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

Classes
class	GridSearchIterator
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::owning_ptr < GridSearchIterator >	GridSearchIteratorOP
typedef utility::pointer::owning_ptr < GridSearchIterator const >	GridSearchIteratorCOP
typedef utility::pointer::owning_ptr < PcsDataCenter >	PcsDataCenterOP
typedef utility::pointer::owning_ptr < PcsDataCenter const >	PcsDataCenterCOP
typedef utility::pointer::owning_ptr < PcsDataCenterManager >	PcsDataCenterManagerOP
typedef utility::pointer::owning_ptr < PcsEnergy >	PcsEnergyOP
typedef utility::pointer::owning_ptr < PcsEnergy const >	PcsEnergyCOP
typedef utility::pointer::owning_ptr < PcsInputCenter >	PcsInputCenterOP
typedef utility::pointer::owning_ptr < PcsInputCenter const >	PcsInputCenterCOP

Functions
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)
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManager &m)
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManagerSingleton &m)
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)
std::ostream &	operator<< (std::ostream &out, const PcsEnergyParameter &me)
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)
std::ostream &	operator<< (std::ostream &out, const PcsInputCenter &me)
std::ostream &	operator<< (std::ostream &out, const PcsInputCenterManager &me)
std::ostream &	operator<< (std::ostream &out, const PcsInputFile &me)
std::ostream &	operator<< (std::ostream &out, const PcsInputLine &me)
std::ostream &	operator<< (std::ostream &out, const PcsTensor &me)

Variables
basic::Tracer	TR_PcsDataCenter ("protocols.scoring.methods.pcs.PcsDataCenter")
basic::Tracer	TR_PcsDataCenterManager ("protocols.scoring.methods.pcs.PcsDataCenterManager")
basic::Tracer	TR_PcsDataCenterManagerSingleton ("protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton")
basic::Tracer	TR_PcsDataLanthanide ("protocols.scoring.methods.pcs.PcsDataLanthanide")
basic::Tracer	TR_PcsEnergy ("protocols.scoring.methods.pcs.PcsEnergy")
basic::Tracer	TR_PcsEnergyParameter ("protocols.scoring.methods.pcs.PcsEnergyParameter")
basic::Tracer	TR_PcsEnergyParameterManager ("protocols.scoring.methods.pcs.PcsEnergyParameterManager")
basic::Tracer	TR_PcsInputCenter ("protocols.scoring.methods.pcs.PcsInputCenter")
basic::Tracer	TR_PcsInputCenterManager ("protocols.scoring.methods.pcs.PcsInputCenterManager")
basic::Tracer	TR_PcsInputFile ("protocols.scoring.methods.pcs.PcsInputFile")
basic::Tracer	TR_PcsInputLine ("protocols.scoring.methods.pcs.PcsInputLine")
basic::Tracer	TR_TensorsOptimizer ("protocols.scoring.methods.pcs.TensorsOptimizer")
basic::Tracer	TR_TensorsOptimizerFix ("protocols.scoring.methods.pcs.TensorsOptimizerFix")
basic::Tracer	TR_TensorsOptimizerSvd ("protocols.scoring.methods.pcs.TensorsOptimizerSvd")

Typedef Documentation

typedef utility::pointer::owning_ptr< GridSearchIterator const > protocols::scoring::methods::pcs2::GridSearchIteratorCOP

typedef utility::pointer::owning_ptr< GridSearchIterator > protocols::scoring::methods::pcs2::GridSearchIteratorOP

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

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

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

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

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

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

typedef utility::pointer::owning_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 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 r2, and z2.

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, r2, and z2.

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 protocols::scoring::methods::pcs2::PcsInputCenterManager::PcsInputCenter_all_.

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

References protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::get_n_multi_data(), and protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::PCS_data_all_.

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

References protocols::scoring::methods::pcs2::PcsDataCenterManager::get_n_multi_data(), and protocols::scoring::methods::pcs2::PcsDataCenterManager::PCS_data_all_.

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

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

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(), and protocols::scoring::methods::pcs2::PcsTensor::label_.

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 PcsInputFile &	me
	)

References protocols::scoring::methods::pcs2::PcsInputFile::get_filename(), 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_, 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_, 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(), and protocols::scoring::methods::pcs2::PcsDataLanthanide::get_n_pcs().

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

(

core::Size

id

)

References utility_exit_with_message.

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().

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().

Variable Documentation

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

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

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

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

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

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

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().

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

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

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

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

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

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

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

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

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

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

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

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

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