#include <RDCMultiSet.hh>

Public Types
enum	COMPUTATION_TYPE { SVD = 1, NLS = 2, NLSDA = 3, NLSR = 4, NLSDAR = 5 }
	type of tensor and score calculation SVD = singular value decomposition (coupled with grid search) NLS = non-linear least squares fitting NLSDA = non-linear least squares fitting with known alignment magnitude NLSR = non-linear least squares fitting with known rhombicity NLSDAR = non-linear least squares fitting with known alignment magnitude and rhombicity More...

typedef std::pair< Vector, Vector >	SpinPairCoordinates

Public Member Functions
	RDCMultiSet (utility::vector1< std::string > const &filenames, std::string const &medium_label, pose::Pose const &pose)
	construct from data files set default values for RDCMultiSet weight and computation_type More...

	RDCMultiSet (utility::vector1< std::string > const &filenames, std::string const &medium_label, pose::Pose const &pose, Real const weight, std::string computation_type="SVD")
	constructor with full argument list More...

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

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

	~RDCMultiSet ()
	destructor More...

void	update_spin_coordinates (pose::Pose const &pose)
	updates the spin coordinates every time the pose is changed make sure that this function is called before update_matrix_A() is called More...

void	update_matrix_A ()
	builds matrix_A from the spin coordinates and hands it over to the SVD solver More...

void	update_single_rdc_weighting ()
	updates the array holding the single RDC weights that are used during score calculation needs to be called e.g. when the weighting scheme of one of the RDCSingleSets was changed More...

Real	solve_tensor_and_compute_score_by_svd ()
	solves the RDC tensor using SVD and returns the weighted RDC score according to the single RDC weighting scheme and the weights of the individual experiments More...

Real	solve_tensor_and_compute_score_by_nls ()
	solves the RDC tensor using NLS and returns the weighted RDC score according to the single RDC weighting scheme and the weights of the individual experiments More...

Real	compute_rdc_values_and_score_from_tensor (RDCTensor const &tensor)
	calculate RDC values from a given tensor, set values in the RDCSingle vector and return the RDC score More...

Real	compute_rdc_values_and_score_from_tensor ()
	calculate RDC values and the RDC score from the dataset's current tensor More...

void	set_atom_derivatives (pose::Pose const &pose)
	sets the xyz derivative of the RDC RDCTensor must be determined before first call solve_tensor_and_compute_score_by_svd() or solve_tensor_and_compute_score_by_nls() before setting derivatives More...

Real	get_weight () const

Size	get_total_number_rdc () const

Size	get_number_experiments () const

std::string	get_alignment_medium_label () const

utility::vector1 < RDCSingleSetOP > &	get_rdc_singleset_vec ()

utility::vector1 < RDCSingleSetOP > const &	get_rdc_singleset_vec () const

ObjexxFCL::FArray2D< Real > const &	get_matrix_A () const

ObjexxFCL::FArray1D< Real > const &	get_rdc_values () const

ObjexxFCL::FArray1D< Real > const &	get_rdc_single_weights () const

RDCTensorCOP	get_tensor_const () const

RDCTensorOP	get_tensor ()

COMPUTATION_TYPE	get_computation_type () const

NMR_VALUE_AVERAGING_TYPE	get_averaging_type () const

utility::vector1 < utility::vector1 < RDCMultiSet::SpinPairCoordinates > > const &	get_spin_coordinates () const

RDC_NORM_TYPE	get_normalization_type () const

bool	symmetric_rdc_calc () const

bool	correct_sign () const

bool	tensor_fixed () const

void	set_weight (Real weight)

void	set_tensor (RDCTensorOP const &tensor)

void	set_computation_type (std::string const &type)

void	set_averaging_type (std::string const &type)

void	fix_tensor ()

void	unfix_tensor ()

void	show (std::ostream &TR) const

Private Member Functions
	RDCMultiSet ()
	default constructor More...

void	init_from_rdc_filedata (utility::vector1< std::string > const &filenames, pose::Pose const &pose)
	utility function used in constructor to initialize RDCMultiSet object from data files. More...

void	register_options ()
	register options More...

void	init_from_cml ()

void	convert_string_to_computation_type (std::string const &computation_type)
	utility function to convert string to class computation type enum More...

void	deep_copy_rdc_single_set_vec (utility::vector1< RDCSingleSetOP > const &other_vec)

void	fill_matrix_A_row (utility::fixedsizearray1< Real, 5 > &A_row, utility::vector1< SpinPairCoordinates > const &spin_coord, Real const &Dmax)
	utility function to fill matrix_A that is used for SVD More...

Real	basic_rdc_equation (utility::fixedsizearray1< Real, 2 > const &par, SpinPairCoordinates const &spin_coord, Real const &Dmax, Matrix const &rotM)
	utility function that calculates one single RDC value given the input arguments Da, R, the spin coordinates, the maximal dipolar coupling constant and a rotation matrix More...

Real	frdc (Real const *par, utility::vector1< SpinPairCoordinates > const &spin_coord, Real const &Dmax, Matrix const &rotM)
	utility functions to calculate the RDC from different sets of input arguments arguments are a pointer to the parameters (Da, R), the coordinates of equivalent spins, the maximal dipolar coupling constant and a rotation matrix that must be previously constructed from the Euler angles. Fixed values of Da and R can be provided. More...

Real	frdc_Da (Real const *par, Real const &Da, utility::vector1< SpinPairCoordinates > const &spin_coord, Real const &Dmax, Matrix const &rotM)

Real	frdc_R (Real const *par, Real const &R, utility::vector1< SpinPairCoordinates > const &spin_coord, Real const &Dmax, Matrix const &rotM)

Real	frdc_Da_R (Real const &Da, Real const &R, utility::vector1< SpinPairCoordinates > const &spin_coord, Real const &Dmax, Matrix const &rotM)

Private Attributes
std::string	alignment_medium_

utility::vector1< RDCSingleSetOP >	rdc_singleset_vec_

Real	weight_

Size	total_number_rdc_

Size	number_experiments_

ObjexxFCL::FArray2D< Real >	matrix_A_

ObjexxFCL::FArray1D< Real >	rdc_values_

ObjexxFCL::FArray1D< Real >	rdc_single_weights_

basic::svd::SVD_SolverOP	svd_solver_

RDCTensorOP	tensor_

COMPUTATION_TYPE	computation_type_

utility::vector1 < utility::vector1 < SpinPairCoordinates > >	spin_coordinates_

RDC_NORM_TYPE	norm_type_

bool	symmetric_rdc_calc_

bool	correct_sign_

NMR_VALUE_AVERAGING_TYPE	ave_type_

Size	nls_repeats_

bool	fixed_tensor_

Friends
void	rdc_erf (Real const par, int m_dat, void const data, Real fvec, int )
	rdc error function used in the lmmin function More...

Member Typedef Documentation

typedef std::pair< Vector, Vector > core::scoring::nmr::rdc::RDCMultiSet::SpinPairCoordinates

Member Enumeration Documentation

enum core::scoring::nmr::rdc::RDCMultiSet::COMPUTATION_TYPE

type of tensor and score calculation SVD = singular value decomposition (coupled with grid search) NLS = non-linear least squares fitting NLSDA = non-linear least squares fitting with known alignment magnitude NLSR = non-linear least squares fitting with known rhombicity NLSDAR = non-linear least squares fitting with known alignment magnitude and rhombicity

Enumerator
SVD
NLS
NLSDA
NLSR
NLSDAR

Constructor & Destructor Documentation

core::scoring::nmr::rdc::RDCMultiSet::RDCMultiSet	(	utility::vector1< std::string > const &	filenames,
		std::string const &	medium_label,
		pose::Pose const &	pose
	)

construct from data files set default values for RDCMultiSet weight and computation_type

References init_from_cml(), init_from_rdc_filedata(), and register_options().

core::scoring::nmr::rdc::RDCMultiSet::RDCMultiSet	(	utility::vector1< std::string > const &	filenames,
		std::string const &	medium_label,
		pose::Pose const &	pose,
		Real const	weight,
		std::string	computation_type = `"SVD"`
	)

constructor with full argument list

References convert_string_to_computation_type(), init_from_cml(), init_from_rdc_filedata(), and register_options().

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

copy constructor

References deep_copy_rdc_single_set_vec(), and rdc_singleset_vec_.

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

destructor

core::scoring::nmr::rdc::RDCMultiSet::RDCMultiSet ( )

private

default constructor

Member Function Documentation

Real core::scoring::nmr::rdc::RDCMultiSet::basic_rdc_equation	(	utility::fixedsizearray1< Real, 2 > const &	par,
		SpinPairCoordinates const &	spin_coord,
		Real const &	Dmax,
		Matrix const &	rotM
	)

private

utility function that calculates one single RDC value given the input arguments Da, R, the spin coordinates, the maximal dipolar coupling constant and a rotation matrix

References correct_sign_, norm_type_, core::scoring::nmr::NORM_TYPE_CH, core::scoring::nmr::NORM_TYPE_NH, core::scoring::nmr::NORM_TYPE_NONE, core::scoring::rdc, core::scoring::nmr::rdc::rdc_D_max(), core::scoring::nmr::RDC_TYPE_CAHA, and core::scoring::nmr::RDC_TYPE_NH.

Referenced by frdc(), frdc_Da(), frdc_Da_R(), and frdc_R().

Real core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor ( RDCTensor const & tensor )

calculate RDC values from a given tensor, set values in the RDCSingle vector and return the RDC score

Real core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor ( )

calculate RDC values and the RDC score from the dataset's current tensor

References tensor_.

void core::scoring::nmr::rdc::RDCMultiSet::convert_string_to_computation_type ( std::string const & computation_type )

private

utility function to convert string to class computation type enum

References computation_type_, NLS, NLSDA, NLSDAR, NLSR, and SVD.

Referenced by RDCMultiSet(), and set_computation_type().

bool core::scoring::nmr::rdc::RDCMultiSet::correct_sign ( ) const

inline

References correct_sign_.

void core::scoring::nmr::rdc::RDCMultiSet::deep_copy_rdc_single_set_vec ( utility::vector1< RDCSingleSetOP > const & other_vec )

private

References rdc_singleset_vec_.

Referenced by operator=(), and RDCMultiSet().

void core::scoring::nmr::rdc::RDCMultiSet::fill_matrix_A_row	(	utility::fixedsizearray1< Real, 5 > &	A_row,
		utility::vector1< SpinPairCoordinates > const &	spin_coord,
		Real const &	Dmax
	)

private

utility function to fill matrix_A that is used for SVD

References ave_type_, core::scoring::nmr::MEAN, norm_type_, core::scoring::nmr::NORM_TYPE_CH, core::scoring::nmr::NORM_TYPE_NH, and core::scoring::nmr::NORM_TYPE_NONE.

Referenced by compute_rdc_values_and_score_from_tensor(), and update_matrix_A().

void core::scoring::nmr::rdc::RDCMultiSet::fix_tensor ( )

inline

References fixed_tensor_.

Real core::scoring::nmr::rdc::RDCMultiSet::frdc	(	Real const *	par,
		utility::vector1< SpinPairCoordinates > const &	spin_coord,
		Real const &	Dmax,
		Matrix const &	rotM
	)

private

utility functions to calculate the RDC from different sets of input arguments arguments are a pointer to the parameters (Da, R), the coordinates of equivalent spins, the maximal dipolar coupling constant and a rotation matrix that must be previously constructed from the Euler angles. Fixed values of Da and R can be provided.

References ave_type_, basic_rdc_equation(), core::scoring::nmr::MEAN, and core::scoring::rdc.

Referenced by compute_rdc_values_and_score_from_tensor(), core::scoring::nmr::rdc::rdc_erf(), set_atom_derivatives(), and solve_tensor_and_compute_score_by_nls().

Real core::scoring::nmr::rdc::RDCMultiSet::frdc_Da	(	Real const *	par,
		Real const &	Da,
		utility::vector1< SpinPairCoordinates > const &	spin_coord,
		Real const &	Dmax,
		Matrix const &	rotM
	)

private

References ave_type_, basic_rdc_equation(), core::scoring::nmr::MEAN, and core::scoring::rdc.

Referenced by core::scoring::nmr::rdc::rdc_erf().

Real core::scoring::nmr::rdc::RDCMultiSet::frdc_Da_R	(	Real const &	Da,
		Real const &	R,
		utility::vector1< SpinPairCoordinates > const &	spin_coord,
		Real const &	Dmax,
		Matrix const &	rotM
	)

private

References ave_type_, basic_rdc_equation(), core::scoring::nmr::MEAN, and core::scoring::rdc.

Referenced by core::scoring::nmr::rdc::rdc_erf().

Real core::scoring::nmr::rdc::RDCMultiSet::frdc_R	(	Real const *	par,
		Real const &	R,
		utility::vector1< SpinPairCoordinates > const &	spin_coord,
		Real const &	Dmax,
		Matrix const &	rotM
	)

private

References ave_type_, basic_rdc_equation(), core::scoring::nmr::MEAN, and core::scoring::rdc.

Referenced by core::scoring::nmr::rdc::rdc_erf().

std::string core::scoring::nmr::rdc::RDCMultiSet::get_alignment_medium_label ( ) const

inline

References alignment_medium_.

NMR_VALUE_AVERAGING_TYPE core::scoring::nmr::rdc::RDCMultiSet::get_averaging_type ( ) const

inline

References ave_type_.

COMPUTATION_TYPE core::scoring::nmr::rdc::RDCMultiSet::get_computation_type ( ) const

inline

References computation_type_.

ObjexxFCL::FArray2D<Real> const& core::scoring::nmr::rdc::RDCMultiSet::get_matrix_A ( ) const

inline

References matrix_A_.

RDC_NORM_TYPE core::scoring::nmr::rdc::RDCMultiSet::get_normalization_type ( ) const

inline

References norm_type_.

Size core::scoring::nmr::rdc::RDCMultiSet::get_number_experiments ( ) const

inline

References number_experiments_.

ObjexxFCL::FArray1D<Real> const& core::scoring::nmr::rdc::RDCMultiSet::get_rdc_single_weights ( ) const

inline

References rdc_single_weights_.

utility::vector1< RDCSingleSetOP >& core::scoring::nmr::rdc::RDCMultiSet::get_rdc_singleset_vec ( )

inline

References rdc_singleset_vec_.

utility::vector1< RDCSingleSetOP > const& core::scoring::nmr::rdc::RDCMultiSet::get_rdc_singleset_vec ( ) const

inline

References rdc_singleset_vec_.

ObjexxFCL::FArray1D<Real> const& core::scoring::nmr::rdc::RDCMultiSet::get_rdc_values ( ) const

inline

References rdc_values_.

utility::vector1< utility::vector1< RDCMultiSet::SpinPairCoordinates > > const& core::scoring::nmr::rdc::RDCMultiSet::get_spin_coordinates ( ) const

inline

References spin_coordinates_.

RDCTensorOP core::scoring::nmr::rdc::RDCMultiSet::get_tensor ( )

inline

References tensor_.

RDCTensorCOP core::scoring::nmr::rdc::RDCMultiSet::get_tensor_const ( ) const

inline

References tensor_.

Size core::scoring::nmr::rdc::RDCMultiSet::get_total_number_rdc ( ) const

inline

References total_number_rdc_.

Real core::scoring::nmr::rdc::RDCMultiSet::get_weight ( ) const

inline

References weight_.

void core::scoring::nmr::rdc::RDCMultiSet::init_from_cml ( )

private

References core::scoring::nmr::convert_string_to_normalization_type(), correct_sign_, nls_repeats_, norm_type_, and symmetric_rdc_calc_.

Referenced by RDCMultiSet().

void core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata	(	utility::vector1< std::string > const &	filenames,
		pose::Pose const &	pose
	)

private

utility function used in constructor to initialize RDCMultiSet object from data files.

References core::scoring::nmr::CONST, core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), matrix_A_, norm_type_, core::scoring::nmr::NORM_TYPE_CH, core::scoring::nmr::NORM_TYPE_NH, number_experiments_, core::scoring::nmr::OBSIG, core::scoring::nmr::rdc::rdc_scaling_factor_toCH(), core::scoring::nmr::rdc::rdc_scaling_factor_toNH(), rdc_single_weights_, rdc_singleset_vec_, rdc_values_, core::scoring::nmr::SIGMA, spin_coordinates_, symmetric_rdc_calc_, core::pose::symmetry::symmetry_info(), and total_number_rdc_.

Referenced by RDCMultiSet().

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

assignment operator

References alignment_medium_, ave_type_, computation_type_, correct_sign_, deep_copy_rdc_single_set_vec(), fixed_tensor_, matrix_A_, nls_repeats_, norm_type_, number_experiments_, rdc_single_weights_, rdc_singleset_vec_, rdc_values_, spin_coordinates_, svd_solver_, symmetric_rdc_calc_, tensor_, total_number_rdc_, and weight_.

void core::scoring::nmr::rdc::RDCMultiSet::register_options ( )

private

register options

Referenced by RDCMultiSet().

void core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives ( pose::Pose const & pose )

sets the xyz derivative of the RDC RDCTensor must be determined before first call solve_tensor_and_compute_score_by_svd() or solve_tensor_and_compute_score_by_nls() before setting derivatives

void core::scoring::nmr::rdc::RDCMultiSet::set_averaging_type ( std::string const & type )

References ave_type_, and core::scoring::nmr::convert_string_to_averaging_type().

void core::scoring::nmr::rdc::RDCMultiSet::set_computation_type ( std::string const & type )

References convert_string_to_computation_type().

void core::scoring::nmr::rdc::RDCMultiSet::set_tensor ( RDCTensorOP const & tensor )

inline

References tensor_.

void core::scoring::nmr::rdc::RDCMultiSet::set_weight ( Real weight )

inline

References weight_.

void core::scoring::nmr::rdc::RDCMultiSet::show ( std::ostream & TR ) const

References alignment_medium_, computation_type_, core::scoring::nmr::convert_rdc_type_to_string(), number_experiments_, rdc_singleset_vec_, SVD, tensor_, and total_number_rdc_.

Real core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls ( )

solves the RDC tensor using NLS and returns the weighted RDC score according to the single RDC weighting scheme and the weights of the individual experiments

Real core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_svd ( )

solves the RDC tensor using SVD and returns the weighted RDC score according to the single RDC weighting scheme and the weights of the individual experiments

References alignment_medium_, matrix_A_, number_experiments_, rdc_single_weights_, rdc_singleset_vec_, rdc_values_, spin_coordinates_, svd_solver_, tensor_, total_number_rdc_, core::scoring::total_score, core::scoring::nmr::rdc::TR(), and update_matrix_A().

bool core::scoring::nmr::rdc::RDCMultiSet::symmetric_rdc_calc ( ) const

inline

References symmetric_rdc_calc_.

bool core::scoring::nmr::rdc::RDCMultiSet::tensor_fixed ( ) const

inline

References fixed_tensor_.

void core::scoring::nmr::rdc::RDCMultiSet::unfix_tensor ( )

inline

References fixed_tensor_.

void core::scoring::nmr::rdc::RDCMultiSet::update_matrix_A ( )

builds matrix_A from the spin coordinates and hands it over to the SVD solver

References correct_sign_, fill_matrix_A_row(), matrix_A_, norm_type_, core::scoring::nmr::NORM_TYPE_CH, core::scoring::nmr::NORM_TYPE_NH, core::scoring::nmr::NORM_TYPE_NONE, number_experiments_, core::scoring::nmr::rdc::rdc_D_max(), core::scoring::nmr::rdc::rdc_scaling_factor_toCH(), core::scoring::nmr::rdc::rdc_scaling_factor_toNH(), rdc_singleset_vec_, rdc_values_, spin_coordinates_, svd_solver_, and total_number_rdc_.

Referenced by set_atom_derivatives(), and solve_tensor_and_compute_score_by_svd().

void core::scoring::nmr::rdc::RDCMultiSet::update_single_rdc_weighting ( )

updates the array holding the single RDC weights that are used during score calculation needs to be called e.g. when the weighting scheme of one of the RDCSingleSets was changed

References core::scoring::nmr::CONST, number_experiments_, core::scoring::nmr::OBSIG, rdc_single_weights_, rdc_singleset_vec_, rdc_values_, core::scoring::nmr::SIGMA, spin_coordinates_, and total_number_rdc_.

void core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates ( pose::Pose const & pose )

updates the spin coordinates every time the pose is changed make sure that this function is called before update_matrix_A() is called

References core::conformation::Residue::atom(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), number_experiments_, rdc_singleset_vec_, core::pose::Pose::residue(), spin_coordinates_, symmetric_rdc_calc_, core::pose::symmetry::symmetry_info(), and core::conformation::Atom::xyz().

Friends And Related Function Documentation

void rdc_erf	(	Real const *	par,
		int	m_dat,
		void const *	data,
		Real *	fvec,
		int *
	)

friend

rdc error function used in the lmmin function

par is an array of fit parameters [alpha, beta, gamma, (Da, R)]
data is a pointer to the the RDCMultiSet object i.e. to all data needed for RDC calculation and NLS fitting
fvc is an array holding the residuals of the fit calculation

Referenced by solve_tensor_and_compute_score_by_nls().