protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 Class Reference

#include <PseudocontactShiftEnergy.hh>

Public Types
typedef core::scoring::methods::WholeStructureEnergy	parent

Public Member Functions
	PCS_Energy_Ts3 ()
	c-tor More...
	~PCS_Energy_Ts3 ()
PCS_Energy_Ts3 &	operator= (PCS_Energy_Ts3 const &other)
	PCS_Energy_Ts3 (PCS_Energy_Ts3 const &other)
virtual core::scoring::methods::EnergyMethodOP	clone () const
	clone More...
void	indicate_required_context_graphs (utility::vector1< bool > &) const
void	finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) const
core::Real	calculate_pcs_score (core::pose::Pose &pose, bool print_to_tracer) const
core::Real	calculate_scores_and_tensors_from_pose_and_PCS_data (utility::vector1< core::Real > &vec_best_score, utility::vector1< PCS_tensor_Ts3 > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, core::pose::Pose const &pdb, PCS_data_Ts3 &pcs_d) const
core::Real	minimize_tensors_from_PCS_data (utility::vector1< PCS_tensor_Ts3 > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, PCS_data_Ts3 const &pcs_d) const
PCS_data_Ts3 &	PCS_data_from_pose (core::pose::Pose &pose) const
void	dump_PCS_info (utility::vector1< PCS_tensor_Ts3 > const &vec_tensor, numeric::xyzVector< core::Real > const &best_coo, PCS_data_Ts3 const &pcs_d) const
virtual core::Size	version () const

Member Typedef Documentation

typedef core::scoring::methods::WholeStructureEnergy protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::parent

Constructor & Destructor Documentation

protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::PCS_Energy_Ts3

(

)

c-tor

Referenced by clone().

protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::~PCS_Energy_Ts3

(

)

protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::PCS_Energy_Ts3

(

PCS_Energy_Ts3 const &

other

)

Member Function Documentation

core::Real protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_pcs_score	(	core::pose::Pose &	pose,
		bool	print_to_tracer
	)		const

References calculate_scores_and_tensors_from_pose_and_PCS_data(), dump_PCS_info(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_instance(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_minimize_best_tensor(), minimize_tensors_from_PCS_data(), PCS_data_from_pose(), tolerance, and protocols::scoring::methods::pcsTs3::TR_PCS_Energy_Ts3.

Referenced by finalize_total_energy().

core::Real protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data	(	utility::vector1< core::Real > &	vec_best_score,
		utility::vector1< PCS_tensor_Ts3 > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		core::pose::Pose const &	pdb,
		PCS_data_Ts3 &	pcs_d
	)		const

References numeric::xyzVector< class >::assign(), core::conformation::Residue::atom(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_instance(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_n_lanthanides(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_pcs_data_per_lanthanides_all(), core::conformation::Residue::has(), protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3::next_center(), core::pose::Pose::residue(), score, core::pose::Pose::total_residue(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_matrix_A_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), utility_exit_with_message, numeric::xyzVector< class >::x(), core::conformation::Atom::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by calculate_pcs_score().

core::scoring::methods::EnergyMethodOP protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::clone ( ) const

virtual

clone

References PCS_Energy_Ts3().

void protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::dump_PCS_info	(	utility::vector1< PCS_tensor_Ts3 > const &	vec_tensor,
		numeric::xyzVector< core::Real > const &	best_coo,
		PCS_data_Ts3 const &	pcs_d
	)		const

References protocols::scoring::methods::pcsTs3::fill_A_line(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_n_lanthanides(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_PCS_data_line_all_spin(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_pcs_data_per_lanthanides_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_X_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_Y_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_Z_all(), option, user, utility_exit, basic::options::OptionKeys::PCSTS3::write_extra, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by calculate_pcs_score().

void protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::finalize_total_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	,
		core::scoring::EnergyMap &	totals
	)		const

References calculate_pcs_score(), and core::scoring::pcsTs3.

void protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::indicate_required_context_graphs

(

utility::vector1< bool > &

)

const

core::Real protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::minimize_tensors_from_PCS_data	(	utility::vector1< PCS_tensor_Ts3 > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		PCS_data_Ts3 const &	pcs_d
	)		const

References numeric::xyzVector< class >::assign(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::get_n_lanthanides(), options, core::optimization::Minimizer::run(), utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by calculate_pcs_score().

PCS_Energy_Ts3 & protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::operator=

(

PCS_Energy_Ts3 const &

other

)

References utility_exit_with_message.

PCS_data_Ts3 & protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::PCS_data_from_pose

(

core::pose::Pose &

pose

)

const

References core::pose::Pose::data(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::exclude_residues_vector_is_current(), protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3::get_input_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_instance(), protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3::get_instance(), basic::datacache::BasicDataCache::get_ptr(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_vector_exclude_residues(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_vector_filename(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::get_vector_weight(), basic::datacache::BasicDataCache::has(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::has_exclude_residues_vector(), protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3::has_exclude_residues_vector_changed(), basic::datacache::BasicDataCache::set(), protocols::scoring::methods::pcsTs3::TR_PCS_Energy_Ts3, core::pose::datacache::CacheableDataType::TS3_PSEUDOCONTACT_SHIFT_DATA, and utility_exit_with_message.

Referenced by calculate_pcs_score().

core::Size protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::version ( ) const

virtual

---

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

• src/protocols/scoring/methods/pcsTs3/PseudocontactShiftEnergy.hh
• src/protocols/scoring/methods/pcsTs3/PseudocontactShiftEnergy.cc