protocols::scoring::methods::pcs2::PcsEnergy Class Reference

#include <PcsEnergy.hh>

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

Public Member Functions
	PcsEnergy ()
	c-tor More...
	~PcsEnergy ()
PcsEnergy &	operator= (PcsEnergy const &other)
	PcsEnergy (PcsEnergy 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
	This is called to start the PCS machinerie and get the score (set in totals) More...
core::Real	calculate_pcs_score_on_PCS_data_center_CA (core::pose::Pose &pose, bool print_to_tracer, PcsDataCenter &pcs_d, core::Size i_multi_data, GridSearchIteratorCA &grid_it) const
	Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number. More...
core::Real	CA_search_scores_and_tensors (utility::vector1< core::Real > &vec_best_score, utility::vector1< PcsTensor > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, core::pose::Pose const &pdb, PcsDataCenter &pcs_d, core::Size i_multi_data, GridSearchIteratorCA &grid_it) const
	Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number, return the vec of best score, vec of best tensor, and the vec of best x-y-z coordinate. More...
core::Real	CA_search_scores_and_tensors_with_svd (utility::vector1< core::Real > &vec_best_score, utility::vector1< PcsTensor > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, core::pose::Pose const &, PcsDataCenter &pcs_d_c, core::Size, GridSearchIteratorCA &grid_it) const
core::Real	minimize_tensors_from_PCS_data (utility::vector1< PcsTensor > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, PcsDataCenter const &pcs_d, core::optimization::Minimizer &minimizer, utility::vector1< core::Real > &vect_to_opti) const
core::Real	minimize_tensors_from_PCS_data_with_svd (utility::vector1< PcsTensor > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, PcsDataCenter const &, core::optimization::Minimizer &minimizer, utility::vector1< core::Real > &vect_to_opti) const
core::Real	minimize_tensors_fix_from_PCS_data (utility::vector1< PcsTensor > &vec_best_tensor, PcsDataCenter const &pcs_d) const
PcsDataCenterManager &	PCS_multi_data_from_pose (core::pose::Pose &pose) const
PcsDataCenterManagerSingleton &	PCS_multi_data_from_noone () const
void	dump_PCS_info (utility::vector1< PcsTensor > const &vec_tensor, numeric::xyzVector< core::Real > const &best_coo, PcsDataCenter const &pcs_d) const
virtual core::Size	version () const

Member Typedef Documentation

typedef core::scoring::methods::WholeStructureEnergy protocols::scoring::methods::pcs2::PcsEnergy::parent

Constructor & Destructor Documentation

protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy

(

)

c-tor

Referenced by clone().

protocols::scoring::methods::pcs2::PcsEnergy::~PcsEnergy

(

)

protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy

(

PcsEnergy const &

other

)

Member Function Documentation

core::Real protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors	(	utility::vector1< core::Real > &	vec_best_score,
		utility::vector1< PcsTensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		core::pose::Pose const &	pdb,
		PcsDataCenter &	pcs_d,
		core::Size	i_multi_data,
		GridSearchIteratorCA &	grid_it
	)		const

Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number, return the vec of best score, vec of best tensor, and the vec of best x-y-z coordinate.

References numeric::xyzVector< class >::assign(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd(), epsilon, protocols::scoring::methods::pcs2::PcsTensor::get_chi_xx(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_xy(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_xz(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_yy(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_yz(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), minimize_tensors_from_PCS_data(), minimizer, protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(), options, protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset(), score, protocols::scoring::methods::pcs2::TR_PcsEnergy, protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_svd(), utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by calculate_pcs_score_on_PCS_data_center_CA().

core::Real protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd	(	utility::vector1< core::Real > &	vec_best_score,
		utility::vector1< PcsTensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		core::pose::Pose const &	,
		PcsDataCenter &	pcs_d_c,
		core::Size	,
		GridSearchIteratorCA &	grid_it
	)		const

References numeric::xyzVector< class >::assign(), epsilon, protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), minimize_tensors_from_PCS_data_with_svd(), minimizer, protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(), options, protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset(), score, protocols::scoring::methods::pcs2::TR_PcsEnergy, utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

core::Real protocols::scoring::methods::pcs2::PcsEnergy::calculate_pcs_score_on_PCS_data_center_CA	(	core::pose::Pose &	pose,
		bool	print_to_tracer,
		PcsDataCenter &	pcs_d,
		core::Size	i_multi_data,
		GridSearchIteratorCA &	grid_it
	)		const

Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number.

References CA_search_scores_and_tensors(), dump_PCS_info(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_instance(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), and protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all().

Referenced by finalize_total_energy().

core::scoring::methods::EnergyMethodOP protocols::scoring::methods::pcs2::PcsEnergy::clone ( ) const

virtual

clone

References PcsEnergy().

void protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info	(	utility::vector1< PcsTensor > const &	vec_tensor,
		numeric::xyzVector< core::Real > const &	best_coo,
		PcsDataCenter const &	pcs_d
	)		const

References FACT_USI_PRECALC_FOR_A_3, protocols::scoring::methods::pcs2::fill_A_line_fast(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_PCS_data_line_all_spin(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_X_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_Y_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_Z_all(), j, option, user, utility_exit, basic::options::OptionKeys::PCS::write_extra, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by calculate_pcs_score_on_PCS_data_center_CA().

void protocols::scoring::methods::pcs2::PcsEnergy::finalize_total_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	,
		core::scoring::EnergyMap &	totals
	)		const

This is called to start the PCS machinerie and get the score (set in totals)

References calculate_pcs_score_on_PCS_data_center_CA(), protocols::scoring::methods::pcs2::PcsDataCenterManager::get_n_multi_data(), protocols::scoring::methods::pcs2::PcsDataCenterManager::get_PCS_data_all(), core::scoring::pcs2, PCS_multi_data_from_pose(), protocols::scoring::methods::pcs2::TR_PcsEnergy, and protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all().

void protocols::scoring::methods::pcs2::PcsEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

)

const

core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_fix_from_PCS_data	(	utility::vector1< PcsTensor > &	vec_best_tensor,
		PcsDataCenter const &	pcs_d
	)		const

References protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), minimizer, options, core::optimization::Minimizer::run(), and utility_exit_with_message.

core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_from_PCS_data	(	utility::vector1< PcsTensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		PcsDataCenter const &	pcs_d,
		core::optimization::Minimizer &	minimizer,
		utility::vector1< core::Real > &	vect_to_opti
	)		const

References numeric::xyzVector< class >::assign(), and core::optimization::Minimizer::run().

Referenced by CA_search_scores_and_tensors().

core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_from_PCS_data_with_svd	(	utility::vector1< PcsTensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		PcsDataCenter const &	,
		core::optimization::Minimizer &	minimizer,
		utility::vector1< core::Real > &	vect_to_opti
	)		const

References numeric::xyzVector< class >::assign(), and core::optimization::Minimizer::run().

Referenced by CA_search_scores_and_tensors_with_svd().

PcsEnergy & protocols::scoring::methods::pcs2::PcsEnergy::operator=

(

PcsEnergy const &

other

)

References utility_exit_with_message.

PcsDataCenterManagerSingleton & protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_noone

(

)

const

References protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_instance(), and protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::get_instance().

PcsDataCenterManager & protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_pose

(

core::pose::Pose &

pose

)

const

References core::pose::Pose::data(), end, protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_instance(), protocols::scoring::methods::pcs2::PcsInputCenterManager::get_instance(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_n_multi_data(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_PcsEnergyParameter_for(), protocols::scoring::methods::pcs2::PcsInputCenterManager::get_PcsInputCenter_for(), basic::datacache::BasicDataCache::get_ptr(), protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_filename(), protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_weight(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::PSEUDOCONTACT_SHIFT_MULTI_DATA, basic::datacache::BasicDataCache::set(), protocols::loops::start, and utility_exit_with_message.

Referenced by finalize_total_energy().

core::Size protocols::scoring::methods::pcs2::PcsEnergy::version ( ) const

virtual

---

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

• symlinks/rosetta/src/protocols/scoring/methods/pcs2/PcsEnergy.hh
• symlinks/rosetta/src/protocols/scoring/methods/pcs2/PcsEnergy.cc