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
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)
basic::Tracer	TR_PcsDataCenterManager ("protocols.scoring.methods.pcs.PcsDataCenterManager")
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManager &m)
basic::Tracer	TR_PcsDataCenterManagerSingleton ("protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton")
std::ostream &	operator<< (std::ostream &out, const PcsDataCenterManagerSingleton &m)
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)
basic::Tracer	TR_PcsEnergy ("protocols.scoring.methods.pcs.PcsEnergy")
basic::Tracer	TR_PcsEnergyParameter ("protocols.scoring.methods.pcs.PcsEnergyParameter")
std::ostream &	operator<< (std::ostream &out, const PcsEnergyParameter &me)
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)
basic::Tracer	TR_PcsInputCenter ("protocols.scoring.methods.pcs.PcsInputCenter")
std::ostream &	operator<< (std::ostream &out, const PcsInputCenter &me)
basic::Tracer	TR_PcsInputCenterManager ("protocols.scoring.methods.pcs.PcsInputCenterManager")
std::ostream &	operator<< (std::ostream &out, const PcsInputCenterManager &me)
basic::Tracer	TR_PcsInputFile ("protocols.scoring.methods.pcs.PcsInputFile")
std::ostream &	operator<< (std::ostream &out, const PcsInputFile &me)
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)
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

Definition at line 31 of file GridSearchIterator.fwd.hh.

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

Definition at line 28 of file GridSearchIterator.fwd.hh.

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

Definition at line 30 of file PcsDataCenter.fwd.hh.

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

Definition at line 28 of file PcsDataCenterManager.fwd.hh.

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

Definition at line 27 of file PcsDataCenter.fwd.hh.

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

Definition at line 33 of file PcsEnergy.fwd.hh.

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

Definition at line 30 of file PcsEnergy.fwd.hh.

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

Definition at line 35 of file PcsInputCenter.fwd.hh.

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

Definition at line 32 of file PcsInputCenter.fwd.hh.

Function Documentation

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

Definition at line 285 of file PcsDataLanthanide.cc.

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
	)

Definition at line 105 of file PcsDataCenter.cc.

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
	)

Definition at line 141 of file PcsDataCenter.cc.

References OTHER_FACT_USI_PRECALC_FOR_A_3().

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
	)

Definition at line 77 of file PcsInputCenterManager.cc.

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

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

Definition at line 101 of file PcsDataCenterManager.cc.

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 PcsEnergyParameterManager &	me
	)

Definition at line 108 of file PcsEnergyParameterManager.cc.

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 PcsDataCenterManagerSingleton &	m
	)

Definition at line 110 of file PcsDataCenterManagerSingleton.cc.

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 PcsInputCenter &	me
	)

Definition at line 110 of file PcsInputCenter.cc.

References protocols::scoring::methods::pcs2::PcsInputCenter::PcsInputFile_all_.

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

Definition at line 118 of file PcsEnergyParameter.cc.

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
	)

Definition at line 122 of file PcsInputLine.cc.

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
	)

Definition at line 131 of file PcsTensor.cc.

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 PcsInputFile &	me
	)

Definition at line 139 of file PcsInputFile.cc.

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
	)

Definition at line 165 of file PcsGridSearchParameter.cc.

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
	)

Definition at line 394 of file PcsDataCenter.cc.

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
	)

Definition at line 445 of file PcsDataLanthanide.cc.

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)

Definition at line 206 of file PcsGridSearchParameter.cc.

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
	)

Definition at line 299 of file PcsDataLanthanide.cc.

References do_I_skip().

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

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"

)

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

Definition at line 217 of file PcsGridSearchParameter.cc.

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