protocols::scoring::methods::pcs2 Namespace Reference

Classes
class	GridSearchIteratorCA
class	PcsDataCenter
class	PcsDataCenterManager
class	PcsDataCenterManagerSingleton
class	PcsDataLanthanide
class	PcsEnergy
class	PcsEnergyCreator
class	PcsEnergyParameter
class	PcsEnergyParameterManager
class	PcsGridSearchParameter
class	PcsGridSearchParameterManager
class	PcsInputCenter
	PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set. More...
class	PcsInputCenterManager
class	PcsInputFile
	PcsInputFile contain all the information of a .npc file one per lanthanide. More...
class	PcsInputLine
	PcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file. More...
class	PcsTensor
class	TensorsOptimizer
class	TensorsOptimizerFix
class	TensorsOptimizerSvd

Typedefs
typedef utility::pointer::shared_ptr < PcsDataCenter >	PcsDataCenterOP
typedef utility::pointer::shared_ptr < PcsDataCenter const >	PcsDataCenterCOP
typedef utility::pointer::shared_ptr < PcsDataCenterManager >	PcsDataCenterManagerOP
typedef utility::pointer::shared_ptr < PcsEnergy >	PcsEnergyOP
typedef utility::pointer::shared_ptr < PcsEnergy const >	PcsEnergyCOP
typedef utility::pointer::shared_ptr < PcsInputCenter >	PcsInputCenterOP
typedef utility::pointer::shared_ptr < PcsInputCenter const >	PcsInputCenterCOP

Functions
static basic::Tracer	TR_PcsDataCenter ("protocols.scoring.methods.pcs.PcsDataCenter")
core::Real	fill_A_line_fast (utility::vector1< core::Real > &A_line, core::Real const xM, core::Real const yM, core::Real const zM, core::Real const x, core::Real const y, core::Real const z)
void	fill_A_line_slow (utility::vector1< core::Real > &A_line, core::Real const xM, core::Real const yM, core::Real const zM, core::Real const x, core::Real const y, core::Real const z)
std::ostream &	operator<< (std::ostream &out, const PcsDataCenter &me)
static basic::Tracer	TR_PcsDataCenterManager ("protocols.scoring.methods.pcs.PcsDataCenterManager")
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManager &m)
static basic::Tracer	TR_PcsDataCenterManagerSingleton ("protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton")
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManagerSingleton &m)
static basic::Tracer	TR_PcsDataLanthanide ("protocols.scoring.methods.pcs.PcsDataLanthanide")
bool	do_I_skip (PcsInputLine &pcs_i_l, core::Size start, core::Size end)
core::Size	reduced_size (utility::vector1< PcsInputLine > const &pcs_i_l_v, core::Size start, core::Size end)
std::ostream &	operator<< (std::ostream &out, const PcsDataLanthanide &me)
static basic::Tracer	TR_PcsEnergy ("protocols.scoring.methods.pcs.PcsEnergy")
static basic::Tracer	TR_PcsEnergyParameter ("protocols.scoring.methods.pcs.PcsEnergyParameter")
std::ostream &	operator<< (std::ostream &out, const PcsEnergyParameter &me)
static basic::Tracer	TR_PcsEnergyParameterManager ("protocols.scoring.methods.pcs.PcsEnergyParameterManager")
std::ostream &	operator<< (std::ostream &out, const PcsEnergyParameterManager &me)
std::ostream &	operator<< (std::ostream &out, const PcsGridSearchParameter &me)
void	output_error_message (core::Size id)
bool	valide_include_only_stage (core::Size start, core::Size end)
static basic::Tracer	TR_PcsInputCenter ("protocols.scoring.methods.pcs.PcsInputCenter")
std::ostream &	operator<< (std::ostream &out, const PcsInputCenter &me)
static basic::Tracer	TR_PcsInputCenterManager ("protocols.scoring.methods.pcs.PcsInputCenterManager")
std::ostream &	operator<< (std::ostream &out, const PcsInputCenterManager &me)
static basic::Tracer	TR_PcsInputFile ("protocols.scoring.methods.pcs.PcsInputFile")
std::ostream &	operator<< (std::ostream &out, const PcsInputFile &me)
static basic::Tracer	TR_PcsInputLine ("protocols.scoring.methods.pcs.PcsInputLine")
std::ostream &	operator<< (std::ostream &out, const PcsInputLine &me)
std::ostream &	operator<< (std::ostream &out, const PcsTensor &me)
static basic::Tracer	TR_TensorsOptimizer ("protocols.scoring.methods.pcs.TensorsOptimizer")
static basic::Tracer	TR_TensorsOptimizerFix ("protocols.scoring.methods.pcs.TensorsOptimizerFix")
static basic::Tracer	TR_TensorsOptimizerSvd ("protocols.scoring.methods.pcs.TensorsOptimizerSvd")

Typedef Documentation

typedef utility::pointer::shared_ptr< PcsDataCenter const > protocols::scoring::methods::pcs2::PcsDataCenterCOP

typedef utility::pointer::shared_ptr< PcsDataCenterManager > protocols::scoring::methods::pcs2::PcsDataCenterManagerOP

typedef utility::pointer::shared_ptr< PcsDataCenter > protocols::scoring::methods::pcs2::PcsDataCenterOP

typedef utility::pointer::shared_ptr< PcsEnergy const > protocols::scoring::methods::pcs2::PcsEnergyCOP

typedef utility::pointer::shared_ptr< PcsEnergy > protocols::scoring::methods::pcs2::PcsEnergyOP

typedef utility::pointer::shared_ptr< PcsInputCenter const > protocols::scoring::methods::pcs2::PcsInputCenterCOP

typedef utility::pointer::shared_ptr< PcsInputCenter > protocols::scoring::methods::pcs2::PcsInputCenterOP

Function Documentation

bool protocols::scoring::methods::pcs2::do_I_skip	(	PcsInputLine &	pcs_i_l,
		core::Size	start,
		core::Size	end
	)

References core::sequence::end, and protocols::scoring::methods::pcs2::PcsInputLine::get_residue_num().

Referenced by protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter(), protocols::scoring::methods::pcs2::PcsDataLanthanide::PcsDataLanthanide(), and reduced_size().

core::Real protocols::scoring::methods::pcs2::fill_A_line_fast	(	utility::vector1< core::Real > &	A_line,
		core::Real const	xM,
		core::Real const	yM,
		core::Real const	zM,
		core::Real const	x,
		core::Real const	y,
		core::Real const	z
	)

References protocols::hybridization::r2.

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

void protocols::scoring::methods::pcs2::fill_A_line_slow	(	utility::vector1< core::Real > &	A_line,
		core::Real const	xM,
		core::Real const	yM,
		core::Real const	zM,
		core::Real const	x,
		core::Real const	y,
		core::Real const	z
	)

References OTHER_FACT_USI_PRECALC_FOR_A_3(), and protocols::hybridization::r2.

Referenced by protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_cstyle(), and protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_svd().

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsInputCenterManager &	me
	)

References core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsInputCenterManager::PcsInputCenter_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsDataCenterManager &	m
	)

References protocols::scoring::methods::pcs2::PcsDataCenterManager::get_n_multi_data(), core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsDataCenterManager::PCS_data_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsDataCenterManagerSingleton &	m
	)

References protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::get_n_multi_data(), core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::PCS_data_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsEnergyParameterManager &	me
	)

References protocols::scoring::methods::pcs2::PcsEnergyParameterManager::pcs_e_p_all_, protocols::scoring::methods::pcs2::PcsEnergyParameterManager::vec_filename_all_, and protocols::scoring::methods::pcs2::PcsEnergyParameterManager::vec_individual_weight_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsInputCenter &	me
	)

References core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsInputCenter::PcsInputFile_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsEnergyParameter &	me
	)

References protocols::scoring::methods::pcs2::PcsEnergyParameter::include_only_end_, protocols::scoring::methods::pcs2::PcsEnergyParameter::include_only_start_, protocols::scoring::methods::pcs2::PcsEnergyParameter::n_trial_min_, core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsEnergyParameter::pcs_weight_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsInputLine &	me
	)

References protocols::scoring::methods::pcs2::PcsInputLine::get_atom_name(), protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_experimental(), protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_tolerance(), protocols::scoring::methods::pcs2::PcsInputLine::get_residue_num(), and core::conformation::membrane::out.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsTensor &	me
	)

References protocols::scoring::methods::pcs2::PcsTensor::chi_xx_, protocols::scoring::methods::pcs2::PcsTensor::chi_xy_, protocols::scoring::methods::pcs2::PcsTensor::chi_xz_, protocols::scoring::methods::pcs2::PcsTensor::chi_yy_, protocols::scoring::methods::pcs2::PcsTensor::chi_yz_, protocols::scoring::methods::pcs2::PcsTensor::get_chi_zz(), protocols::scoring::methods::pcs2::PcsTensor::label_, and core::conformation::membrane::out.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsInputFile &	me
	)

References protocols::scoring::methods::pcs2::PcsInputFile::get_filename(), core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsInputFile::PcsInputLine_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsGridSearchParameter &	me
	)

References protocols::scoring::methods::pcs2::PcsGridSearchParameter::filenames_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_weights_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage4_, core::conformation::membrane::out, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage3_, and protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage4_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsDataCenter &	me
	)

References protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::n_lanthanides_, protocols::scoring::methods::pcs2::PcsDataCenter::n_pcs_spin_, core::conformation::membrane::out, and protocols::scoring::methods::pcs2::PcsDataCenter::PCS_data_per_lanthanides_all_.

std::ostream& protocols::scoring::methods::pcs2::operator<<	(	std::ostream &	out,
		const PcsDataLanthanide &	me
	)

References protocols::scoring::methods::pcs2::PcsDataLanthanide::A_index_, protocols::scoring::methods::pcs2::PcsDataLanthanide::cstyle_b_, protocols::scoring::methods::pcs2::PcsDataLanthanide::get_filename(), protocols::scoring::methods::pcs2::PcsDataLanthanide::get_n_pcs(), and core::conformation::membrane::out.

void protocols::scoring::methods::pcs2::output_error_message

(

core::Size

id

)

Referenced by protocols::scoring::methods::pcs2::PcsGridSearchParameter::control_grid_param().

core::Size protocols::scoring::methods::pcs2::reduced_size	(	utility::vector1< PcsInputLine > const &	pcs_i_l_v,
		core::Size	start,
		core::Size	end
	)

References do_I_skip().

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

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenter ( "protocols.scoring.methods.pcs.PcsDataCenter"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenterManager ( "protocols.scoring.methods.pcs.PcsDataCenterManager"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenterManagerSingleton ( "protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataLanthanide ( "protocols.scoring.methods.pcs.PcsDataLanthanide"  )

static

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

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergy ( "protocols.scoring.methods.pcs.PcsEnergy"  )

static

Referenced by protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd(), and protocols::scoring::methods::pcs2::PcsEnergy::finalize_total_energy().

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergyParameter ( "protocols.scoring.methods.pcs.PcsEnergyParameter"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergyParameterManager ( "protocols.scoring.methods.pcs.PcsEnergyParameterManager"  )

static

Referenced by protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_PcsEnergyParameter_for().

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputCenter ( "protocols.scoring.methods.pcs.PcsInputCenter"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputCenterManager ( "protocols.scoring.methods.pcs.PcsInputCenterManager"  )

static

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

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputFile ( "protocols.scoring.methods.pcs.PcsInputFile"  )

static

Referenced by protocols::scoring::methods::pcs2::PcsInputFile::read_PCS_file().

static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputLine ( "protocols.scoring.methods.pcs.PcsInputLine"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizer ( "protocols.scoring.methods.pcs.TensorsOptimizer"  )

static

static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizerFix ( "protocols.scoring.methods.pcs.TensorsOptimizerFix"  )

static

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

static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizerSvd ( "protocols.scoring.methods.pcs.TensorsOptimizerSvd"  )

static

bool protocols::scoring::methods::pcs2::valide_include_only_stage	(	core::Size	start,
		core::Size	end
	)

Referenced by protocols::scoring::methods::pcs2::PcsGridSearchParameter::control_grid_param().