#include <PCSTensor.hh>

Inheritance diagram for core::scoring::nmr::pcs::PCSTensor:

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

	PCSTensor (utility::vector1< Real > const &tensor_params)
	constructor with arguments initializes tensor with upper diagonal elements and the coordinates of the metal center parameters in vector should be in order chi__xx, chi_xy, chi_xz, chi_yy, chi_yz, xM, yM, zM More...

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

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

	~PCSTensor () 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 delta chi tensor as it exists in the arbitrary frame resets the tensor upper diagonal elements and the coordinates of the metal center parameters in vector should be in order chi__xx, chi_xy, chi_xz, chi_yy, chi_yz, xM, yM, zM More...

void	set_tensor_in_pas (utility::vector1< Real > const &tensor_params) override
	sets the delta chi tensor as it exists in the principal axis system (PAS) resets the tensor principal values, the axial and rhombic component, the three Euler angles and the coordinates of the metal center parameters in vector should be in order alpha, beta, gamma, xM, yM, zM, ax, rh More...

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

void	reorder_tensor () override
	brings delta chi tensor principal values in correct order and reconfigures 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 a PCSTensor to a json_spirit object More...

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

bool	is_pcs_tensor_in_arbitrary_frame () const

bool	is_pcs_tensor_in_pas () const

bool	is_pcs_tensor_diagonalized () const

bool	is_pcs_tensor_reconfigured () const

Vector const &	get_metal_center () const

void	set_metal_center (Real xM, Real yM, Real zM)

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	ax_rh_from_eigenvalues ()
	converts tensor principal values into its axial and rhombic component More...

void	ax_rh_to_eigenvalues ()
	converts axial and rhombic component into the tensor principal values More...

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

Private Attributes
bool	pcs_tensor_in_arbitrary_frame_

bool	pcs_tensor_in_pas_

bool	pcs_tensor_diagonalized_

bool	pcs_tensor_reconfigured_

Vector	metal_center_

Constructor & Destructor Documentation

core::scoring::nmr::pcs::PCSTensor::PCSTensor ( )

default constructor

core::scoring::nmr::pcs::PCSTensor::PCSTensor ( utility::vector1< Real > const & tensor_params )

constructor with arguments initializes tensor with upper diagonal elements and the coordinates of the metal center parameters in vector should be in order chi__xx, chi_xy, chi_xz, chi_yy, chi_yz, xM, yM, zM

References set_tensor_in_arbitrary_frame().

core::scoring::nmr::pcs::PCSTensor::PCSTensor ( PCSTensor const & other )

copy constructor

core::scoring::nmr::pcs::PCSTensor::~PCSTensor ( )

override

virtual destructor

Member Function Documentation

void core::scoring::nmr::pcs::PCSTensor::ax_rh_from_eigenvalues ( )

private

converts tensor principal values into its axial and rhombic component

converts delta chi tensor principal values into its axial and rhombic component

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

Referenced by diagonalize_tensor(), and reorder_tensor().

void core::scoring::nmr::pcs::PCSTensor::ax_rh_to_eigenvalues ( )

private

converts axial and rhombic component into the tensor principal values

converts axial and rhombic component into the delta chi tensor principal values

References core::scoring::nmr::NMRTensor::get_ax(), core::scoring::nmr::NMRTensor::get_rh(), core::scoring::nmr::NMRTensor::set_Eig_xx(), core::scoring::nmr::NMRTensor::set_Eig_yy(), and core::scoring::nmr::NMRTensor::set_Eig_zz().

Referenced by set_tensor_in_pas().

Matrix core::scoring::nmr::pcs::PCSTensor::build_tensor_matrix ( )

private

returns the delta chi tensor in 3x3 matrix form

return the delta chi 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::pcs::PCSTensor::deserialize ( utility::json_spirit::mObject data )

overridevirtual

deserialize a json_spirit object to a PCSTensor

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

References core::scoring::nmr::NMRTensor::deserialize(), metal_center_, pcs_tensor_diagonalized_, pcs_tensor_in_arbitrary_frame_, pcs_tensor_in_pas_, and pcs_tensor_reconfigured_.

void core::scoring::nmr::pcs::PCSTensor::diagonalize_tensor ( )

overridevirtual

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

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

References core::scoring::angles(), ax_rh_from_eigenvalues(), build_tensor_matrix(), core::scoring::nmr::euler_angles_from_rotation_matrix(), core::scoring::nmr::NMRTensor::get_euler_convention(), pcs_tensor_diagonalized_, pcs_tensor_in_arbitrary_frame_, pcs_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().

Vector const& core::scoring::nmr::pcs::PCSTensor::get_metal_center ( ) const

inline

References metal_center_.

Referenced by core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor(), and show_tensor_stats().

bool core::scoring::nmr::pcs::PCSTensor::is_pcs_tensor_diagonalized ( ) const

inline

References pcs_tensor_diagonalized_.

bool core::scoring::nmr::pcs::PCSTensor::is_pcs_tensor_in_arbitrary_frame ( ) const

inline

References pcs_tensor_in_arbitrary_frame_.

Referenced by core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor().

bool core::scoring::nmr::pcs::PCSTensor::is_pcs_tensor_in_pas ( ) const

inline

References pcs_tensor_in_pas_.

Referenced by core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor().

bool core::scoring::nmr::pcs::PCSTensor::is_pcs_tensor_reconfigured ( ) const

inline

References pcs_tensor_reconfigured_.

PCSTensor & core::scoring::nmr::pcs::PCSTensor::operator= ( PCSTensor const & rhs )

assignment operator

References metal_center_, core::scoring::nmr::NMRTensor::operator=(), pcs_tensor_diagonalized_, pcs_tensor_in_arbitrary_frame_, pcs_tensor_in_pas_, and pcs_tensor_reconfigured_.

void core::scoring::nmr::pcs::PCSTensor::reorder_tensor ( )

overridevirtual

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

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

utility::json_spirit::Value core::scoring::nmr::pcs::PCSTensor::serialize ( ) const

overridevirtual

serialize a PCSTensor to a json_spirit object

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

References metal_center_, pcs_tensor_diagonalized_, pcs_tensor_in_arbitrary_frame_, pcs_tensor_in_pas_, pcs_tensor_reconfigured_, and core::scoring::nmr::NMRTensor::serialize().

void core::scoring::nmr::pcs::PCSTensor::set_metal_center	(	Real	xM,
		Real	yM,
		Real	zM
	)

inline

References metal_center_.

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

overridevirtual

sets the delta chi tensor as it exists in the arbitrary frame resets the tensor upper diagonal elements and the coordinates of the metal center parameters in vector should be in order chi__xx, chi_xy, chi_xz, chi_yy, chi_yz, xM, yM, zM

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

References metal_center_, pcs_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 PCSTensor().

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

overridevirtual

sets the delta chi tensor as it exists in the principal axis system (PAS) resets the tensor principal values, the axial and rhombic component, the three Euler angles and the coordinates of the metal center parameters in vector should be in order alpha, beta, gamma, xM, yM, zM, ax, rh

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

References ax_rh_to_eigenvalues(), metal_center_, pcs_tensor_diagonalized_, pcs_tensor_in_pas_, core::scoring::nmr::NMRTensor::set_alpha(), core::scoring::nmr::NMRTensor::set_ax(), core::scoring::nmr::NMRTensor::set_beta(), core::scoring::nmr::NMRTensor::set_gamma(), and core::scoring::nmr::NMRTensor::set_rh().

void core::scoring::nmr::pcs::PCSTensor::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.