#include <RDCTensor.hh>

Inheritance diagram for core::scoring::nmr::rdc::RDCTensor:

Public Member Functions
	RDCTensor ()
	default constructor More...

	RDCTensor (utility::vector1< Real > const &tensor_params)
	constructor with arguments initializes alignment tensor with upper diagonal elements vector should contain tensor parameters in the order A_xx, A_xy, A_xz, A_yy, A_yz More...

	RDCTensor (RDCTensor const &other)
	copy constructor More...

RDCTensor &	operator= (RDCTensor const &rhs)
	assignment operator More...

	~RDCTensor () override
	virtual destructor More...

std::string	tensor_name () const override
	every tensor should offer a function that returns its name More...

void	set_tensor_in_arbitrary_frame (utility::vector1< Real > const &tensor_params) override
	sets the alignment tensor as it exists in the arbitrary frame resets the tensor upper diagonal elements vector should contain tensor parameters in the order A_xx, A_xy, A_xz, A_yy, A_yz More...

void	set_tensor_in_pas (utility::vector1< Real > const &tensor_params) override
	sets the alignment tensor as it exists in the principal axis system (PAS) resets the alignment tensor principal values, the alignment order, the rhombicity, the three Euler angles and the dipolar coupling constant vector should contain tensor parameters in the order alpha, beta, gamma, Da, R, Dmax More...

void	diagonalize_tensor () override
	brings alignment tensor in principal axis frame by diagonalization make sure to call either set_tensor_in_arbitrary_frame() and set_Dmax() or set_tensor_in_pas() first More...

void	reorder_tensor () override
	brings alignment tensor principal values in correct order and reconfigure tensor into unique tensor representation make sure to call set_tensor_in_pas() or diagonalize_tensor() first More...

void	show_tensor_stats (std::ostream &TR, bool show_in_pas=true) const override
	shows summary of tensor statistics More...

utility::json_spirit::Value	serialize () const override
	serialize an RDCTensor to a json_spirit object More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to an RDCTensor More...

Real	get_Da () const

Real	get_R () const

Real	get_Dmax () const

bool	is_rdc_tensor_in_arbitrary_frame () const

bool	is_rdc_tensor_in_pas () const

bool	is_tensor_diagonalized () const

bool	is_tensor_reconfigured () const

void	set_Dmax (Real Dmax)

Public Member Functions inherited from core::scoring::nmr::NMRTensor
	NMRTensor ()
	default constructor More...

	NMRTensor (NMRTensor const &other)
	copy constructor More...

NMRTensor &	operator= (NMRTensor const &rhs)
	assignment operator More...

	~NMRTensor () override
	virtual destructor More...

Real	get_T_xx () const

Real	get_T_xy () const

Real	get_T_xz () const

Real	get_T_yy () const

Real	get_T_yz () const

Real	get_ax () const

Real	get_rh () const

Real	get_Eig_xx () const

Real	get_Eig_yy () const

Real	get_Eig_zz () const

Real	get_alpha () const

Real	get_beta () const

Real	get_gamma () const

EULER_CONVENTION	get_euler_convention () const

void	set_T_xx (Real T_xx)

void	set_T_xy (Real T_xy)

void	set_T_xz (Real T_xz)

void	set_T_yy (Real T_yy)

void	set_T_yz (Real T_yz)

void	set_ax (Real ax)

void	set_rh (Real rh)

void	set_Eig_xx (Real Eig_xx)

void	set_Eig_yy (Real Eig_yy)

void	set_Eig_zz (Real Eig_zz)

void	set_alpha (Real alpha)

void	set_beta (Real beta)

void	set_gamma (Real gamma)

Private Member Functions
void	Da_R_ax_rh_from_eigenvalues ()
	converts alignment tensor principal values into axial and rhombic component, alignment order and rhombicity More...

void	Da_R_to_ax_rh_and_eigenvalues ()
	calculates alignment tensor principal values, its axial and rhombic component from the alignment order and rhombicity More...

Matrix	build_tensor_matrix ()
	returns the alignment tensor in 3x3 matrix form More...

Private Attributes
Real	Da_

Real	R_

Real	Dmax_

bool	rdc_tensor_in_arbitrary_frame_

bool	rdc_tensor_in_pas_

bool	dmax_set_

bool	rdc_tensor_diagonalized_

bool	rdc_tensor_reconfigured_

Constructor & Destructor Documentation

core::scoring::nmr::rdc::RDCTensor::RDCTensor ( )

default constructor

core::scoring::nmr::rdc::RDCTensor::RDCTensor ( utility::vector1< Real > const & tensor_params )

constructor with arguments initializes alignment tensor with upper diagonal elements vector should contain tensor parameters in the order A_xx, A_xy, A_xz, A_yy, A_yz

References set_tensor_in_arbitrary_frame().

core::scoring::nmr::rdc::RDCTensor::RDCTensor ( RDCTensor const & other )

copy constructor

core::scoring::nmr::rdc::RDCTensor::~RDCTensor ( )

override

virtual destructor

Member Function Documentation

Matrix core::scoring::nmr::rdc::RDCTensor::build_tensor_matrix ( )

private

returns the alignment tensor in 3x3 matrix form

References core::scoring::nmr::NMRTensor::get_T_xx(), core::scoring::nmr::NMRTensor::get_T_xy(), core::scoring::nmr::NMRTensor::get_T_xz(), core::scoring::nmr::NMRTensor::get_T_yy(), and core::scoring::nmr::NMRTensor::get_T_yz().

Referenced by diagonalize_tensor().

void core::scoring::nmr::rdc::RDCTensor::Da_R_ax_rh_from_eigenvalues ( )

private

converts alignment tensor principal values into axial and rhombic component, alignment order and rhombicity

References Da_, Dmax_, dmax_set_, core::scoring::nmr::NMRTensor::get_Eig_xx(), core::scoring::nmr::NMRTensor::get_Eig_yy(), core::scoring::nmr::NMRTensor::get_Eig_zz(), R_, core::scoring::nmr::NMRTensor::set_ax(), and core::scoring::nmr::NMRTensor::set_rh().

Referenced by diagonalize_tensor(), and reorder_tensor().

void core::scoring::nmr::rdc::RDCTensor::Da_R_to_ax_rh_and_eigenvalues ( )

private

calculates alignment tensor principal values, its axial and rhombic component from the alignment order and rhombicity

References Da_, Dmax_, dmax_set_, R_, core::scoring::nmr::NMRTensor::set_ax(), core::scoring::nmr::NMRTensor::set_Eig_xx(), core::scoring::nmr::NMRTensor::set_Eig_yy(), core::scoring::nmr::NMRTensor::set_Eig_zz(), and core::scoring::nmr::NMRTensor::set_rh().

Referenced by set_tensor_in_pas().

void core::scoring::nmr::rdc::RDCTensor::deserialize ( utility::json_spirit::mObject data )

overridevirtual

deserialize a json_spirit object to an RDCTensor

deserialize a json_spirit object to a PCSTensor

Reimplemented from core::scoring::nmr::NMRTensor.

References Da_, core::scoring::nmr::NMRTensor::deserialize(), Dmax_, R_, rdc_tensor_diagonalized_, rdc_tensor_in_arbitrary_frame_, rdc_tensor_in_pas_, and rdc_tensor_reconfigured_.

void core::scoring::nmr::rdc::RDCTensor::diagonalize_tensor ( )

overridevirtual

brings alignment tensor in principal axis frame by diagonalization make sure to call either set_tensor_in_arbitrary_frame() and set_Dmax() or set_tensor_in_pas() first

Reimplemented from core::scoring::nmr::NMRTensor.

References core::scoring::angles(), build_tensor_matrix(), Da_R_ax_rh_from_eigenvalues(), dmax_set_, core::scoring::nmr::euler_angles_from_rotation_matrix(), core::scoring::nmr::NMRTensor::get_euler_convention(), rdc_tensor_diagonalized_, rdc_tensor_in_arbitrary_frame_, rdc_tensor_in_pas_, core::scoring::nmr::NMRTensor::set_alpha(), core::scoring::nmr::NMRTensor::set_beta(), core::scoring::nmr::NMRTensor::set_Eig_xx(), core::scoring::nmr::NMRTensor::set_Eig_yy(), core::scoring::nmr::NMRTensor::set_Eig_zz(), and core::scoring::nmr::NMRTensor::set_gamma().

Referenced by reorder_tensor(), and protocols::nmr::rdc::RDCEnergy::show_additional_info().

Real core::scoring::nmr::rdc::RDCTensor::get_Da ( ) const

inline

References Da_.

Referenced by core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), and show_tensor_stats().

Real core::scoring::nmr::rdc::RDCTensor::get_Dmax ( ) const

inline

References Dmax_.

Real core::scoring::nmr::rdc::RDCTensor::get_R ( ) const

inline

References R_.

Referenced by core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), and show_tensor_stats().

bool core::scoring::nmr::rdc::RDCTensor::is_rdc_tensor_in_arbitrary_frame ( ) const

inline

References rdc_tensor_in_arbitrary_frame_.

Referenced by core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor().

bool core::scoring::nmr::rdc::RDCTensor::is_rdc_tensor_in_pas ( ) const

inline

References rdc_tensor_in_pas_.

Referenced by core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor().

bool core::scoring::nmr::rdc::RDCTensor::is_tensor_diagonalized ( ) const

inline

References rdc_tensor_diagonalized_.

bool core::scoring::nmr::rdc::RDCTensor::is_tensor_reconfigured ( ) const

inline

References rdc_tensor_reconfigured_.

RDCTensor & core::scoring::nmr::rdc::RDCTensor::operator= ( RDCTensor const & rhs )

assignment operator

References Da_, Dmax_, dmax_set_, core::scoring::nmr::NMRTensor::operator=(), R_, rdc_tensor_diagonalized_, rdc_tensor_in_arbitrary_frame_, rdc_tensor_in_pas_, and rdc_tensor_reconfigured_.

void core::scoring::nmr::rdc::RDCTensor::reorder_tensor ( )

overridevirtual

brings alignment tensor principal values in correct order and reconfigure tensor into unique tensor representation make sure to call set_tensor_in_pas() or diagonalize_tensor() first

Reimplemented from core::scoring::nmr::NMRTensor.

Referenced by protocols::nmr::rdc::RDCEnergy::show_additional_info().

utility::json_spirit::Value core::scoring::nmr::rdc::RDCTensor::serialize ( ) const

overridevirtual

serialize an RDCTensor to a json_spirit object

serialize a PCSTensor to a json_spirit object

Reimplemented from core::scoring::nmr::NMRTensor.

References Da_, Dmax_, R_, rdc_tensor_diagonalized_, rdc_tensor_in_arbitrary_frame_, rdc_tensor_in_pas_, rdc_tensor_reconfigured_, and core::scoring::nmr::NMRTensor::serialize().

void core::scoring::nmr::rdc::RDCTensor::set_Dmax ( Real Dmax )

inline

References Dmax_, and dmax_set_.

Referenced by set_tensor_in_pas(), and protocols::nmr::rdc::RDCEnergy::show_additional_info().

void core::scoring::nmr::rdc::RDCTensor::set_tensor_in_arbitrary_frame ( utility::vector1< Real > const & tensor_params )

overridevirtual

sets the alignment tensor as it exists in the arbitrary frame resets the tensor upper diagonal elements vector should contain tensor parameters in the order A_xx, A_xy, A_xz, A_yy, A_yz

Implements core::scoring::nmr::NMRTensor.

References rdc_tensor_in_arbitrary_frame_, core::scoring::nmr::NMRTensor::set_T_xx(), core::scoring::nmr::NMRTensor::set_T_xy(), core::scoring::nmr::NMRTensor::set_T_xz(), core::scoring::nmr::NMRTensor::set_T_yy(), and core::scoring::nmr::NMRTensor::set_T_yz().

Referenced by RDCTensor().

void core::scoring::nmr::rdc::RDCTensor::set_tensor_in_pas ( utility::vector1< Real > const & tensor_params )

overridevirtual

sets the alignment tensor as it exists in the principal axis system (PAS) resets the alignment tensor principal values, the alignment order, the rhombicity, the three Euler angles and the dipolar coupling constant vector should contain tensor parameters in the order alpha, beta, gamma, Da, R, Dmax

Implements core::scoring::nmr::NMRTensor.

References Da_, Da_R_to_ax_rh_and_eigenvalues(), R_, rdc_tensor_diagonalized_, rdc_tensor_in_pas_, core::scoring::nmr::NMRTensor::set_alpha(), core::scoring::nmr::NMRTensor::set_beta(), set_Dmax(), and core::scoring::nmr::NMRTensor::set_gamma().

void core::scoring::nmr::rdc::RDCTensor::show_tensor_stats	(	std::ostream &	tracer,
		bool	show_in_pas = `true`
	)		const

overridevirtual

shows summary of tensor statistics

If show_in_pas is true and tensor has been set or transformed in the principal axis system, show tensor parameters in PAS. If either of the two conditions is not fulfilled show tensor matrix in arbitrary frame.

Reimplemented from core::scoring::nmr::NMRTensor.