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

typedef linear_algebra::GeneralizedEigenSolver < Matrix16 >	SolverType

typedef vector1< Real >	PseudoVector

typedef vector1< PseudoVector >	PseudoMatrix

typedef struct numeric::kinematic_closure::p	poly

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

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

typedef utility::vector1 < Coordinate >	CoordinateList

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

typedef utility::vector1 < ParameterList >	ParameterMatrix

Functions
void	triangle (const utility::vector1< Real > &vbond, utility::vector1< Real > &calpha, utility::vector1< Real > &salpha)

void	sincos (const utility::vector1< Real > &theta, const int flag, utility::vector1< Real > &cosine, utility::vector1< Real > &sine)

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

void	cross (const utility::vector1< Real > &L, const utility::vector1< Real > &r0, utility::vector1< Real > &r)

void	frame (const utility::vector1< utility::vector1< Real > > &R, utility::vector1< utility::vector1< Real > > &U)

Real	eucDistance (const utility::vector1< Real > &a, const utility::vector1< Real > &b)

Real	scpn (const utility::vector1< Real > &a, const utility::vector1< Real > &b, const utility::vector1< Real > &c)

Real	bondangle (const utility::vector1< Real > &a, const utility::vector1< Real > &b, const utility::vector1< Real > &c)

Real	torsion (const utility::vector1< Real > &a, const utility::vector1< Real > &b, const utility::vector1< Real > &c, const utility::vector1< Real > &d)

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

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

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

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

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

void	bridgeObjects (const utility::vector1< utility::vector1< Real > > &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 ()

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

void	point_value2 (const utility::vector1< Real > &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::vector1< Real > &A, const utility::vector1< Real > &B, utility::vector1< Real > &C)

void	polyProduct4x2 (const utility::vector1< Real > &A, const utility::vector1< Real > &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 (PseudoMatrix const &u, PseudoMatrix &sin, PseudoMatrix &cos)

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

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

void	printVector (const utility::vector1< Real > &V)
	helper functions /// More...

void	printMatrix (const utility::vector1< utility::vector1< Real > > &M)
	prints the matrix More...

void	printTranspose (const utility::vector1< utility::vector1< Real > > &M)

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

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

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

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::vector1<numeric::Real> numeric::kinematic_closure::Coordinate

Definition at line 24 of file types.hh.

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

Definition at line 25 of file types.hh.

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

Definition at line 23 of file types.hh.

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

Definition at line 51 of file dixon.cc.

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

Definition at line 50 of file dixon.cc.

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

Definition at line 27 of file types.hh.

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

Definition at line 28 of file types.hh.

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

typedef vector1<PseudoVector> numeric::kinematic_closure::PseudoMatrix

Definition at line 62 of file dixon.cc.

typedef vector1<Real> numeric::kinematic_closure::PseudoVector

Definition at line 61 of file dixon.cc.

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

Definition at line 53 of file dixon.cc.

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

Definition at line 52 of file dixon.cc.

Function Documentation

numeric::Real numeric::kinematic_closure::bondangle	(	const utility::vector1< Real > &	a,
		const utility::vector1< Real > &	b,
		const utility::vector1< Real > &	c
	)

Definition at line 281 of file bridgeObjects.cc.

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

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

void numeric::kinematic_closure::bridgeObjects	(	const utility::vector1< utility::vector1< Real > > &	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

Definition at line 680 of file bridgeObjects.cc.

References ObjexxFCL::format::A(), 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 test_bridgeObjects().

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
	)

Definition at line 372 of file dixon.cc.

Referenced by dixon_eig().

void numeric::kinematic_closure::build_sin_and_cos	(	PseudoMatrix const &	u,
		PseudoMatrix &	sin,
		PseudoMatrix &	cos
	)

Definition at line 405 of file dixon.cc.

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

Referenced by dixon_eig().

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

inline

Definition at line 136 of file sturm.hh.

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::vector1< Real > > &	atoms,
		Real &	vbond,
		Real &	xi,
		Real &	eta,
		Real &	delta,
		utility::vector1< Real > &	R0,
		utility::vector1< utility::vector1< Real > > &	Q
	)

Definition at line 329 of file bridgeObjects.cc.

References bondangle(), eucDistance(), frame(), and torsion().

Referenced by bridgeObjects(), and test_chainParams().

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

Definition at line 576 of file bridgeObjects.cc.

References 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< Real > &	b_len1,
		const utility::vector1< Real > &	b_ang1,
		const utility::vector1< Real > &	t_ang1,
		const bool	space,
		const utility::vector1< Real > &	R0,
		const utility::vector1< utility::vector1< Real > > &	Q,
		utility::vector1< utility::vector1< Real > > &	atoms
	)

Definition at line 365 of file bridgeObjects.cc.

References 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::vector1< Real > > &	atoms
	)

Definition at line 549 of file bridgeObjects.cc.

References chainXYZ().

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

Definition at line 30 of file vector.cc.

void numeric::kinematic_closure::cross	(	const utility::vector1< Real > &	L,
		const utility::vector1< Real > &	r0,
		utility::vector1< Real > &	r
	)

Definition at line 230 of file bridgeObjects.cc.

Referenced by HDmakerMover::apply(), frame(), slice_ellipsoid_envelope(), test_cross(), and torsion().

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

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

Definition at line 431 of file dixon.cc.

References ObjexxFCL::abs(), build_dixon_matrices(), build_sin_and_cos(), ObjexxFCL::format::I(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::num_real_solutions(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvalues(), and numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvectors().

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

void numeric::kinematic_closure::dixon_sturm	(	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,
		const utility::vector1< int > &	order,
		utility::vector1< utility::vector1< Real > > &	cos,
		utility::vector1< utility::vector1< Real > > &	sin,
		utility::vector1< utility::vector1< Real > > &	tau,
		int &	nsol
	)

Definition at line 492 of file dixon.cc.

References ObjexxFCL::format::A(), C, initialize_sturm(), basic::options::OptionKeys::frags::j, point_value2(), point_value4(), point_value6(), point_value8(), polyProduct12x4(), polyProduct2x2(), polyProduct4sq(), polyProduct4x2(), polyProduct4x4(), polyProduct6x6(), polyProduct8sq(), polyProduct8x8(), PP4x2_VECSIZE, solve_sturm(), vectorDiff(), basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

Referenced by test_triaxialCoefficients().

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
	)

Definition at line 279 of file dixon.cc.

References ObjexxFCL::format::A(), C, DIXON_RESULTANT_SIZE, and DIXON_SIZE.

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

Definition at line 26 of file vector.cc.

Real numeric::kinematic_closure::eucDistance	(	const utility::vector1< Real > &	a,
		const utility::vector1< Real > &	b
	)

Definition at line 269 of file bridgeObjects.cc.

References ObjexxFCL::pow().

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

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

inline

Definition at line 247 of file sturm.hh.

References demo.D060_Folding::f.

Referenced by numchanges().

void numeric::kinematic_closure::frame	(	const utility::vector1< utility::vector1< Real > > &	R,
		utility::vector1< utility::vector1< Real > > &	U
	)

Definition at line 244 of file bridgeObjects.cc.

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

Definition at line 62 of file sturm.hh.

References x().

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

inline

Definition at line 54 of file sturm.hh.

References MAX_ITER_SECANT, MAXIT, and RELERROR.

Referenced by dixon_sturm().

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

inline

Definition at line 88 of file sturm.hh.

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

Definition at line 300 of file sturm.hh.

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

Referenced by sbisect().

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

Definition at line 62 of file kinematic_closure_helpers.cc.

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

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

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

Definition at line 83 of file kinematic_closure_helpers.cc.

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 )

Definition at line 40 of file vector.cc.

Referenced by numeric::distance(), numeric::model_quality::fixEigenvector(), numeric::model_quality::rsym_eigenval(), and numeric::model_quality::rsym_rotation().

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

inline

Definition at line 269 of file sturm.hh.

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

Definition at line 187 of file sturm.hh.

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
	)

Definition at line 96 of file vector.cc.

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

Definition at line 106 of file vector.cc.

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

Definition at line 76 of file vector.cc.

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

Definition at line 86 of file vector.cc.

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

Definition at line 116 of file vector.cc.

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

Definition at line 126 of file vector.cc.

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

Definition at line 56 of file vector.cc.

References basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::antibody::prefix, and basic::options::OptionKeys::out::suffix.

template<class T >

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

Definition at line 72 of file vector.hh.

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

template<class T >

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

Definition at line 61 of file vector.hh.

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
	)

Definition at line 66 of file vector.cc.

References basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::antibody::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
	)

Definition at line 104 of file dixon.cc.

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

dixon functions ///

Definition at line 68 of file dixon.cc.

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
	)

Definition at line 77 of file dixon.cc.

Referenced by dixon_sturm().

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

Definition at line 86 of file dixon.cc.

Referenced by dixon_sturm().

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

Definition at line 95 of file dixon.cc.

Referenced by dixon_sturm().

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

Definition at line 192 of file dixon.cc.

Referenced by dixon_sturm().

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

Definition at line 114 of file dixon.cc.

References PP4x2_VECSIZE.

Referenced by dixon_sturm(), and test_polyProduct2x2().

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

Definition at line 156 of file dixon.cc.

Referenced by dixon_sturm(), and test_polyProduct4sq().

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

Definition at line 126 of file dixon.cc.

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
	)

Definition at line 140 of file dixon.cc.

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
	)

Definition at line 172 of file dixon.cc.

Referenced by dixon_sturm(), and test_polyProduct6x6().

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

Definition at line 240 of file dixon.cc.

Referenced by dixon_sturm().

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

Definition at line 216 of file dixon.cc.

Referenced by dixon_sturm().

void numeric::kinematic_closure::printMatrix ( const utility::vector1< utility::vector1< Real > > & 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.

Definition at line 42 of file kinematic_closure_helpers.cc.

References utility::io::oc::cout, basic::options::OptionKeys::frags::j, and test.T007_TracerIO::M.

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

void numeric::kinematic_closure::printTranspose ( const utility::vector1< utility::vector1< Real > > & M )

Definition at line 51 of file kinematic_closure_helpers.cc.

References utility::io::oc::cout, basic::options::OptionKeys::frags::j, and test.T007_TracerIO::M.

void numeric::kinematic_closure::printVector ( const utility::vector1< Real > & V )

helper functions ///

Definition at line 30 of file kinematic_closure_helpers.cc.

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::vector1< Real > > &	R,
		const Real &	c,
		const Real &	s,
		utility::vector1< utility::vector1< Real > > &	Rx
	)

Definition at line 610 of file bridgeObjects.cc.

References amino_acids::size.

Referenced by bridgeObjects(), and test_rotateX().

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

Definition at line 621 of file bridgeObjects.cc.

References amino_acids::size.

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

Definition at line 632 of file bridgeObjects.cc.

References amino_acids::size.

Referenced by bridgeObjects().

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

inline

Definition at line 395 of file sturm.hh.

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::vector1< Real > &	a,
		const utility::vector1< Real > &	b,
		const utility::vector1< Real > &	c
	)

Definition at line 273 of file bridgeObjects.cc.

Referenced by bondangle(), and test_scpn().

void numeric::kinematic_closure::sincos	(	const utility::vector1< Real > &	theta,
		const int	flag,
		utility::vector1< Real > &	cosine,
		utility::vector1< Real > &	sine
	)

Definition at line 55 of file bridgeObjects.cc.

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

inline

Definition at line 491 of file sturm.hh.

References buildsturm(), numeric::kinematic_closure::p::coef, numeric::max(), MAX_ORDER, MAXPOW, numeric::min(), numchanges(), numroots(), and sbisect().

Referenced by dixon_sturm().

void numeric::kinematic_closure::test_bondangle ( )

Definition at line 1268 of file bridgeObjects.cc.

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 ( )

Definition at line 892 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_chainParams ( )

Definition at line 1215 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_chainTORS ( )

Definition at line 1065 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_chainXYZ ( )

Definition at line 1110 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_cross ( )

Definition at line 1331 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_dixon ( )

Definition at line 966 of file dixon.cc.

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

void numeric::kinematic_closure::test_eucDistance ( )

Definition at line 1300 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_frame ( )

Definition at line 1313 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_point_value2 ( )

Definition at line 851 of file dixon.cc.

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

void numeric::kinematic_closure::test_polyProduct2x2 ( )

Definition at line 951 of file dixon.cc.

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

void numeric::kinematic_closure::test_polyProduct4sq ( )

Definition at line 901 of file dixon.cc.

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

void numeric::kinematic_closure::test_polyProduct4x2 ( )

Definition at line 934 of file dixon.cc.

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

void numeric::kinematic_closure::test_polyProduct4x4 ( )

Definition at line 915 of file dixon.cc.

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

void numeric::kinematic_closure::test_polyProduct6x6 ( )

Definition at line 878 of file dixon.cc.

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

void numeric::kinematic_closure::test_rotateX ( )

Definition at line 1048 of file bridgeObjects.cc.

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

void numeric::kinematic_closure::test_scpn ( )

Definition at line 1284 of file bridgeObjects.cc.

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 ( )

Definition at line 1392 of file bridgeObjects.cc.

References sincos().

void numeric::kinematic_closure::test_torsion ( )

Definition at line 1249 of file bridgeObjects.cc.

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 ( )

Definition at line 1402 of file bridgeObjects.cc.

References printVector(), and triangle().

void numeric::kinematic_closure::test_triaxialCoefficients ( )

Definition at line 1343 of file bridgeObjects.cc.

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

numeric::Real numeric::kinematic_closure::torsion	(	const utility::vector1< Real > &	a,
		const utility::vector1< Real > &	b,
		const utility::vector1< Real > &	c,
		const utility::vector1< Real > &	d
	)

Definition at line 287 of file bridgeObjects.cc.

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

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

void numeric::kinematic_closure::triangle	(	const utility::vector1< Real > &	vbond,
		utility::vector1< Real > &	calpha,
		utility::vector1< Real > &	salpha
	)

Definition at line 39 of file bridgeObjects.cc.

Referenced by test_triangle(), and triaxialCoefficients().

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