#include <RG_Energy_RNA.hh>

Inheritance diagram for core::scoring::rna::RG_Energy_RNA:

Collaboration diagram for core::scoring::rna::RG_Energy_RNA:

Public Member Functions
	RG_Energy_RNA ()
	Defines a center of mass based RG calculation that is O(n) rather than O(n^2). Not tested yet.
virtual methods::EnergyMethodOP	clone () const
	clone
void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, 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.
void	eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &, EnergyMap const &weights, 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.
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.
Public Attributes
	__pad0__:WholeStructureEnergy parent

Constructor & Destructor Documentation

core::scoring::rna::RG_Energy_RNA::RG_Energy_RNA ( )

Defines a center of mass based RG calculation that is O(n) rather than O(n^2). Not tested yet.

c-tor

Referenced by clone().

Member Function Documentation

methods::EnergyMethodOP core::scoring::rna::RG_Energy_RNA::clone ( ) const [virtual]

clone

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

References RG_Energy_RNA().

void core::scoring::rna::RG_Energy_RNA::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 `[virtual]`

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.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

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

References core::id::AtomID::atomno(), core::scoring::rna::first_base_atom_index(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna_rg, core::scoring::rna::rna_scoring_info_from_pose(), core::id::AtomID::rsd(), and core::pose::Pose::total_residue().

void core::scoring::rna::RG_Energy_RNA::finalize_total_energy	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn,
		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.

References core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna_rg, and core::scoring::rna::RNA_CentroidInfo::set_calculated().

void core::scoring::rna::RG_Energy_RNA::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const [inline, 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.