#include <PcsDataLanthanide.hh>

Public Member Functions
void	update_my_A_matrix_for_cstyle (utility::vector1< utility::vector1< core::Real > > &A_all)

	PcsDataLanthanide (std::string const &, core::Real const weight, utility::vector1< PcsInputLine > &pcs_i_l, core::Size start, core::Size end, core::Real individual_scale)

	~PcsDataLanthanide ()

	PcsDataLanthanide (PcsDataLanthanide const &other)

PcsDataLanthanide &	operator= (PcsDataLanthanide const &other)

void	set_A_index (core::Size j, core::Size n_pcs_spin_)
	Set a value of the A_index_ vector. More...

void	update_my_A_matrix_for_svd (utility::vector1< utility::vector1< core::Real > > &A_all)
	update the A matrix given A_all matrix. Dimensions of A_all >= dimension of A. A_all is common to all the lanthanide sharing the same center More...

core::Real	get_weight () const
	give me the weight associated with this PCS data More...

core::Real	get_individual_scale () const

core::Real	get_normalization_factor () const
	give me the normalization factor associated with this PCS data More...

core::Real	get_normalization_factor_inversed () const
	give me the normalization factor associated with this PCS data More...

std::string	get_filename () const
	give me the filename associated with this PCS data More...

core::Size	get_n_pcs () const
	give me the number of PCS data More...

utility::vector1< core::Size > const &	get_A_index () const
	Give me the A_index_ vector. More...

const utility::vector1< utility::vector1< core::Real > > &	get_cstyle_A () const
	return the b vector in FArray1D format More...

const utility::vector1< core::Real > &	get_cstyle_b () const

const utility::vector1< core::Real > &	get_cstyle_b_individual_scale () const

core::Real	calculate_tensor_and_cost_with_svd (PcsTensor &pcs_t)
	@This return the score and populate the PcsTensor with svd. More...

core::Real	calculate_cost_only_with_svd ()

void	calculate_tensor_only_with_svd (PcsTensor &pcs_t)
	@This populate the PcsTensor with svd. More...

void	retrieve_tensor_from_svd (PcsTensor &pcs_t)

Private Member Functions
	PcsDataLanthanide ()

Private Attributes
std::string const	filename_

core::Real const	weight_

core::Size	n_pcs_

utility::vector1< core::Size >	A_index_

utility::vector1< utility::vector1< core::Real > >	cstyle_A_

utility::vector1< core::Real >	cstyle_b_

utility::vector1< core::Real >	cstyle_b_individual_scale_

basic::svd::SVD_Solver	svd_s_

core::Real	normalization_1_

core::Real	normalization_2_

core::Real	normalization_3_

core::Real	normalization_factor_

core::Real	normalization_factor_inversed_

core::Real	individual_scale_

Friends
std::ostream &	operator<< (std::ostream &out, const PcsDataLanthanide &me)
	@Print me More...

Constructor & Destructor Documentation

◆ PcsDataLanthanide() [1/3]

protocols::scoring::methods::pcs2::PcsDataLanthanide::PcsDataLanthanide	(	std::string const &	filename,
		core::Real const	weight,
		utility::vector1< PcsInputLine > &	pcs_i_l,
		core::Size	start,
		core::Size	end,
		core::Real	individual_scale
	)

◆ PcsDataLanthanide() [2/3]

protocols::scoring::methods::pcs2::PcsDataLanthanide::PcsDataLanthanide ( )

private

◆ ~PcsDataLanthanide()

protocols::scoring::methods::pcs2::PcsDataLanthanide::~PcsDataLanthanide ( )

default

◆ PcsDataLanthanide() [3/3]

protocols::scoring::methods::pcs2::PcsDataLanthanide::PcsDataLanthanide ( PcsDataLanthanide const & other )

References A_index_, cstyle_A_, cstyle_b_, cstyle_b_individual_scale_, individual_scale_, n_pcs_, normalization_1_, normalization_2_, normalization_3_, normalization_factor_, and normalization_factor_inversed_.

Member Function Documentation

◆ calculate_cost_only_with_svd()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_cost_only_with_svd ( )

References normalization_factor_, protocols::hybridization::score, svd_s_, and weight_.

◆ calculate_tensor_and_cost_with_svd()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_and_cost_with_svd ( PcsTensor & pcs_t )

@This return the score and populate the PcsTensor with svd.

References cstyle_A_, normalization_factor_, protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), protocols::hybridization::score, svd_s_, and weight_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func().

◆ calculate_tensor_only_with_svd()

void protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd ( PcsTensor & pcs_t )

@This populate the PcsTensor with svd.

References protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), and svd_s_.

Referenced by protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors().

◆ get_A_index()

const utility::vector1< core::Size > & protocols::scoring::methods::pcs2::PcsDataLanthanide::get_A_index ( ) const

Give me the A_index_ vector.

References A_index_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), and protocols::scoring::methods::pcs2::TensorsOptimizerFix::func().

◆ get_cstyle_A()

const utility::vector1< utility::vector1< core::Real > > & protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_A ( ) const

return the b vector in FArray1D format

References cstyle_A_.

◆ get_cstyle_b()

const utility::vector1< core::Real > & protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_b ( ) const

References cstyle_b_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), and protocols::scoring::methods::pcs2::TensorsOptimizerFix::func().

◆ get_cstyle_b_individual_scale()

const utility::vector1< core::Real > & protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_b_individual_scale ( ) const

References cstyle_b_individual_scale_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), and protocols::scoring::methods::pcs2::TensorsOptimizer::func().

◆ get_filename()

std::string protocols::scoring::methods::pcs2::PcsDataLanthanide::get_filename ( ) const

give me the filename associated with this PCS data

References filename_.

Referenced by protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info().

◆ get_individual_scale()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::get_individual_scale ( ) const

References individual_scale_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), and protocols::scoring::methods::pcs2::TensorsOptimizer::func().

◆ get_n_pcs()

core::Size protocols::scoring::methods::pcs2::PcsDataLanthanide::get_n_pcs ( ) const

give me the number of PCS data

References n_pcs_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), and protocols::scoring::methods::pcs2::TensorsOptimizerFix::func().

◆ get_normalization_factor()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::get_normalization_factor ( ) const

give me the normalization factor associated with this PCS data

References normalization_factor_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), and protocols::scoring::methods::pcs2::TensorsOptimizerFix::func().

◆ get_normalization_factor_inversed()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::get_normalization_factor_inversed ( ) const

give me the normalization factor associated with this PCS data

References normalization_factor_inversed_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), and protocols::scoring::methods::pcs2::TensorsOptimizer::func().

◆ get_weight()

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::get_weight ( ) const

give me the weight associated with this PCS data

References weight_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), and protocols::scoring::methods::pcs2::TensorsOptimizerFix::func().

◆ operator=()

PcsDataLanthanide & protocols::scoring::methods::pcs2::PcsDataLanthanide::operator= ( PcsDataLanthanide const & other )

References A_index_, cstyle_A_, cstyle_b_, cstyle_b_individual_scale_, individual_scale_, n_pcs_, normalization_1_, normalization_2_, normalization_3_, normalization_factor_, normalization_factor_inversed_, and svd_s_.

◆ retrieve_tensor_from_svd()

void protocols::scoring::methods::pcs2::PcsDataLanthanide::retrieve_tensor_from_svd ( PcsTensor & pcs_t )

References protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), and svd_s_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact().

◆ set_A_index()

void protocols::scoring::methods::pcs2::PcsDataLanthanide::set_A_index	(	core::Size	j,
		core::Size	n_pcs_spin_
	)

Set a value of the A_index_ vector.

References A_index_.

Referenced by protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter().

◆ update_my_A_matrix_for_cstyle()

void protocols::scoring::methods::pcs2::PcsDataLanthanide::update_my_A_matrix_for_cstyle ( utility::vector1< utility::vector1< core::Real > > & A_all )

References A_index_, and cstyle_A_.

◆ update_my_A_matrix_for_svd()

void protocols::scoring::methods::pcs2::PcsDataLanthanide::update_my_A_matrix_for_svd ( utility::vector1< utility::vector1< core::Real > > & A_all )

update the A matrix given A_all matrix. Dimensions of A_all >= dimension of A. A_all is common to all the lanthanide sharing the same center

References A_index_, cstyle_A_, and svd_s_.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const PcsDataLanthanide &	me
	)

friend

@Print me

Member Data Documentation

◆ A_index_

utility::vector1<core::Size> protocols::scoring::methods::pcs2::PcsDataLanthanide::A_index_

private

Referenced by get_A_index(), operator=(), PcsDataLanthanide(), set_A_index(), update_my_A_matrix_for_cstyle(), and update_my_A_matrix_for_svd().

◆ cstyle_A_

utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::pcs2::PcsDataLanthanide::cstyle_A_

private

Referenced by calculate_tensor_and_cost_with_svd(), get_cstyle_A(), operator=(), PcsDataLanthanide(), update_my_A_matrix_for_cstyle(), and update_my_A_matrix_for_svd().

◆ cstyle_b_

utility::vector1<core::Real> protocols::scoring::methods::pcs2::PcsDataLanthanide::cstyle_b_

private

Referenced by get_cstyle_b(), operator=(), and PcsDataLanthanide().

◆ cstyle_b_individual_scale_

utility::vector1<core::Real> protocols::scoring::methods::pcs2::PcsDataLanthanide::cstyle_b_individual_scale_

private

Referenced by get_cstyle_b_individual_scale(), operator=(), and PcsDataLanthanide().

◆ filename_

std::string const protocols::scoring::methods::pcs2::PcsDataLanthanide::filename_

private

Referenced by get_filename(), and PcsDataLanthanide().

◆ individual_scale_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::individual_scale_

private

Referenced by get_individual_scale(), operator=(), and PcsDataLanthanide().

◆ n_pcs_

core::Size protocols::scoring::methods::pcs2::PcsDataLanthanide::n_pcs_

private

Referenced by get_n_pcs(), operator=(), and PcsDataLanthanide().

◆ normalization_1_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::normalization_1_

private

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

◆ normalization_2_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::normalization_2_

private

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

◆ normalization_3_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::normalization_3_

private

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

◆ normalization_factor_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::normalization_factor_

private

Referenced by calculate_cost_only_with_svd(), calculate_tensor_and_cost_with_svd(), get_normalization_factor(), operator=(), and PcsDataLanthanide().

◆ normalization_factor_inversed_

core::Real protocols::scoring::methods::pcs2::PcsDataLanthanide::normalization_factor_inversed_

private

Referenced by get_normalization_factor_inversed(), operator=(), and PcsDataLanthanide().

◆ svd_s_

basic::svd::SVD_Solver protocols::scoring::methods::pcs2::PcsDataLanthanide::svd_s_

private

Referenced by calculate_cost_only_with_svd(), calculate_tensor_and_cost_with_svd(), calculate_tensor_only_with_svd(), operator=(), PcsDataLanthanide(), retrieve_tensor_from_svd(), and update_my_A_matrix_for_svd().

◆ weight_

core::Real const protocols::scoring::methods::pcs2::PcsDataLanthanide::weight_

private

Referenced by calculate_cost_only_with_svd(), calculate_tensor_and_cost_with_svd(), and get_weight().

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

src/protocols/scoring/methods/pcs2/PcsDataLanthanide.hh
src/protocols/scoring/methods/pcs2/PcsDataLanthanide.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ PcsDataLanthanide() [1/3]

◆ PcsDataLanthanide() [2/3]

◆ ~PcsDataLanthanide()

◆ PcsDataLanthanide() [3/3]

Member Function Documentation

◆ calculate_cost_only_with_svd()

◆ calculate_tensor_and_cost_with_svd()

◆ calculate_tensor_only_with_svd()

◆ get_A_index()

◆ get_cstyle_A()

◆ get_cstyle_b()

◆ get_cstyle_b_individual_scale()

◆ get_filename()

◆ get_individual_scale()

◆ get_n_pcs()

◆ get_normalization_factor()

◆ get_normalization_factor_inversed()

◆ get_weight()

◆ operator=()

◆ retrieve_tensor_from_svd()

◆ set_A_index()

◆ update_my_A_matrix_for_cstyle()

◆ update_my_A_matrix_for_svd()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ A_index_

◆ cstyle_A_

◆ cstyle_b_

◆ cstyle_b_individual_scale_

◆ filename_

◆ individual_scale_

◆ n_pcs_

◆ normalization_1_

◆ normalization_2_

◆ normalization_3_

◆ normalization_factor_

◆ normalization_factor_inversed_

◆ svd_s_

◆ weight_