#include <PcsEnergy.hh>

Inheritance diagram for protocols::scoring::methods::pcs2::PcsEnergy:

Collaboration diagram for protocols::scoring::methods::pcs2::PcsEnergy:

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

Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::pointer::ReferenceCount	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
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

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
	Return the version of the energy method. More...

Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
	WholeStructureEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...

virtual	~WholeStructureEnergy ()

EnergyMethodType	method_type () const
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

virtual Distance	atomic_interaction_cutoff () const
	how far apart must two heavy atoms be to have a zero interaction energy? More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. More...

virtual void	setup_for_scoring (pose::Pose &, ScoreFunction const &) const

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

Detailed Description

Definition at line 68 of file PcsEnergy.hh.

Member Typedef Documentation

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

Definition at line 70 of file PcsEnergy.hh.

Constructor & Destructor Documentation

protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy ( )

c-tor

Definition at line 123 of file PcsEnergy.cc.

Referenced by clone().

protocols::scoring::methods::pcs2::PcsEnergy::~PcsEnergy ( )

Definition at line 119 of file PcsEnergy.cc.

protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy ( PcsEnergy const & other)

Definition at line 113 of file PcsEnergy.cc.

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.

Definition at line 482 of file PcsEnergy.cc.

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

Definition at line 672 of file PcsEnergy.cc.

References 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(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset(), and protocols::scoring::methods::pcs2::TR_PcsEnergy().

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.

Definition at line 345 of file PcsEnergy.cc.

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

Implements core::scoring::methods::EnergyMethod.

Definition at line 131 of file PcsEnergy.cc.

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

Definition at line 266 of file PcsEnergy.cc.

References protocols::comparative_modeling::features::A, 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(), and protocols::scoring::methods::pcs2::PcsDataCenter::get_Z_all().

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

virtual

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

Reimplemented from core::scoring::methods::EnergyMethod.

Definition at line 141 of file PcsEnergy.cc.

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 > & context_graphs_required) const

virtual

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

Implements core::scoring::methods::EnergyMethod.

Definition at line 101 of file PcsEnergy.cc.

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

Definition at line 435 of file PcsEnergy.cc.

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

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

Definition at line 393 of file PcsEnergy.cc.

References 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