protocols::scoring::methods::pcs Namespace Reference

Classes
class	GridSearchIterator
class	PCS_data_per_lanthanides
class	PCS_data
class	PCS_Energy
class	PCS_Energy_parameters_manager
class	PseudocontactShiftEnergyCreator
class	PCS_line_data
	PCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file. More...
class	PCS_file_data
	PCS_file_data contain all the information of a .npc file one per lanthanide. More...
class	PCS_data_input
	PCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files. More...
class	PCS_data_input_manager
class	PCS_tensor
class	TensorsOptimizer

Typedefs
typedef utility::pointer::owning_ptr < GridSearchIterator >	GridSearchIteratorOP
typedef utility::pointer::owning_ptr < GridSearchIterator const >	GridSearchIteratorCOP
typedef utility::pointer::owning_ptr < PCS_data >	PCS_dataOP
typedef utility::pointer::owning_ptr < PCS_Energy >	PCS_EnergyOP
typedef utility::pointer::owning_ptr < PCS_Energy const >	PCS_EnergyCOP

Functions
basic::Tracer	TR_pcs_d_p_l ("protocols.scoring.methods.pcs.PCS_data_per_lanthanides")
basic::Tracer	TR_pcs_d ("protocols.scoring.methods.pcs.PCS_data")
void	fill_A_line (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 PCS_data &P_d)
std::ostream &	operator<< (std::ostream &out, const PCS_data_per_lanthanides &PCS_d_p_l)
basic::Tracer	TR_PCS_Energy ("protocols.scoring.methods.pcs.PCS_Energy")
basic::Tracer	TR_PCS_d_i ("protocols.scoring.methods.pcs.PCS_data_input")
std::ostream &	operator<< (std::ostream &out, const PCS_line_data &PCS_l_d)
std::ostream &	operator<< (std::ostream &out, const PCS_file_data &PCS_f_d)
std::ostream &	operator<< (std::ostream &out, const PCS_data_input &PCS_d_i)
std::ostream &	operator<< (std::ostream &out, const PCS_tensor &PCS_t)
basic::Tracer	TR_tsr_opt ("protocols.scoring.methods.pcs.TensorsOptimizer")

Typedef Documentation

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

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

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

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

typedef utility::pointer::owning_ptr< PCS_data > protocols::scoring::methods::pcs::PCS_dataOP

Definition at line 29 of file PseudocontactShiftData.fwd.hh.

typedef utility::pointer::owning_ptr< PCS_Energy const > protocols::scoring::methods::pcs::PCS_EnergyCOP

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

typedef utility::pointer::owning_ptr< PCS_Energy > protocols::scoring::methods::pcs::PCS_EnergyOP

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

Function Documentation

void protocols::scoring::methods::pcs::fill_A_line	(	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 184 of file PseudocontactShiftData.cc.

References FACT_USI_PRECALC_FOR_A_3().

Referenced by protocols::scoring::methods::pcs::TensorsOptimizer::dfunc(), protocols::scoring::methods::pcs::PCS_Energy::dump_PCS_info(), protocols::scoring::methods::pcs::TensorsOptimizer::operator()(), and protocols::scoring::methods::pcs::PCS_data::update_matrix_A_all().

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_tensor &	PCS_t
	)

Definition at line 130 of file PseudocontactShiftTensor.cc.

References protocols::scoring::methods::pcs::PCS_tensor::a_, protocols::scoring::methods::pcs::PCS_tensor::ax_, protocols::scoring::methods::pcs::PCS_tensor::b_, protocols::scoring::methods::pcs::PCS_tensor::chi_xx_, protocols::scoring::methods::pcs::PCS_tensor::chi_xy_, protocols::scoring::methods::pcs::PCS_tensor::chi_xz_, protocols::scoring::methods::pcs::PCS_tensor::chi_yy_, protocols::scoring::methods::pcs::PCS_tensor::chi_yz_, protocols::scoring::methods::pcs::PCS_tensor::delta_chi_zz(), protocols::scoring::methods::pcs::PCS_tensor::delta_X_xx(), protocols::scoring::methods::pcs::PCS_tensor::delta_X_yy(), protocols::scoring::methods::pcs::PCS_tensor::delta_X_zz(), protocols::scoring::methods::pcs::PCS_tensor::g_, protocols::scoring::methods::pcs::PCS_tensor::label_, and protocols::scoring::methods::pcs::PCS_tensor::rh_.

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_line_data &	PCS_l_d
	)

Definition at line 244 of file PseudocontactShiftInput.cc.

References protocols::scoring::methods::pcs::PCS_line_data::atom_name(), protocols::scoring::methods::pcs::PCS_line_data::PCS_experimental(), protocols::scoring::methods::pcs::PCS_line_data::PCS_tolerance(), and protocols::scoring::methods::pcs::PCS_line_data::residue_num().

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_file_data &	PCS_f_d
	)

Definition at line 253 of file PseudocontactShiftInput.cc.

References protocols::scoring::methods::pcs::PCS_file_data::PCS_data_line_all_.

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_data_input &	PCS_d_i
	)

Definition at line 266 of file PseudocontactShiftInput.cc.

References protocols::scoring::methods::pcs::PCS_data_input::PCS_filename_and_data_.

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_data &	P_d
	)

Definition at line 712 of file PseudocontactShiftData.cc.

References protocols::scoring::methods::pcs::PCS_data::get_n_lanthanides(), protocols::scoring::methods::pcs::PCS_data::n_lanthanides_, protocols::scoring::methods::pcs::PCS_data::n_pcs_spin_, and protocols::scoring::methods::pcs::PCS_data::PCS_data_per_lanthanides_all_.

std::ostream& protocols::scoring::methods::pcs::operator<<	(	std::ostream &	out,
		const PCS_data_per_lanthanides &	PCS_d_p_l
	)

Definition at line 724 of file PseudocontactShiftData.cc.

References protocols::scoring::methods::pcs::PCS_data_per_lanthanides::A_index_, protocols::scoring::methods::pcs::PCS_data_per_lanthanides::fstyle_A_, protocols::scoring::methods::pcs::PCS_data_per_lanthanides::fstyle_b_, protocols::scoring::methods::pcs::PCS_data_per_lanthanides::get_filename(), protocols::scoring::methods::pcs::PCS_data_per_lanthanides::get_n_pcs(), and protocols::scoring::methods::pcs::PCS_data_per_lanthanides::n_pcs_.

basic::Tracer protocols::scoring::methods::pcs::TR_pcs_d

(

"protocols.scoring.methods.pcs.PCS_data"

)

Referenced by protocols::scoring::methods::pcs::PCS_data::PCS_data().

basic::Tracer protocols::scoring::methods::pcs::TR_PCS_d_i

(

"protocols.scoring.methods.pcs.PCS_data_input"

)

Referenced by protocols::scoring::methods::pcs::PCS_data_input_manager::get_input_data(), and protocols::scoring::methods::pcs::PCS_file_data::read_PCS_file().

basic::Tracer protocols::scoring::methods::pcs::TR_pcs_d_p_l

(

"protocols.scoring.methods.pcs.PCS_data_per_lanthanides"

)

Referenced by protocols::scoring::methods::pcs::PCS_data_per_lanthanides::PCS_data_per_lanthanides().

basic::Tracer protocols::scoring::methods::pcs::TR_PCS_Energy

(

"protocols.scoring.methods.pcs.PCS_Energy"

)

Referenced by protocols::scoring::methods::pcs::PCS_Energy::calculate_pcs_score(), and protocols::scoring::methods::pcs::PCS_Energy::PCS_data_from_pose().

basic::Tracer protocols::scoring::methods::pcs::TR_tsr_opt

(

"protocols.scoring.methods.pcs.TensorsOptimizer"

)

Referenced by protocols::scoring::methods::pcs::TensorsOptimizer::operator()().