numeric::kinematic_closure::radians Namespace Reference

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, bool &feasible_triangle)
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	to_radians (utility::vector1< Real > &degrees)
void	to_degrees (utility::vector1< Real > &radians)
void	bridge_objects (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	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::fixedsizearray1< numeric::Real, 3 > &R0, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &Q, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &atoms)

Function Documentation

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

Returns

the bond angle between the given vectors in radians.

References eucDistance(), and scpn().

Referenced by chainParams(), and chainTORS().

void numeric::kinematic_closure::radians::bridge_objects	(	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 coordinates of N-CA-C atoms indexed as atoms[atom][dimension]
[in]	dt	- desired torsions for each atom (radians)
[in]	da	- desired bond angle for each atom (radians)
[in]	db	- desired bond length for each atom (radians)
[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] (radians)
[out]	b_ang	- matrix giving bond angles for each atom for each solution, indexed as b_ang[solution][atom] (radians)
[out]	b_len	- matrix giving bond lengths for each atom for each solution, indexed as b_len[solution][atom] (radians)
[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, numeric::kinematic_closure::dixon_eig(), basic::options::OptionKeys::frags::j, test.G201_Module_Structure::l1, test.G200_Module_Region::loop, numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), rotateX(), rotateZ(), torsion(), and triaxialCoefficients().

void numeric::kinematic_closure::radians::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 bridge_objects().

void numeric::kinematic_closure::radians::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().

void numeric::kinematic_closure::radians::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::fixedsizearray1< numeric::Real, 3 > &	R0,
		const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &	Q,
		utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &	atoms
	)

void numeric::kinematic_closure::radians::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, basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::s, and test.T850_SubClassing::v.

Referenced by bridge_objects(), and chainXYZ().

void numeric::kinematic_closure::radians::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().

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

Referenced by frame(), and torsion().

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

References ObjexxFCL::pow().

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

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

References cross().

Referenced by chainParams(), and chainTORS().

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

Referenced by bridge_objects().

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

Referenced by bridge_objects().

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

Referenced by bondangle().

void numeric::kinematic_closure::radians::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 triaxialCoefficients().

void numeric::kinematic_closure::radians::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::radians::to_degrees

(

utility::vector1< Real > &

radians

)

References numeric::conversions::to_degrees().

void numeric::kinematic_closure::radians::to_radians

(

utility::vector1< Real > &

degrees

)

References numeric::conversions::to_radians().

numeric::Real numeric::kinematic_closure::radians::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
	)

Returns

the torsion angle between the given vectors in radians.

References cross(), demo.D060_Folding::f, numeric::constants::r::pi, ObjexxFCL::pow(), basic::options::OptionKeys::in::file::s, numeric::wrap_2pi(), numeric::crick_equations::y(), and numeric::crick_equations::z().

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

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

Referenced by triaxialCoefficients().

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

void numeric::kinematic_closure::radians::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,
		bool &	feasible_triangle
	)

References ObjexxFCL::format::A(), ObjexxFCL::abs(), basic::options::OptionKeys::score::fiber_diffraction::b, C, basic::options::OptionKeys::frags::j, ObjexxFCL::format::L(), test.T007_TracerIO::M, basic::options::OptionKeys::score::fiber_diffraction::p, sincos(), and triangle().

Referenced by bridge_objects().