#include <PCSSingleSet.hh>

Public Types
enum	COMPUTATION_TYPE { SVD = 1, NLS = 2, NLSAX = 3, NLSRH = 4, NLSAXRH = 5 }
	type of tensor and score calculation SVD = singular value decomposition (coupled with grid search) NLS = non-linear least squares fitting NLSAX = non-linear least squares fitting with fixed axial tensor component NLSRH = non-linear least squares fitting with fixed rhombic tensor component NLSAXRH = non-linear least squares fitting with fixed axial and rhombic tensor component More...

Public Member Functions
	PCSSingleSet (std::string const &filename, std::string const &metal_ion_label, pose::Pose const &pose)
	construct from pcs datafile set default values for PCSSingleSet weight, single_pcs_weighting_scheme and computation type More...

	PCSSingleSet (std::string const &filename, std::string const &metal_ion_label, pose::Pose const &pose, Real const weight, std::string single_pcs_weigting="CONST", std::string computation_type="SVD")
	constructor with full argument list More...

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

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

	~PCSSingleSet ()
	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 (Vector const &metal_coord)
	updates matrix_A using the metal coordinates it gets from the grid search of the PCSMultiSet object hands matrix_A over to the SVD solver too More...

Real	solve_tensor_and_compute_score_by_svd (Vector const &metal_coord)
	solves the PCS tensor using SVD and returns the weighted PCS score according to the single PCS weighting scheme More...

Real	solve_tensor_and_compute_score_by_nls (Vector const &metal_coord)
	solves the PCS tensor using NLS and returns the weighted PCS score according to the single PCS weighting scheme More...

Real	compute_pcs_values_and_score_from_tensor (PCSTensor const &tensor)
	calculate PCS values from a given tensor, set values in the PCSSingle vector and return the PCS score More...

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

void	set_atom_derivatives (pose::Pose &pose)
	sets the xyz derivative of the PCS PCSTensor 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

Real	get_scaling_factor () const

Size	get_number_pcs () const

std::string	get_dataset_name () const

std::string	get_metal_ion_label () const

utility::vector1< PCSSingle > const &	get_single_pcs_vec () const

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

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

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

PCSTensorCOP	get_tensor_const () const

PCSTensorOP	get_tensor ()

COMPUTATION_TYPE	get_computation_type () const

NMR_VALUE_AVERAGING_TYPE	get_averaging_type () const

utility::vector1 < utility::vector1 < utility::vector1< Vector > > > const &	get_spin_coordinates () const

utility::fixedsizearray1< Real, 6 > const &	get_metal_coord_bounds () const

bool	normalized_data () const

bool	symmetric_pcs_calc () const

void	set_weight (Real weight)

void	set_tensor (PCSTensorOP const &tensor)

void	set_metal_coord_bounds (utility::fixedsizearray1< Real, 6 > const &metal_coord_bounds)

void	set_computation_type (std::string const &type)

void	set_averaging_type (std::string const &type)

void	show (std::ostream &TR) const

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

void	init_from_pcs_filedata (std::string const &filename, pose::Pose const &pose)
	utility function used in constructor to initialize PCSSingelSet object from pcs data file and pose. More...

void	register_options ()
	register options More...

void	init_from_cml ()

void	fill_matrix_A_row (utility::fixedsizearray1< Real, 5 > &A_row, utility::vector1< Vector > const &spin_coords, Vector const &metal_coord, Real const &scal=1.0)
	utility function to fill matrix_A that is used for SVD in PCSSingleSet We average the PCS here over the number of equivalent spins (e.g. methyl protons). More...

void	convert_string_to_computation_type (std::string const &computation_type)
	utility functions to convert string to class specific enums More...

Real	basic_pcs_equation (utility::fixedsizearray1< Real, 5 > const &par, Vector const &spin_coord, Matrix const &rotM, Real const &scal=1.0)
	utility function that calculates one single PCS value given the input arguments xM, yM, zM, Xax, Xrh, the spin coordinates, a rotation matrix and a scaling factor More...

Real	fpcs (Real const *par, utility::vector1< Vector > const &spin_coord, Matrix const &rotM, Real const &scal=1.0)
	utility functions to calculate the PCS from different sets of input arguments arguments are a pointer to the parameters (xM, yM, zM, Xax, Xrh), the coordinates of equivalent spins, a rotation matrix that must be previously constructed from the Euler angles and a scaling factor. Fixed values of Xax and Xrh can be provided. More...

Real	fpcs_Xax (Real const *par, Real const &Xax, utility::vector1< Vector > const &spin_coord, Matrix const &rotM, Real const &scal=1.0)

Real	fpcs_Xrh (Real const *par, Real const &Xrh, utility::vector1< Vector > const &spin_coord, Matrix const &rotM, Real const &scal=1.0)

Real	fpcs_Xax_Xrh (Real const *par, Real const &Xax, Real const &Xrh, utility::vector1< Vector > const &spin_coord, Matrix const &rotM, Real const &scal=1.0)

Private Attributes
std::string	dataset_name_

std::string	metal_ion_label_

utility::vector1< PCSSingle >	pcs_single_vec_

Real	weight_

Real	scaling_factor_

Size	number_pcs_

ObjexxFCL::FArray2D< Real >	matrix_A_

ObjexxFCL::FArray1D< Real >	pcs_values_

ObjexxFCL::FArray1D< Real >	pcs_single_weights_

PCSTensorOP	tensor_

basic::svd::SVD_SolverOP	svd_solver_

SINGLE_NMR_VALUE_WEIGHTING	single_pcs_weighting_scheme_

COMPUTATION_TYPE	computation_type_

utility::vector1 < utility::vector1 < utility::vector1< Vector > > >	spin_coordinates_

utility::fixedsizearray1< Real, 6 >	metal_coord_bounds_

bool	normalized_data_

bool	symmetric_pcs_calc_

NMR_VALUE_AVERAGING_TYPE	ave_type_

Size	nls_repeats_

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

Member Enumeration Documentation

enum core::scoring::nmr::pcs::PCSSingleSet::COMPUTATION_TYPE

type of tensor and score calculation SVD = singular value decomposition (coupled with grid search) NLS = non-linear least squares fitting NLSAX = non-linear least squares fitting with fixed axial tensor component NLSRH = non-linear least squares fitting with fixed rhombic tensor component NLSAXRH = non-linear least squares fitting with fixed axial and rhombic tensor component

Enumerator
SVD
NLS
NLSAX
NLSRH
NLSAXRH

Constructor & Destructor Documentation

core::scoring::nmr::pcs::PCSSingleSet::PCSSingleSet	(	std::string const &	filename,
		std::string const &	metal_ion_label,
		pose::Pose const &	pose
	)

construct from pcs datafile set default values for PCSSingleSet weight, single_pcs_weighting_scheme and computation type

constructor with arguments set default values for PCSSingleSet weight, single_pcs_weighting_scheme and computation type

References computation_type_, core::scoring::nmr::CONST, init_from_cml(), init_from_pcs_filedata(), register_options(), single_pcs_weighting_scheme_, and SVD.

core::scoring::nmr::pcs::PCSSingleSet::PCSSingleSet	(	std::string const &	filename,
		std::string const &	metal_ion_label,
		pose::Pose const &	pose,
		Real const	weight,
		std::string	single_pcs_weigting = `"CONST"`,
		std::string	computation_type = `"SVD"`
	)

constructor with full argument list

References convert_string_to_computation_type(), core::scoring::nmr::convert_string_to_weighting_scheme(), init_from_cml(), init_from_pcs_filedata(), register_options(), and single_pcs_weighting_scheme_.

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

copy constructor

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

destructor

core::scoring::nmr::pcs::PCSSingleSet::PCSSingleSet ( )

private

default constructor

Member Function Documentation

Real core::scoring::nmr::pcs::PCSSingleSet::basic_pcs_equation	(	utility::fixedsizearray1< Real, 5 > const &	par,
		Vector const &	spin_coord,
		Matrix const &	rotM,
		Real const &	scal = `1.0`
	)

private

utility function that calculates one single PCS value given the input arguments xM, yM, zM, Xax, Xrh, the spin coordinates, a rotation matrix and a scaling factor

References core::scoring::pcs, and protocols::hybridization::r2.

Referenced by fpcs(), fpcs_Xax(), fpcs_Xax_Xrh(), and fpcs_Xrh().

Real core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor ( PCSTensor const & tensor )

calculate PCS values from a given tensor, set values in the PCSSingle vector and return the PCS score

calculate PCS values from a given tensor and set values in the PCSSingle vector

Real core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor ( )

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

References tensor_.

void core::scoring::nmr::pcs::PCSSingleSet::convert_string_to_computation_type ( std::string const & computation_type )

private

utility functions to convert string to class specific enums

References computation_type_, NLS, NLSAX, NLSAXRH, NLSRH, protocols::kinmatch::str(), and SVD.

Referenced by PCSSingleSet(), and set_computation_type().

void core::scoring::nmr::pcs::PCSSingleSet::fill_matrix_A_row	(	utility::fixedsizearray1< Real, 5 > &	A_row,
		utility::vector1< Vector > const &	spin_coords,
		Vector const &	metal_coord,
		Real const &	scal = `1.0`
	)

private

utility function to fill matrix_A that is used for SVD in PCSSingleSet We average the PCS here over the number of equivalent spins (e.g. methyl protons).

References ave_type_, core::scoring::nmr::MEAN, and protocols::hybridization::r2.

Referenced by compute_pcs_values_and_score_from_tensor(), and update_matrix_A().

Real core::scoring::nmr::pcs::PCSSingleSet::fpcs	(	Real const *	par,
		utility::vector1< Vector > const &	spin_coord,
		Matrix const &	rotM,
		Real const &	scal = `1.0`
	)

private

utility functions to calculate the PCS from different sets of input arguments arguments are a pointer to the parameters (xM, yM, zM, Xax, Xrh), the coordinates of equivalent spins, a rotation matrix that must be previously constructed from the Euler angles and a scaling factor. Fixed values of Xax and Xrh can be provided.

utility functions to calculate the PCS from different sets of input arguments arguments are a pointer to the parameters (xM, yM, zM, Xax, Xrh), the coordinates of equivalent spins, a rotation matrix that must be previously constructed from the Euler angles and a scaling factor. Fixed values of Xax and Xrh can be provided. We average the PCS here over the number of equivalent spins (e.g. methyl protons).

References ave_type_, basic_pcs_equation(), core::scoring::nmr::MEAN, and core::scoring::pcs.

Referenced by compute_pcs_values_and_score_from_tensor(), core::scoring::nmr::pcs::pcs_erf(), set_atom_derivatives(), and solve_tensor_and_compute_score_by_nls().

Real core::scoring::nmr::pcs::PCSSingleSet::fpcs_Xax	(	Real const *	par,
		Real const &	Xax,
		utility::vector1< Vector > const &	spin_coord,
		Matrix const &	rotM,
		Real const &	scal = `1.0`
	)

private

References ave_type_, basic_pcs_equation(), core::scoring::nmr::MEAN, and core::scoring::pcs.

Referenced by core::scoring::nmr::pcs::pcs_erf().

Real core::scoring::nmr::pcs::PCSSingleSet::fpcs_Xax_Xrh	(	Real const *	par,
		Real const &	Xax,
		Real const &	Xrh,
		utility::vector1< Vector > const &	spin_coord,
		Matrix const &	rotM,
		Real const &	scal = `1.0`
	)

private

References ave_type_, basic_pcs_equation(), core::scoring::nmr::MEAN, and core::scoring::pcs.

Referenced by core::scoring::nmr::pcs::pcs_erf().

Real core::scoring::nmr::pcs::PCSSingleSet::fpcs_Xrh	(	Real const *	par,
		Real const &	Xrh,
		utility::vector1< Vector > const &	spin_coord,
		Matrix const &	rotM,
		Real const &	scal = `1.0`
	)

private

References ave_type_, basic_pcs_equation(), core::scoring::nmr::MEAN, and core::scoring::pcs.

Referenced by core::scoring::nmr::pcs::pcs_erf().

NMR_VALUE_AVERAGING_TYPE core::scoring::nmr::pcs::PCSSingleSet::get_averaging_type ( ) const

inline

References ave_type_.

COMPUTATION_TYPE core::scoring::nmr::pcs::PCSSingleSet::get_computation_type ( ) const

inline

References computation_type_.

std::string core::scoring::nmr::pcs::PCSSingleSet::get_dataset_name ( ) const

inline

References dataset_name_.

ObjexxFCL::FArray2D<Real> const& core::scoring::nmr::pcs::PCSSingleSet::get_matrix_A ( ) const

inline

References matrix_A_.

utility::fixedsizearray1<Real,6> const& core::scoring::nmr::pcs::PCSSingleSet::get_metal_coord_bounds ( ) const

inline

References metal_coord_bounds_.

std::string core::scoring::nmr::pcs::PCSSingleSet::get_metal_ion_label ( ) const

inline

References metal_ion_label_.

Size core::scoring::nmr::pcs::PCSSingleSet::get_number_pcs ( ) const

inline

References number_pcs_.

ObjexxFCL::FArray1D<Real> const& core::scoring::nmr::pcs::PCSSingleSet::get_pcs_single_weights ( ) const

inline

References pcs_single_weights_.

ObjexxFCL::FArray1D<Real> const& core::scoring::nmr::pcs::PCSSingleSet::get_pcs_values ( ) const

inline

References pcs_values_.

Real core::scoring::nmr::pcs::PCSSingleSet::get_scaling_factor ( ) const

inline

References scaling_factor_.

utility::vector1<PCSSingle> const& core::scoring::nmr::pcs::PCSSingleSet::get_single_pcs_vec ( ) const

inline

References pcs_single_vec_.

utility::vector1< utility::vector1< utility::vector1< Vector > > > const& core::scoring::nmr::pcs::PCSSingleSet::get_spin_coordinates ( ) const

inline

References spin_coordinates_.

PCSTensorOP core::scoring::nmr::pcs::PCSSingleSet::get_tensor ( )

inline

References tensor_.

PCSTensorCOP core::scoring::nmr::pcs::PCSSingleSet::get_tensor_const ( ) const

inline

References tensor_.

Real core::scoring::nmr::pcs::PCSSingleSet::get_weight ( ) const

inline

References weight_.

void core::scoring::nmr::pcs::PCSSingleSet::init_from_cml ( )

private

References nls_repeats_, normalized_data_, and symmetric_pcs_calc_.

Referenced by PCSSingleSet().

void core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata	(	std::string const &	filename,
		pose::Pose const &	pose
	)

private

utility function used in constructor to initialize PCSSingelSet object from pcs data file and pose.

utility function used in constructor to initialize PCSSingelSet object from filedata and pose.

References core::scoring::nmr::CONST, dataset_name_, core::scoring::nmr::pcs::PCSSingle::get_protein_spins(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), matrix_A_, core::simple_metrics::metrics::mean, normalized_data_, number_pcs_, core::scoring::nmr::OBSIG, pcs_single_vec_, pcs_single_weights_, pcs_values_, core::io::nmr::read_pcs_datafile(), scaling_factor_, core::scoring::nmr::SIGMA, single_pcs_weighting_scheme_, spin_coordinates_, symmetric_pcs_calc_, core::pose::symmetry::symmetry_info(), and core::scoring::nmr::pcs::TR().

Referenced by PCSSingleSet().

bool core::scoring::nmr::pcs::PCSSingleSet::normalized_data ( ) const

inline

References normalized_data_.

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

assignment operator

References ave_type_, computation_type_, dataset_name_, matrix_A_, metal_coord_bounds_, metal_ion_label_, nls_repeats_, normalized_data_, number_pcs_, pcs_single_vec_, pcs_single_weights_, pcs_values_, scaling_factor_, single_pcs_weighting_scheme_, spin_coordinates_, svd_solver_, symmetric_pcs_calc_, tensor_, and weight_.

void core::scoring::nmr::pcs::PCSSingleSet::register_options ( )

private

register options

Referenced by PCSSingleSet().

void core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives ( pose::Pose & pose )

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

sets the xyz derivative of the PCS PCSTensor must be determined previously call solve_tensor_and_compute_score_by_svd() or solve_tensor_and_compute_score_by_nls() first

References core::scoring::nmr::apply_tensor_transformation(), core::scoring::nmr::apply_vector_transformation(), fpcs(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), matrix_A_, number_pcs_, pcs_single_vec_, pcs_single_weights_, pcs_values_, protocols::hybridization::r2, core::scoring::nmr::rotation_matrix_from_euler_angles(), scaling_factor_, spin_coordinates_, core::pose::symmetry::symmetry_info(), tensor_, and update_matrix_A().

void core::scoring::nmr::pcs::PCSSingleSet::set_averaging_type ( std::string const & type )

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

void core::scoring::nmr::pcs::PCSSingleSet::set_computation_type ( std::string const & type )

References convert_string_to_computation_type().

void core::scoring::nmr::pcs::PCSSingleSet::set_metal_coord_bounds ( utility::fixedsizearray1< Real, 6 > const & metal_coord_bounds )

inline

References metal_coord_bounds_.

void core::scoring::nmr::pcs::PCSSingleSet::set_tensor ( PCSTensorOP const & tensor )

inline

References tensor_.

void core::scoring::nmr::pcs::PCSSingleSet::set_weight ( Real weight )

inline

References weight_.

void core::scoring::nmr::pcs::PCSSingleSet::show ( std::ostream & TR ) const

References computation_type_, dataset_name_, number_pcs_, pcs_single_vec_, SVD, tensor_, and weight_.

Real core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_nls ( Vector const & metal_coord )

solves the PCS tensor using NLS and returns the weighted PCS score according to the single PCS weighting scheme

References computation_type_, dataset_name_, fpcs(), NLS, nls_repeats_, NLSAX, NLSAXRH, NLSRH, number_pcs_, pcs_erf, pcs_single_vec_, pcs_single_weights_, pcs_values_, core::scoring::nmr::rotation_matrix_from_euler_angles(), scaling_factor_, protocols::hybridization::score, spin_coordinates_, SVD, core::id::swap(), tensor_, and core::scoring::nmr::pcs::TR().

Real core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_svd ( Vector const & metal_coord )

solves the PCS tensor using SVD and returns the weighted PCS score according to the single PCS weighting scheme

solves the PCS tensor using SVD and returns the weighted PCS score according to the single PCS weighting scheme matrix A and spin coordinates must have been updated before calling this function for the first time

References dataset_name_, matrix_A_, number_pcs_, pcs_single_vec_, pcs_single_weights_, pcs_values_, protocols::hybridization::score, svd_solver_, tensor_, core::scoring::nmr::pcs::TR(), and update_matrix_A().

bool core::scoring::nmr::pcs::PCSSingleSet::symmetric_pcs_calc ( ) const

inline

References symmetric_pcs_calc_.

void core::scoring::nmr::pcs::PCSSingleSet::update_matrix_A ( Vector const & metal_coord )

updates matrix_A using the metal coordinates it gets from the grid search of the PCSMultiSet object hands matrix_A over to the SVD solver too

References fill_matrix_A_row(), matrix_A_, number_pcs_, pcs_values_, scaling_factor_, spin_coordinates_, and svd_solver_.

Referenced by set_atom_derivatives(), and solve_tensor_and_compute_score_by_svd().

void core::scoring::nmr::pcs::PCSSingleSet::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_pcs_, pcs_single_vec_, core::pose::Pose::residue(), spin_coordinates_, symmetric_pcs_calc_, core::pose::symmetry::symmetry_info(), and core::conformation::Atom::xyz().

Friends And Related Function Documentation

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

friend

pcs error function used in the lmmin function

par is an array of fit parameters [alpha, beta, gamma, xM, yM, zM, scal, (Xax, Xrh)]
data is a pointer to the the PCSSingleSet object i.e. to all data needed for PCS calculation and NLS fitting
fvc is an array holding the residuals of the fit calculation
par is an array of fit parameters [alpha, beta, gamma, xM, yM, zM, (Xax, Xrh)]
data is a pointer to the the PCSSingleSet object i.e. to all data needed for PCS calculation and NLS fitting
fvc is an array holding the residuals of the fit calculation

Referenced by solve_tensor_and_compute_score_by_nls().