protocols::scoring::methods::pcs2::PcsDataLanthanide Class Reference

#include <PcsDataLanthanide.hh>

Public Member Functions
void	update_my_A_matrix_for_cstyle (utility::vector1< utility::vector1< core::Real > > &A_all)
	PcsDataLanthanide ()
	~PcsDataLanthanide ()
	PcsDataLanthanide (PcsDataLanthanide const &other)
PcsDataLanthanide &	operator= (PcsDataLanthanide const &other)
	PcsDataLanthanide (std::string, core::Real const weight, utility::vector1< PcsInputLine > &pcs_i_l, core::Size start, core::Size end, core::Real individual_scale)
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)
	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)
	populate the PcsTensor with svd. More...
void	retrieve_tensor_from_svd (PcsTensor &pcs_t)

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)
	me More...

Constructor & Destructor Documentation

protocols::scoring::methods::pcs2::PcsDataLanthanide::PcsDataLanthanide

(

)

References utility_exit_with_message.

protocols::scoring::methods::pcs2::PcsDataLanthanide::~PcsDataLanthanide

(

)

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_.

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

References A_index_, cstyle_A_, cstyle_b_, cstyle_b_individual_scale_, protocols::scoring::methods::pcs2::do_I_skip(), filename_, protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_experimental(), individual_scale_, N, n_pcs_, normalization_1_, normalization_2_, normalization_3_, normalization_factor_, normalization_factor_inversed_, basic::options::OptionKeys::PCS::normalization_id, option, protocols::scoring::methods::pcs2::reduced_size(), basic::svd::SVD_Solver::set_vector_b(), sum(), svd_s_, protocols::scoring::methods::pcs2::TR_PcsDataLanthanide, user, and utility_exit_with_message.

Member Function Documentation

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

(

)

References normalization_factor_, basic::svd::SVD_Solver::run_decomp_svd(), basic::svd::SVD_Solver::run_score_svd_without_solving(), score, svd_s_, and weight_.

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

(

PcsTensor &

pcs_t

)

return the score and populate the PcsTensor with svd.

References cstyle_A_, basic::svd::SVD_Solver::get_svd_solution(), normalization_factor_, protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), basic::svd::SVD_Solver::run_decomp_svd(), basic::svd::SVD_Solver::run_score_svd_on_matrix(), basic::svd::SVD_Solver::run_score_svd_without_solving(), basic::svd::SVD_Solver::run_solve_svd(), score, svd_s_, and weight_.

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

void protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd

(

PcsTensor &

pcs_t

)

populate the PcsTensor with svd.

References basic::svd::SVD_Solver::get_svd_solution(), protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), basic::svd::SVD_Solver::run_decomp_svd(), basic::svd::SVD_Solver::run_solve_svd(), and svd_s_.

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

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

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_.

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

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().

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::operator<<().

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().

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::TensorsOptimizerSvd::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(), and protocols::scoring::methods::pcs2::operator<<().

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().

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().

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

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_.

void protocols::scoring::methods::pcs2::PcsDataLanthanide::retrieve_tensor_from_svd

(

PcsTensor &

pcs_t

)

References basic::svd::SVD_Solver::get_svd_solution(), protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), and svd_s_.

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

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().

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_.

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_, basic::svd::SVD_Solver::set_matrix_A(), and svd_s_.

Friends And Related Function Documentation

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

friend

me

Member Data Documentation

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

private

Referenced by get_A_index(), protocols::scoring::methods::pcs2::operator<<(), operator=(), PcsDataLanthanide(), set_A_index(), update_my_A_matrix_for_cstyle(), and update_my_A_matrix_for_svd().

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().

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

private

Referenced by get_cstyle_b(), protocols::scoring::methods::pcs2::operator<<(), operator=(), and PcsDataLanthanide().

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

private

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

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

private

Referenced by get_filename(), and PcsDataLanthanide().

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

private

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

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

private

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

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

private

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

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

private

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

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

private

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

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().

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

private

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

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().

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