protocols::scoring::methods::pcs2::PcsDataCenter Class Reference

#include <PcsDataCenter.hh>

Inheritance diagram for protocols::scoring::methods::pcs2::PcsDataCenter:

Public Member Functions
	PcsDataCenter ()
	~PcsDataCenter () override
	PcsDataCenter (PcsDataCenter const &other)
PcsDataCenter &	operator= (PcsDataCenter const &src)
	PcsDataCenter (PcsInputCenter &pcs_i_c, core::Size start, core::Size end, core::Real individual_scale)
core::Size	get_n_lanthanides () const
	Give me the number of lanthanides for this center. More...
utility::vector1< utility::vector1< core::Real > > const &	get_A_all () const
	Give me the matrix A_all_. More...
utility::vector1< core::Real > const &	get_X_all () const
	Give me the vector X_all_. More...
utility::vector1< core::Real > const &	get_Y_all () const
	Give me the vector Y_all_. More...
utility::vector1< core::Real > const &	get_Z_all () const
	Give me the vector Z_all_. More...
core::Size	where_is_line (PcsInputLine &pcs_i_l)
	Give the index number of the PcsInputLine given. More...
void	update_X_Y_Z_all (core::pose::Pose const &pose)
	This is called each time the pose is changed. More...
void	update_matrix_A_all (core::Real const X, core::Real const Y, core::Real const Z)
	Call update_my_A_matrix for all lanthanide data. X Y Z are the new coordinate of the center. More...
void	update_matrix_A_all_for_svd (core::Real const X, core::Real const Y, core::Real const Z)
	Call update_my_A_matrix for all lanthanide data. X Y Z are the new coordinate of the center It also update individual smaller matrice for svd. More...
void	update_matrix_A_all_for_cstyle (core::Real const X, core::Real const Y, core::Real const Z)
utility::vector1< PcsDataLanthanide > &	get_pcs_data_per_lanthanides_all ()
	Give me the vector PCS_data_per_lanthanides_all_. More...
const utility::vector1< PcsInputLine > &	get_PCS_data_line_all_spin () const
	Give me the vector PCS_data_line_all_spin_. More...
const utility::vector1< PcsDataLanthanide > &	get_pcs_data_per_lanthanides_all () const
	Give me the vector PCS_data_per_lanthanides_all_ (const version) More...

Private Member Functions
void	update_matrix_A ()
void	update_matrix_A_cstyle ()

Private Attributes
core::Size	n_lanthanides_
core::Size	n_pcs_spin_
utility::vector1< PcsInputLine >	PCS_data_line_all_spin_
utility::vector1< PcsDataLanthanide >	PCS_data_per_lanthanides_all_
utility::vector1< utility::vector1< core::Real > >	A_all_
utility::vector1< core::Real >	X_all_
utility::vector1< core::Real >	Y_all_
utility::vector1< core::Real >	Z_all_

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

Constructor & Destructor Documentation

PcsDataCenter() [1/3]

protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter

(

)

~PcsDataCenter()

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

overridedefault

PcsDataCenter() [2/3]

protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter

(

PcsDataCenter const &

other

)

References A_all_, n_lanthanides_, n_pcs_spin_, PCS_data_line_all_spin_, PCS_data_per_lanthanides_all_, X_all_, Y_all_, and Z_all_.

PcsDataCenter() [3/3]

protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter	(	PcsInputCenter &	pcs_i_c,
		core::Size	start,
		core::Size	end,
		core::Real	individual_scale
	)

References A_all_, protocols::scoring::methods::pcs2::do_I_skip(), core::sequence::end, protocols::abinitio::filename(), protocols::scoring::methods::pcs2::PcsInputCenter::get_PcsInputFile_all(), protocols::scoring::methods::pcs2::PcsInputFile::get_PcsInputLine_all(), protocols::scoring::methods::pcs2::PcsInputFile::get_weight(), n_lanthanides_, n_pcs_spin_, PCS_data_line_all_spin_, PCS_data_per_lanthanides_all_, protocols::scoring::methods::pcs2::PcsDataLanthanide::set_A_index(), protocols::loops::start, where_is_line(), X_all_, Y_all_, and Z_all_.

Member Function Documentation

get_A_all()

const utility::vector1< utility::vector1< core::Real > > & protocols::scoring::methods::pcs2::PcsDataCenter::get_A_all

(

)

const

Give me the matrix A_all_.

References A_all_.

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().

get_n_lanthanides()

core::Size protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides

(

)

const

Give me the number of lanthanides for this center.

References n_lanthanides_.

Referenced by protocols::scoring::methods::pcs2::TensorsOptimizer::abort_min(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::abort_min(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd(), protocols::scoring::methods::pcs2::PcsEnergy::calculate_pcs_score_on_PCS_data_center_CA(), 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(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func(), and protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_fix_from_PCS_data().

get_PCS_data_line_all_spin()

const utility::vector1< PcsInputLine > & protocols::scoring::methods::pcs2::PcsDataCenter::get_PCS_data_line_all_spin

(

)

const

Give me the vector PCS_data_line_all_spin_.

References PCS_data_line_all_spin_.

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

get_pcs_data_per_lanthanides_all() [1/2]

utility::vector1< PcsDataLanthanide > & protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all

(

)

Give me the vector PCS_data_per_lanthanides_all_.

References PCS_data_per_lanthanides_all_.

Referenced by protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd(), protocols::scoring::methods::pcs2::PcsEnergy::calculate_pcs_score_on_PCS_data_center_CA(), 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(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(), and protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func().

get_pcs_data_per_lanthanides_all() [2/2]

const utility::vector1< PcsDataLanthanide > & protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all

(

)

const

Give me the vector PCS_data_per_lanthanides_all_ (const version)

References PCS_data_per_lanthanides_all_.

get_X_all()

const utility::vector1< core::Real > & protocols::scoring::methods::pcs2::PcsDataCenter::get_X_all

(

)

const

Give me the vector X_all_.

References X_all_.

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

get_Y_all()

const utility::vector1< core::Real > & protocols::scoring::methods::pcs2::PcsDataCenter::get_Y_all

(

)

const

Give me the vector Y_all_.

References Y_all_.

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

get_Z_all()

const utility::vector1< core::Real > & protocols::scoring::methods::pcs2::PcsDataCenter::get_Z_all

(

)

const

Give me the vector Z_all_.

References Z_all_.

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

operator=()

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

(

PcsDataCenter const &

src

)

References A_all_, n_lanthanides_, n_pcs_spin_, PCS_data_line_all_spin_, PCS_data_per_lanthanides_all_, X_all_, Y_all_, and Z_all_.

update_matrix_A()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A ( )

private

References A_all_, and PCS_data_per_lanthanides_all_.

Referenced by update_matrix_A_all_for_svd().

update_matrix_A_all()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all	(	core::Real const	X,
		core::Real const	Y,
		core::Real const	Z
	)

Call update_my_A_matrix for all lanthanide data. X Y Z are the new coordinate of the center.

References A_all_, protocols::scoring::methods::pcs2::fill_A_line_slow(), n_pcs_spin_, protocols::comparative_modeling::features::X, X_all_, core::chemical::element::Y, Y_all_, and Z_all_.

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

update_matrix_A_all_for_cstyle()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_cstyle	(	core::Real const	X,
		core::Real const	Y,
		core::Real const	Z
	)

References A_all_, protocols::scoring::methods::pcs2::fill_A_line_slow(), n_pcs_spin_, update_matrix_A_cstyle(), protocols::comparative_modeling::features::X, X_all_, core::chemical::element::Y, Y_all_, and Z_all_.

update_matrix_A_all_for_svd()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_svd	(	core::Real const	X,
		core::Real const	Y,
		core::Real const	Z
	)

Call update_my_A_matrix for all lanthanide data. X Y Z are the new coordinate of the center It also update individual smaller matrice for svd.

References A_all_, protocols::scoring::methods::pcs2::fill_A_line_slow(), n_pcs_spin_, update_matrix_A(), protocols::comparative_modeling::features::X, X_all_, core::chemical::element::Y, Y_all_, and Z_all_.

Referenced by protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors(), and protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func().

update_matrix_A_cstyle()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_cstyle ( )

private

References A_all_, and PCS_data_per_lanthanides_all_.

Referenced by update_matrix_A_all_for_cstyle().

update_X_Y_Z_all()

void protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all

(

core::pose::Pose const &

pose

)

This is called each time the pose is changed.

References core::conformation::Residue::atom(), core::conformation::Residue::has(), PCS_data_line_all_spin_, core::pose::Pose::residue(), core::pose::Pose::size(), X_all_, core::conformation::Atom::xyz(), Y_all_, and Z_all_.

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

where_is_line()

core::Size protocols::scoring::methods::pcs2::PcsDataCenter::where_is_line

(

PcsInputLine &

pcs_i_l

)

Give the index number of the PcsInputLine given.

References protocols::scoring::methods::pcs2::PcsInputLine::get_atom_name(), protocols::scoring::methods::pcs2::PcsInputLine::get_residue_num(), and PCS_data_line_all_spin_.

Referenced by PcsDataCenter().

Friends And Related Function Documentation

operator<<

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

friend

Print me.

Member Data Documentation

A_all_

utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::pcs2::PcsDataCenter::A_all_

private

Referenced by get_A_all(), operator=(), PcsDataCenter(), update_matrix_A(), update_matrix_A_all(), update_matrix_A_all_for_cstyle(), update_matrix_A_all_for_svd(), and update_matrix_A_cstyle().

n_lanthanides_

core::Size protocols::scoring::methods::pcs2::PcsDataCenter::n_lanthanides_

private

Referenced by get_n_lanthanides(), operator=(), and PcsDataCenter().

n_pcs_spin_

core::Size protocols::scoring::methods::pcs2::PcsDataCenter::n_pcs_spin_

private

Referenced by operator=(), PcsDataCenter(), update_matrix_A_all(), update_matrix_A_all_for_cstyle(), and update_matrix_A_all_for_svd().

PCS_data_line_all_spin_

utility::vector1<PcsInputLine> protocols::scoring::methods::pcs2::PcsDataCenter::PCS_data_line_all_spin_

private

Referenced by get_PCS_data_line_all_spin(), operator=(), PcsDataCenter(), update_X_Y_Z_all(), and where_is_line().

PCS_data_per_lanthanides_all_

utility::vector1<PcsDataLanthanide> protocols::scoring::methods::pcs2::PcsDataCenter::PCS_data_per_lanthanides_all_

private

Referenced by get_pcs_data_per_lanthanides_all(), operator=(), PcsDataCenter(), update_matrix_A(), and update_matrix_A_cstyle().

X_all_

utility::vector1<core::Real> protocols::scoring::methods::pcs2::PcsDataCenter::X_all_

private

Referenced by get_X_all(), operator=(), PcsDataCenter(), update_matrix_A_all(), update_matrix_A_all_for_cstyle(), update_matrix_A_all_for_svd(), and update_X_Y_Z_all().

Y_all_

utility::vector1<core::Real> protocols::scoring::methods::pcs2::PcsDataCenter::Y_all_

private

Referenced by get_Y_all(), operator=(), PcsDataCenter(), update_matrix_A_all(), update_matrix_A_all_for_cstyle(), update_matrix_A_all_for_svd(), and update_X_Y_Z_all().

Z_all_

utility::vector1<core::Real> protocols::scoring::methods::pcs2::PcsDataCenter::Z_all_

private

Referenced by get_Z_all(), operator=(), PcsDataCenter(), update_matrix_A_all(), update_matrix_A_all_for_cstyle(), update_matrix_A_all_for_svd(), and update_X_Y_Z_all().

---

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

• src/protocols/scoring/methods/pcs2/PcsDataCenter.hh
• src/protocols/scoring/methods/pcs2/PcsDataCenter.cc