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

#include <PcsDataLanthanide.hh>

Collaboration diagram for protocols::scoring::methods::pcs2::PcsDataLanthanide:

List of all members.

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.
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
core::Real	get_weight () const
	give me the weight associated with this PCS data
core::Real	get_individual_scale () const
core::Real	get_normalization_factor () const
	give me the normalization factor associated with this PCS data
core::Real	get_normalization_factor_inversed () const
	give me the normalization factor associated with this PCS data
std::string	get_filename () const
	give me the filename associated with this PCS data
core::Size	get_n_pcs () const
	give me the number of PCS data
utility::vector1< core::Size > const &	get_A_index () const
	Give me the A_index_ vector.
const utility::vector1 < utility::vector1< core::Real > > &	get_cstyle_A () const
	return the b vector in FArray1D format
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.
core::Real	calculate_cost_only_with_svd ()
void	calculate_tensor_only_with_svd (PcsTensor &pcs_t)
	populate the PcsTensor with svd.
void	retrieve_tensor_from_svd (PcsTensor &pcs_t)
Friends
std::ostream &	operator<< (std::ostream &out, const PcsDataLanthanide &me)
	me

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Constructor & Destructor Documentation

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

(

)

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

(

)

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

(

PcsDataLanthanide const &

other

)

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 protocols::scoring::methods::pcs2::do_I_skip(), protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_experimental(), protocols::forge::build::SegmentInsertConnectionScheme::N, protocols::scoring::methods::pcs2::reduced_size(), and protocols::scoring::methods::pcs2::TR_PcsDataLanthanide().

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Member Function Documentation

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

(

)

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 make_table_of_pilot_apps::f, and protocols::scoring::methods::pcs2::PcsTensor::reset_tensor().

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 make_table_of_pilot_apps::f, and protocols::scoring::methods::pcs2::PcsTensor::reset_tensor().

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.

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

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

(

)

const

return the b vector in FArray1D format

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

(

)

const

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

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

(

)

const

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

Referenced by protocols::scoring::methods::pcs2::operator<<().

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

(

)

const

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

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

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

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

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

PcsDataLanthanide & protocols::scoring::methods::pcs2::PcsDataLanthanide::operator=

(

PcsDataLanthanide const &

other

)

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

(

PcsTensor &

pcs_t

)

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

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.

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

)

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

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Friends And Related Function Documentation

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

me

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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