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core::scoring::nmr::rdc::RDCTensor Class Reference

#include <RDCTensor.hh>

Inheritance diagram for core::scoring::nmr::rdc::RDCTensor:
Inheritance graph
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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...
 
RDCTensoroperator= (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...
 
NMRTensoroperator= (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
void core::scoring::nmr::rdc::RDCTensor::Da_R_ax_rh_from_eigenvalues ( )
private
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
Real core::scoring::nmr::rdc::RDCTensor::get_Da ( ) const
inline
Real core::scoring::nmr::rdc::RDCTensor::get_Dmax ( ) const
inline

References Dmax_.

Real core::scoring::nmr::rdc::RDCTensor::get_R ( ) const
inline
bool core::scoring::nmr::rdc::RDCTensor::is_rdc_tensor_in_arbitrary_frame ( ) const
inline
bool core::scoring::nmr::rdc::RDCTensor::is_rdc_tensor_in_pas ( ) const
inline
bool core::scoring::nmr::rdc::RDCTensor::is_tensor_diagonalized ( ) const
inline
bool core::scoring::nmr::rdc::RDCTensor::is_tensor_reconfigured ( ) const
inline
RDCTensor & core::scoring::nmr::rdc::RDCTensor::operator= ( RDCTensor const &  rhs)
void core::scoring::nmr::rdc::RDCTensor::reorder_tensor ( )
overridevirtual
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
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
std::string core::scoring::nmr::rdc::RDCTensor::tensor_name ( ) const
overridevirtual

every tensor should offer a function that returns its name

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

Member Data Documentation

Real core::scoring::nmr::rdc::RDCTensor::Da_
private
Real core::scoring::nmr::rdc::RDCTensor::Dmax_
private
bool core::scoring::nmr::rdc::RDCTensor::dmax_set_
private
Real core::scoring::nmr::rdc::RDCTensor::R_
private
bool core::scoring::nmr::rdc::RDCTensor::rdc_tensor_diagonalized_
private
bool core::scoring::nmr::rdc::RDCTensor::rdc_tensor_in_arbitrary_frame_
private
bool core::scoring::nmr::rdc::RDCTensor::rdc_tensor_in_pas_
private
bool core::scoring::nmr::rdc::RDCTensor::rdc_tensor_reconfigured_
private

The documentation for this class was generated from the following files: