coordinate numeric::kinematic_closure::norm ( Coordinate const & a )

References pyrosetta.tests.__main__::result.

int numeric::kinematic_closure::numchanges	(	int	np,
		poly *	sseq,
		double	a
	)

inline

References numeric::kinematic_closure::p::coef, evalpoly(), demo.D060_Folding::f, numeric::kinematic_closure::p::ord, and basic::options::OptionKeys::in::file::s.

Referenced by sbisect(), and solve_sturm().

int numeric::kinematic_closure::numroots	(	int	np,
		poly *	sseq,
		int *	atneg,
		int *	atpos
	)

inline

References numeric::kinematic_closure::p::coef, demo.D060_Folding::f, numeric::kinematic_closure::p::ord, and basic::options::OptionKeys::in::file::s.

Referenced by solve_sturm().

Coordinate numeric::kinematic_closure::operator*	(	Coordinate const &	a,
		Real const &	k
	)

References pyrosetta.tests.__main__::result.

Coordinate numeric::kinematic_closure::operator*	(	Real const &	k,
		Coordinate const &	a
	)

References pyrosetta.tests.__main__::result.

Coordinate numeric::kinematic_closure::operator+	(	Coordinate const &	a,
		Coordinate const &	b
	)

References pyrosetta.tests.__main__::result.

Coordinate numeric::kinematic_closure::operator-	(	Coordinate const &	a,
		Coordinate const &	b
	)

References pyrosetta.tests.__main__::result.

Coordinate numeric::kinematic_closure::operator/	(	Coordinate const &	a,
		Real const &	k
	)

References pyrosetta.tests.__main__::result.

Coordinate numeric::kinematic_closure::operator/	(	Real const &	k,
		Coordinate const &	a
	)

References pyrosetta.tests.__main__::result.

std::ostream & numeric::kinematic_closure::operator<<	(	std::ostream &	out,
		ParameterList const &	x
	)

References erraser_single_res_analysis::out, erraser_single_res_analysis::prefix, and basic::options::OptionKeys::out::suffix.

template<class T >

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

References basic::options::OptionKeys::score::fiber_diffraction::a, and basic::options::OptionKeys::score::fiber_diffraction::b.

template<class T >

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

References basic::options::OptionKeys::score::fiber_diffraction::a, and basic::options::OptionKeys::score::fiber_diffraction::b.

std::ostream & numeric::kinematic_closure::operator<<	(	std::ostream &	out,
		ParameterMatrix const &	xx
	)

References erraser_single_res_analysis::out, erraser_single_res_analysis::prefix, and basic::options::OptionKeys::out::suffix.

void numeric::kinematic_closure::point_value16	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	t,
		utility::vector1< Real > &	C
	)

void numeric::kinematic_closure::point_value2	(	const utility::fixedsizearray1< Real, 3 > &	A,
		const utility::vector1< Real > &	t,
		utility::vector1< Real > &	C
	)

dixon functions ///

Referenced by dixon_sturm(), and test_point_value2().

void numeric::kinematic_closure::point_value4	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	t,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

void numeric::kinematic_closure::point_value6	(	const utility::vector1< Real > &	B,
		const utility::vector1< Real > &	t,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

void numeric::kinematic_closure::point_value8	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	t,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

void numeric::kinematic_closure::polyProduct12x4	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	B,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

void numeric::kinematic_closure::polyProduct2x2	(	const utility::fixedsizearray1< Real, 3 > &	A,
		const utility::fixedsizearray1< Real, 3 > &	B,
		utility::vector1< Real > &	C
	)

References PP4x2_VECSIZE.

Referenced by dixon_sturm(), and test_polyProduct2x2().

void numeric::kinematic_closure::polyProduct4sq	(	const utility::vector1< Real > &	A,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm(), and test_polyProduct4sq().

void numeric::kinematic_closure::polyProduct4x2	(	const utility::vector1< Real > &	A,
		const utility::fixedsizearray1< Real, 3 > &	B,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm(), and test_polyProduct4x2().

void numeric::kinematic_closure::polyProduct4x4	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	B,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm(), and test_polyProduct4x4().

void numeric::kinematic_closure::polyProduct6x6	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	B,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm(), and test_polyProduct6x6().

void numeric::kinematic_closure::polyProduct8sq	(	const utility::vector1< Real > &	A,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

void numeric::kinematic_closure::polyProduct8x8	(	const utility::vector1< Real > &	A,
		const utility::vector1< Real > &	B,
		utility::vector1< Real > &	C
	)

Referenced by dixon_sturm().

template<class MatrixLike >

void numeric::kinematic_closure::printMatrix ( const MatrixLike & M )

prints the matrix

This function used to intentionally print the transpose of the matrix. The rational was that "we use row-major indexing". That didn't make any sense to me, and I'd been mislead by the implicit transpose a couple of times, so I got rid of it.

References utility::io::oc::cout.

Referenced by test_chainParams(), test_chainTORS(), test_chainXYZ(), test_dixon(), test_frame(), test_rotateX(), and test_triaxialCoefficients().

template<class MatrixLike >

void numeric::kinematic_closure::printTranspose ( const MatrixLike & M )

References utility::io::oc::cout, and basic::options::OptionKeys::frags::j.

template<class Iterable >

void numeric::kinematic_closure::printVector ( const Iterable & V )

helper functions ///

References utility::io::oc::cout.

Referenced by test_chainParams(), test_chainTORS(), test_cross(), test_point_value2(), test_polyProduct2x2(), test_polyProduct4sq(), test_polyProduct4x2(), test_polyProduct4x4(), test_polyProduct6x6(), and test_triangle().

void numeric::kinematic_closure::rotateX	(	const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	R,
		const Real &	c,
		const Real &	s,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	Rx
	)

Referenced by bridgeObjects(), and test_rotateX().

void numeric::kinematic_closure::rotateY	(	const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	R,
		const Real &	c,
		const Real &	s,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	Ry
	)

void numeric::kinematic_closure::rotateZ	(	const utility::vector1< utility::fixedsizearray1< Real, 3 > > &	R,
		const Real &	c,
		const Real &	s,
		utility::vector1< utility::fixedsizearray1< Real, 3 > > &	Rz
	)

Referenced by bridgeObjects().

void numeric::kinematic_closure::sbisect	(	int	np,
		poly *	sseq,
		double	min,
		double	max,
		int	atmin,
		int	atmax,
		double *	roots
	)

inline

References numeric::kinematic_closure::p::coef, numeric::max(), MAXIT, modrf(), numchanges(), numeric::kinematic_closure::p::ord, and RELERROR.

Referenced by solve_sturm().

Eigen::IOFormat numeric::kinematic_closure::scipy	(	8	,
		0	,
		"	,
		"	,
		"	,
		\n"	,
		""	[","],
		""	[","]
	)

Real numeric::kinematic_closure::scpn	(	const utility::fixedsizearray1< Real, 3 > &	a,
		const utility::fixedsizearray1< Real, 3 > &	b,
		const utility::fixedsizearray1< Real, 3 > &	c
	)

Referenced by bondangle(), and test_scpn().

void numeric::kinematic_closure::sincos	(	const utility::fixedsizearray1< Real, 3 > &	theta,
		const int	flag,
		utility::fixedsizearray1< Real, 3 > &	cosine,
		utility::fixedsizearray1< Real, 3 > &	sine
	)

References basic::options::OptionKeys::score::fiber_diffraction::a, test.Workshop3test::a1, and basic::options::OptionKeys::mh::match::aa.

Referenced by test_sincos(), and triaxialCoefficients().

void numeric::kinematic_closure::sincos	(	const utility::fixedsizearray1< Real, 3 > &	theta,
		const int	flag,
		utility::fixedsizearray1< Real, 4 > &	cosine,
		utility::fixedsizearray1< Real, 4 > &	sine
	)

References basic::options::OptionKeys::score::fiber_diffraction::a, test.Workshop3test::a1, and basic::options::OptionKeys::mh::match::aa.

void numeric::kinematic_closure::solve_sturm	(	const int &	p_order,
		int &	n_root,
		const utility::vector1< double > &	poly_coeffs,
		utility::vector1< double > &	roots
	)

inline

References buildsturm(), numeric::kinematic_closure::p::coef, basic::options::OptionKeys::frags::j, numeric::max(), MAX_ORDER, MAXPOW, numeric::min(), numchanges(), numroots(), and sbisect().

Referenced by dixon_sturm().

void numeric::kinematic_closure::test_bondangle ( )

References basic::options::OptionKeys::score::fiber_diffraction::a, basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::score::fiber_diffraction::b, bondangle(), and utility::io::oc::cout.

void numeric::kinematic_closure::test_bridgeObjects ( )

References erraser_analysis::atoms, bridgeObjects(), and basic::options::OptionKeys::out::path::db.

void numeric::kinematic_closure::test_chainParams ( )

References erraser_analysis::atoms, chainParams(), basic::options::OptionKeys::frags::j, printMatrix(), and printVector().

void numeric::kinematic_closure::test_chainTORS ( )

References erraser_analysis::atoms, chainTORS(), basic::options::OptionKeys::frags::j, printMatrix(), and printVector().

void numeric::kinematic_closure::test_chainXYZ ( )

References erraser_analysis::atoms, chainXYZ(), basic::options::OptionKeys::frags::j, and printMatrix().

void numeric::kinematic_closure::test_cross ( )

References cross(), ObjexxFCL::format::L(), and printVector().

void numeric::kinematic_closure::test_dixon ( )

References ObjexxFCL::format::A(), C, utility::io::oc::cout, basic::options::OptionKeys::frags::j, and printMatrix().

void numeric::kinematic_closure::test_eucDistance ( )

References basic::options::OptionKeys::score::fiber_diffraction::a, basic::options::OptionKeys::score::fiber_diffraction::b, utility::io::oc::cout, and eucDistance().

void numeric::kinematic_closure::test_frame ( )

References frame(), basic::options::OptionKeys::frags::j, and printMatrix().

void numeric::kinematic_closure::test_point_value2 ( )

References ObjexxFCL::format::A(), C, point_value2(), printVector(), and basic::options::OptionKeys::in::file::t.

void numeric::kinematic_closure::test_polyProduct2x2 ( )

References ObjexxFCL::format::A(), C, polyProduct2x2(), and printVector().

void numeric::kinematic_closure::test_polyProduct4sq ( )

References ObjexxFCL::format::A(), C, polyProduct4sq(), and printVector().

void numeric::kinematic_closure::test_polyProduct4x2 ( )

References ObjexxFCL::format::A(), C, polyProduct4x2(), and printVector().

void numeric::kinematic_closure::test_polyProduct4x4 ( )

References ObjexxFCL::format::A(), C, polyProduct4x4(), and printVector().

void numeric::kinematic_closure::test_polyProduct6x6 ( )

References ObjexxFCL::format::A(), C, polyProduct6x6(), and printVector().

void numeric::kinematic_closure::test_rotateX ( )

References basic::options::OptionKeys::frags::j, printMatrix(), and rotateX().

void numeric::kinematic_closure::test_scpn ( )

References basic::options::OptionKeys::score::fiber_diffraction::a, basic::options::OptionKeys::score::fiber_diffraction::b, utility::io::oc::cout, and scpn().

void numeric::kinematic_closure::test_sincos ( )

References sincos().

void numeric::kinematic_closure::test_torsion ( )

References basic::options::OptionKeys::score::fiber_diffraction::a, basic::options::OptionKeys::score::fiber_diffraction::b, utility::io::oc::cout, and torsion().

void numeric::kinematic_closure::test_triangle ( )

References printVector(), and triangle().

void numeric::kinematic_closure::test_triaxialCoefficients ( )

References ObjexxFCL::format::A(), C, dixon_sturm(), demo.D060_Folding::f, printMatrix(), and triaxialCoefficients().

numeric::Real numeric::kinematic_closure::torsion	(	const utility::fixedsizearray1< Real, 3 > &	a,
		const utility::fixedsizearray1< Real, 3 > &	b,
		const utility::fixedsizearray1< Real, 3 > &	c,
		const utility::fixedsizearray1< Real, 3 > &	d
	)

References cross(), demo.D060_Folding::f, pidegs, ObjexxFCL::pow(), rad2deg, basic::options::OptionKeys::in::file::s, numeric::crick_equations::y(), and numeric::crick_equations::z().

Referenced by bridgeObjects(), chainParams(), chainTORS(), and test_torsion().

void numeric::kinematic_closure::triangle	(	const utility::fixedsizearray1< Real, 3 > &	vbond,
		utility::fixedsizearray1< Real, 3 > &	calpha,
		utility::fixedsizearray1< Real, 3 > &	salpha
	)

Referenced by test_triangle(), and triaxialCoefficients().

void numeric::kinematic_closure::triangle	(	const utility::fixedsizearray1< Real, 3 > &	vbond,
		utility::fixedsizearray1< Real, 4 > &	calpha,
		utility::fixedsizearray1< Real, 4 > &	salpha
	)

void numeric::kinematic_closure::triaxialCoefficients	(	const utility::fixedsizearray1< Real, 3 > &	vb,
		const utility::fixedsizearray1< Real, 3 > &	xi,
		const utility::fixedsizearray1< Real, 3 > &	eta,
		const utility::fixedsizearray1< Real, 3 > &	delta,
		const utility::fixedsizearray1< Real, 3 > &	theta,
		const utility::vector1< int > &	order,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	A,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	B,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	C,
		utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &	D,
		utility::fixedsizearray1< Real, 3 > &	cal,
		utility::fixedsizearray1< Real, 3 > &	sal,
		int &	f
	)