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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 (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)
 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 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)
 me More...
 

Constructor & Destructor Documentation

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 
)

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_, core::chemical::element::N, n_pcs_, normalization_1_, normalization_2_, normalization_3_, normalization_factor_, normalization_factor_inversed_, protocols::scoring::methods::pcs2::reduced_size(), core::simple_metrics::metrics::sum, svd_s_, and protocols::scoring::methods::pcs2::TR_PcsDataLanthanide().

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

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

References normalization_factor_, protocols::hybridization::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_, normalization_factor_, protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), protocols::hybridization::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 protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(), 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::PcsEnergy::dump_PCS_info(), and 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 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_, 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:
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