core::scoring::rna::RNA_LowResolutionPotential Class Reference

#include <RNA_LowResolutionPotential.hh>

Collaboration diagram for core::scoring::rna::RNA_LowResolutionPotential:

List of all members.

Public Member Functions
	RNA_LowResolutionPotential ()
void	update_rna_centroid_info (pose::Pose &pose) const
void	update_rna_base_base_interactions (pose::Pose &pose) const
void	update_rna_base_pair_list (pose::Pose &pose) const
void	finalize (pose::Pose &pose) const
Real	rna_base_backbone_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const
Real	rna_backbone_backbone_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
Real	rna_repulsive_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
Real	get_rna_stack_score (Distance const x, Distance const y, Distance const z, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const
void	eval_atom_derivative_base_base (id::AtomID const &atom_id, pose::Pose const &pose, scoring::EnergyMap const &weights, Vector &F1, Vector &F2) const
void	eval_atom_derivative_rna_base_backbone (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const
void	eval_atom_derivative_rna_backbone_backbone (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const
void	eval_atom_derivative_rna_repulsive (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const
bool	check_clear_for_stacking (pose::Pose &pose, Size const &i, int const &sign) const
bool	check_forming_base_pair (pose::Pose &pose, Size const &i, Size const &j) const
void	eval_rna_base_pair_energy (rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const
void	more_precise_base_pair_classification (bool const &value)

---

Constructor & Destructor Documentation

core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential

(

)

---

Member Function Documentation

bool core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking	(	pose::Pose &	pose,
		Size const &	i,
		int const &	sign
	)		const

References core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::pose::Pose::total_residue(), and core::scoring::rna::RNA_CentroidInfo::update().

bool core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair	(	pose::Pose &	pose,
		Size const &	i,
		Size const &	j
	)		const

References core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		scoring::EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

References core::id::AtomID::atomno(), core::scoring::rna::chi1_torsion_atom_index(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_rna_stack_score(), core::kinematics::Stub::M, core::pose::Pose::residue(), core::scoring::rna_base_axis, core::scoring::rna_base_pair, core::scoring::rna_base_stack, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::rna_scoring_info_from_pose(), and core::id::AtomID::rsd().

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative(), and core::scoring::rna::RNA_BaseBaseEnergy::eval_atom_derivative().

void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		Vector &	F1,
		Vector &	F2
	)		const

References core::id::AtomID::atomno(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().

void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		Vector &	F1,
		Vector &	F2
	)		const

References core::id::AtomID::atomno(), core::scoring::rna::chi1_torsion_atom_index(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().

void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		Vector &	F1,
		Vector &	F2
	)		const

References core::id::AtomID::atomno(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().

void core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy	(	rna::RNA_RawBaseBaseInfo &	rna_raw_base_base_info,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		Vector const &	centroid1,
		Vector const &	centroid2,
		core::kinematics::Stub const &	stub1,
		core::kinematics::Stub const &	stub2
	)		const

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().

void core::scoring::rna::RNA_LowResolutionPotential::finalize

(

pose::Pose &

pose

)

const

Referenced by core::scoring::rna::RNA_BaseBaseEnergy::finalize_total_energy().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score	(	Distance const	x,
		Distance const	y,
		Distance const	z,
		Real &	deriv_x = dummy_deriv,
		Real &	deriv_y = dummy_deriv,
		Real &	deriv_z = dummy_deriv
	)		const

References core::scoring::rna::get_fade_correction().

Referenced by eval_atom_derivative_base_base(), and update_rna_base_base_interactions().

void core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification

(

bool const &

value

)

[inline]

Referenced by protocols::rna::RNA_DeNovoProtocol::RNA_DeNovoProtocol().

Real core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)		const

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().

Real core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Vector const &	centroid1,
		Vector const &	centroid2,
		core::kinematics::Stub const &	stub1,
		core::kinematics::Stub const &	stub2
	)		const

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().

Real core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)		const

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().

void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions

(

pose::Pose &

pose

)

const

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_rna_stack_score(), core::scoring::rna::HOOGSTEEN, core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_RawBaseBaseInfo::resize(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), core::scoring::rna::SUGAR, core::pose::Pose::total_residue(), core::scoring::rna::RNA_CentroidInfo::update(), and core::scoring::rna::WATSON_CRICK.

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::scoring::rna::RNA_BaseBaseEnergy::setup_for_derivatives(), and update_rna_base_pair_list().

void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list

(

pose::Pose &

pose

)

const

References core::scoring::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), core::pose::Pose::update_residue_neighbors(), and update_rna_base_base_interactions().

void core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info

(

pose::Pose &

pose

)

const

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

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), and core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_scoring().

---

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

• src/core/scoring/rna/RNA_LowResolutionPotential.hh
• src/core/scoring/rna/RNA_LowResolutionPotential.cc