#include <PseudocontactShiftEnergy.hh>

Inheritance diagram for protocols::scoring::methods::pcs::PCS_Energy:

Collaboration diagram for protocols::scoring::methods::pcs::PCS_Energy:

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
	PCS_Energy ()
	c-tor More...

	~PCS_Energy ()

PCS_Energy &	operator= (PCS_Energy const &other)

	PCS_Energy (PCS_Energy 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
	called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. More...

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 > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, core::pose::Pose const &pdb, PCS_data &pcs_d) const

core::Real	minimize_tensors_from_PCS_data (utility::vector1< PCS_tensor > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, PCS_data const &pcs_d) const

PCS_data &	PCS_data_from_pose (core::pose::Pose &pose) const

void	dump_PCS_info (utility::vector1< PCS_tensor > const &vec_tensor, numeric::xyzVector< core::Real > const &best_coo, PCS_data 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 63 of file PseudocontactShiftEnergy.hh.

Member Typedef Documentation

typedef core::scoring::methods::WholeStructureEnergy protocols::scoring::methods::pcs::PCS_Energy::parent

Definition at line 65 of file PseudocontactShiftEnergy.hh.

Constructor & Destructor Documentation

protocols::scoring::methods::pcs::PCS_Energy::PCS_Energy ( )

c-tor

Definition at line 116 of file PseudocontactShiftEnergy.cc.

Referenced by clone().

protocols::scoring::methods::pcs::PCS_Energy::~PCS_Energy ( )

Definition at line 112 of file PseudocontactShiftEnergy.cc.

protocols::scoring::methods::pcs::PCS_Energy::PCS_Energy ( PCS_Energy const & other)

Definition at line 107 of file PseudocontactShiftEnergy.cc.

Member Function Documentation

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

Definition at line 264 of file PseudocontactShiftEnergy.cc.

References calculate_scores_and_tensors_from_pose_and_PCS_data(), dump_PCS_info(), protocols::scoring::methods::pcs::PCS_Energy_parameters_manager::get_instance(), protocols::scoring::methods::pcs::PCS_Energy_parameters_manager::get_minimize_best_tensor(), minimize_tensors_from_PCS_data(), PCS_data_from_pose(), and protocols::scoring::methods::pcs::TR_PCS_Energy().

Referenced by finalize_total_energy().

core::Real protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data	(	utility::vector1< core::Real > &	vec_best_score,
		utility::vector1< PCS_tensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		core::pose::Pose const &	pdb,
		PCS_data &	pcs_d
	)		const

Definition at line 400 of file PseudocontactShiftEnergy.cc.

References core::conformation::Residue::atom(), protocols::scoring::methods::pcs::PCS_Energy_parameters_manager::get_instance(), protocols::scoring::methods::pcs::PCS_data::get_n_lanthanides(), protocols::scoring::methods::pcs::PCS_data::get_pcs_data_per_lanthanides_all(), core::conformation::Residue::has(), protocols::scoring::methods::pcs::GridSearchIterator::next_center(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::scoring::methods::pcs::PCS_data::update_matrix_A_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), and core::conformation::Atom::xyz().

Referenced by calculate_pcs_score().

core::scoring::methods::EnergyMethodOP protocols::scoring::methods::pcs::PCS_Energy::clone ( ) const

virtual

clone

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

Definition at line 122 of file PseudocontactShiftEnergy.cc.

References PCS_Energy().

void protocols::scoring::methods::pcs::PCS_Energy::dump_PCS_info	(	utility::vector1< PCS_tensor > const &	vec_tensor,
		numeric::xyzVector< core::Real > const &	best_coo,
		PCS_data const &	pcs_d
	)		const

Definition at line 190 of file PseudocontactShiftEnergy.cc.

References protocols::comparative_modeling::features::A, protocols::scoring::methods::pcs::fill_A_line(), protocols::scoring::methods::pcs::PCS_data::get_n_lanthanides(), protocols::scoring::methods::pcs::PCS_data::get_PCS_data_line_all_spin(), protocols::scoring::methods::pcs::PCS_data::get_pcs_data_per_lanthanides_all(), protocols::scoring::methods::pcs::PCS_data::get_X_all(), protocols::scoring::methods::pcs::PCS_data::get_Y_all(), and protocols::scoring::methods::pcs::PCS_data::get_Z_all().

Referenced by calculate_pcs_score().

void protocols::scoring::methods::pcs::PCS_Energy::finalize_total_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::scoring::EnergyMap &	total_energy
	)		const

virtual

called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

called at the end of energy evaluation

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

Definition at line 131 of file PseudocontactShiftEnergy.cc.

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

void protocols::scoring::methods::pcs::PCS_Energy::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 95 of file PseudocontactShiftEnergy.cc.

core::Real protocols::scoring::methods::pcs::PCS_Energy::minimize_tensors_from_PCS_data	(	utility::vector1< PCS_tensor > &	vec_best_tensor,
		numeric::xyzVector< core::Real > &	best_coo,
		PCS_data const &	pcs_d
	)		const