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

#include <RNA_LowResolutionPotential.hh>

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)
Distance	base_backbone_distance_cutoff () const
Distance	base_backbone_z_cutoff () const
Distance	base_backbone_rho_cutoff () const
void	get_zeta_cutoff (conformation::Residue const &res_i, Real &zeta_hoogsteen_cutoff, Real &zeta_sugar_cutoff) const
bool	check_for_base_neighbor (conformation::Residue const &rsd1, Vector const &heavy_atom_j, Real &atom_cutoff_weight) const

Static Public Attributes
static Real	dummy_deriv = 0.0

Private Member Functions
void	eval_rna_base_pair_energy_one_way (rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &res_i, conformation::Residue const &res_j, pose::Pose const &pose, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const
Real	rna_base_backbone_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid1, core::kinematics::Stub const &stub1) const
Size	find_backbone_oxygen_atom (ObjexxFCL::FArray2D< Size > const &atom_number_for_backbone_score_calculations, Size const &i, Size const &atom_num_i) const
Size	find_backbone_oxygen_atom (Size const &atom_num_i) const
void	initialize_rna_basepair_xy ()
void	initialize_rna_axis ()
void	initialize_rna_stagger ()
void	initialize_RNA_backbone_oxygen_atoms ()
void	initialize_atom_numbers_for_backbone_score_calculations ()
void	initialize_rna_base_backbone_xy ()
void	initialize_rna_backbone_backbone_weights ()
void	initialize_rna_backbone_backbone ()
void	initialize_rna_repulsive_weights ()
void	initialize_more_precise_base_pair_cutoffs ()
void	fill_atom_numbers_for_backbone_oxygens (core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa)
bool	check_atom_numbers_for_backbone_oxygens (core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa) const
Real	get_rna_axis_score (Real const cos_theta, Real &deriv=dummy_deriv) const
Real	get_rna_stagger_score (Distance const height, Real &deriv=dummy_deriv) const
Real	get_rna_basepair_xy (Distance const x, Distance const y, Distance const z, Real const cos_theta, conformation::Residue const &res_i, conformation::Residue const &res_j, bool const deriv_check=true, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const
Real	get_rna_backbone_backbone_score (Distance const &r, Size const &atom_num_j_bin, Real &deriv=dummy_deriv) const
Real	get_rna_repulsive_score (Distance const &r, Size const &atom_num_j_bin, Real &deriv=dummy_deriv) const
Real	rna_backbone_backbone_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
Real	rna_repulsive_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
Real	get_rna_base_backbone_xy (Distance const x, Distance const y, Distance const z, conformation::Residue const &res_i, Size const &atom_num_j_bin, bool const deriv_check=false, Real &deriv_x=dummy_deriv, Real &deriv_y=dummy_deriv, Real &deriv_z=dummy_deriv) const
Real	get_rna_backbone_backbone_xy (Distance const x, Distance const y, conformation::Residue const &res_i, Size const &atom_num_j_bin) const
void	setup_precise_zeta_cutoffs (chemical::AA const &na_rad, std::string const &hoogsteen_cutoff_atom, std::string const &sugar_cutoff_atom)

Private Attributes
ObjexxFCL::FArray5D< Real >	rna_basepair_xy_
ObjexxFCL::FArray1D< Real >	rna_stagger_
ObjexxFCL::FArray1D< Real >	rna_axis_
utility::vector1< std::string >	RNA_backbone_oxygen_atoms_
utility::vector1< Size >	atom_numbers_for_backbone_score_calculations_
ObjexxFCL::FArray4D< Real >	rna_base_backbone_xy_
ObjexxFCL::FArray1D< Real >	rna_backbone_backbone_weight_
ObjexxFCL::FArray1D< Real >	rna_backbone_backbone_potential_
ObjexxFCL::FArray1D< Real >	rna_repulsive_weight_
ObjexxFCL::FArray1D< Real >	zeta_hoogsteen_cutoff_precise_
ObjexxFCL::FArray1D< Real >	zeta_sugar_cutoff_precise_
Distance const	rna_basepair_radius_cutoff_
Distance const	rna_basepair_stagger_cutoff_
Real const	rna_basepair_radius_cutoff2_
Distance const	basepair_xy_bin_width_
Size const	basepair_xy_num_bins_
Size const	basepair_xy_table_size_
Distance const	basepair_xy_z_fade_zone_
Distance const	base_stack_min_height_
Distance const	base_stack_max_height_
Distance const	base_stack_radius_
Real const	base_stack_radius2_
Distance const	base_stack_z_fade_zone_
Distance const	base_stack_rho_fade_zone_
Real const	axis_bin_width_
Size const	axis_num_bins_
Size const	stagger_num_bins_
Distance const	stagger_bin_width_
Distance const	stagger_distance_cutoff_
Distance const	base_backbone_bin_width_
Size const	base_backbone_num_bins_
Size const	base_backbone_table_size_
Distance const	base_backbone_distance_cutoff_
Distance const	base_backbone_z_cutoff_
Distance const	base_backbone_rho_cutoff_
Distance const	base_backbone_atom_dist_cutoff_
Distance const	base_backbone_z_fade_zone_
Distance const	base_backbone_rho_fade_zone_
bool const	base_backbone_check_atom_neighbor_
Real const	backbone_backbone_bin_width_
Real const	backbone_backbone_distance_cutoff_
Size const	backbone_backbone_num_bins_
Real const	rna_repulsive_max_penalty_
Real const	rna_repulsive_screen_scale_
Real const	rna_repulsive_distance_cutoff_
Real const	rna_repulse_all_
Size const	num_RNA_base_pair_orientations_
Size const	num_RNA_backbone_oxygen_atoms_
Size const	num_RNA_res_types_
Size	o2prime_index_within_special_backbone_atoms_
Size	o2p_index_within_special_backbone_atoms_
bool const	interpolate_
bool const	fade_
bool const	rna_verbose_
bool	more_precise_base_pair_classification_

Constructor & Destructor Documentation

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

(

)

References axis_num_bins_, backbone_backbone_num_bins_, base_backbone_bin_width_, base_backbone_num_bins_, base_backbone_table_size_, basepair_xy_bin_width_, basepair_xy_num_bins_, basepair_xy_table_size_, initialize_atom_numbers_for_backbone_score_calculations(), initialize_more_precise_base_pair_cutoffs(), initialize_rna_axis(), initialize_rna_backbone_backbone(), initialize_rna_backbone_backbone_weights(), initialize_RNA_backbone_oxygen_atoms(), initialize_rna_base_backbone_xy(), initialize_rna_basepair_xy(), initialize_rna_repulsive_weights(), initialize_rna_stagger(), num_RNA_backbone_oxygen_atoms_, num_RNA_base_pair_orientations_, num_RNA_res_types_, rna_axis_, rna_backbone_backbone_potential_, rna_base_backbone_xy_, rna_basepair_xy_, rna_repulsive_weight_, rna_stagger_, and stagger_num_bins_.

Member Function Documentation

Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff ( ) const

inline

References base_backbone_distance_cutoff_.

Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff ( ) const

inline

References base_backbone_rho_cutoff_.

Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff ( ) const

inline

References base_backbone_z_cutoff_.

bool core::scoring::rna::RNA_LowResolutionPotential::check_atom_numbers_for_backbone_oxygens ( core::chemical::ResidueTypeSetCAP &  rsd_set, core::chemical::AA const &  aa  ) const

private

References atom_numbers_for_backbone_score_calculations_, num_RNA_backbone_oxygen_atoms_, and RNA_backbone_oxygen_atoms_.

Referenced by initialize_atom_numbers_for_backbone_score_calculations().

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

References base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), dot_product(), 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(), core::scoring::tr, and core::scoring::rna::RNA_CentroidInfo::update().

bool core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor	(	conformation::Residue const &	rsd1,
		Vector const &	heavy_atom_j,
		Real &	atom_cutoff_weight
	)		const

References base_backbone_atom_dist_cutoff_, base_backbone_check_atom_neighbor_, core::conformation::Residue::first_sidechain_atom(), core::scoring::rna::get_fade_correction(), core::conformation::Residue::nheavyatoms(), core::pose::num_heavy_atoms(), and core::conformation::Residue::xyz().

Referenced by eval_atom_derivative_rna_base_backbone(), and rna_base_backbone_pair_energy_one_way().

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

References numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), dot_product(), core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, 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::chemical::rna::chi1_torsion_atom_index(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), core::graph::Node::const_edge_list_end(), cross(), dot_product(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Edge::get_node(), get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_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_BaseBaseEnergy::eval_atom_derivative(), and core::scoring::rna::RNA_PairwiseLowResolutionEnergy::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 atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), backbone_backbone_distance_cutoff_, core::graph::Node::const_edge_list_end(), cross(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), core::graph::Edge::get_node(), get_rna_backbone_backbone_score(), interpolate_, numeric::xyzVector< class >::length(), num_RNA_backbone_oxygen_atoms_, o2prime_index_within_special_backbone_atoms_, core::pose::Pose::residue(), rna_backbone_backbone_weight_, and core::id::AtomID::rsd().

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 atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), base_backbone_distance_cutoff_, base_backbone_rho_cutoff_, base_backbone_z_cutoff_, check_for_base_neighbor(), core::chemical::rna::chi1_torsion_atom_index(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), core::graph::Node::const_edge_list_end(), cross(), dot_product(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), core::graph::Edge::get_node(), get_rna_base_backbone_xy(), interpolate_, numeric::xyzVector< class >::length(), core::kinematics::Stub::M, num_RNA_backbone_oxygen_atoms_, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::rna_scoring_info_from_pose(), and core::id::AtomID::rsd().

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 atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), core::graph::Node::const_edge_list_end(), cross(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), core::graph::Edge::get_node(), get_rna_repulsive_score(), num_RNA_backbone_oxygen_atoms_, o2p_index_within_special_backbone_atoms_, core::pose::Pose::residue(), rna_repulse_all_, rna_repulsive_distance_cutoff_, rna_repulsive_weight_, and core::id::AtomID::rsd().

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

References eval_rna_base_pair_energy_one_way().

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

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

private

References numeric::arccos(), core::scoring::rna::RNA_RawBaseBaseInfo::base_axis_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_height_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_axis_array(), base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, core::scoring::rna::RNA_RawBaseBaseInfo::base_stagger_array(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), numeric::conversions::degrees(), dot_product(), core::chemical::element::F, get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), get_zeta_cutoff(), core::chemical::rna::HOOGSTEEN, core::chemical::element::I, core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name3(), core::chemical::rna::NUM_EDGES(), core::scoring::rna::RNA_RawBaseBaseInfo::resize(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, rna_verbose_, core::conformation::Residue::seqpos(), core::chemical::rna::SUGAR, core::pose::Pose::total_residue(), core::scoring::tr, and core::chemical::rna::WATSON_CRICK.

Referenced by eval_rna_base_pair_energy().

void core::scoring::rna::RNA_LowResolutionPotential::fill_atom_numbers_for_backbone_oxygens ( core::chemical::ResidueTypeSetCAP &  rsd_set, core::chemical::AA const &  aa  )

private

References atom_numbers_for_backbone_score_calculations_, num_RNA_backbone_oxygen_atoms_, and RNA_backbone_oxygen_atoms_.

Referenced by initialize_atom_numbers_for_backbone_score_calculations().

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

(

pose::Pose &

pose

)

const

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

Size core::scoring::rna::RNA_LowResolutionPotential::find_backbone_oxygen_atom ( ObjexxFCL::FArray2D< Size > const &  atom_number_for_backbone_score_calculations, Size const &  i, Size const &  atom_num_i  ) const

private

References num_RNA_backbone_oxygen_atoms_.

Referenced by eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), and eval_atom_derivative_rna_repulsive().

Size core::scoring::rna::RNA_LowResolutionPotential::find_backbone_oxygen_atom ( Size const &  atom_num_i ) const

private

References atom_numbers_for_backbone_score_calculations_, and num_RNA_backbone_oxygen_atoms_.

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_axis_score ( Real const  cos_theta, Real &  deriv = dummy_deriv  ) const

private

References axis_bin_width_, axis_num_bins_, interpolate_, core::scoring::interpolate_value_and_deriv(), and rna_axis_.

Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_score ( Distance const &  r, Size const &  atom_num_j_bin, Real &  deriv = dummy_deriv  ) const

private

References backbone_backbone_bin_width_, backbone_backbone_num_bins_, bin, interpolate_, core::scoring::interpolate_value_and_deriv(), rna_backbone_backbone_potential_, and rna_backbone_backbone_weight_.

Referenced by eval_atom_derivative_rna_backbone_backbone(), and rna_backbone_backbone_pair_energy_one_way().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_xy ( Distance const  x, Distance const  y, conformation::Residue const &  res_i, Size const &  atom_num_j_bin  ) const

private

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy ( Distance const  x, Distance const  y, Distance const  z, conformation::Residue const &  res_i, Size const &  atom_num_j_bin, bool const  deriv_check = false, Real &  deriv_x = dummy_deriv, Real &  deriv_y = dummy_deriv, Real &  deriv_z = dummy_deriv  ) const

private

References base_backbone_bin_width_, base_backbone_num_bins_, base_backbone_rho_cutoff_, base_backbone_rho_fade_zone_, base_backbone_table_size_, base_backbone_z_cutoff_, base_backbone_z_fade_zone_, bilinearly_interpolated(), core::chemical::rna::convert_acgu_to_1234(), fade_, core::scoring::rna::get_fade_correction(), interpolate_, core::conformation::Residue::name1(), and rna_base_backbone_xy_.

Referenced by eval_atom_derivative_rna_base_backbone(), and rna_base_backbone_pair_energy_one_way().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy ( Distance const  x, Distance const  y, Distance const  z, Real const  cos_theta, conformation::Residue const &  res_i, conformation::Residue const &  res_j, bool const  deriv_check = true, Real &  deriv_x = dummy_deriv, Real &  deriv_y = dummy_deriv, Real &  deriv_z = dummy_deriv  ) const

private

References base_stack_rho_fade_zone_, basepair_xy_bin_width_, basepair_xy_num_bins_, basepair_xy_table_size_, basepair_xy_z_fade_zone_, bilinearly_interpolated(), core::chemical::rna::convert_acgu_to_1234(), fade_, core::scoring::rna::get_fade_correction(), interpolate_, core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), rna_basepair_radius_cutoff_, rna_basepair_stagger_cutoff_, and rna_basepair_xy_.

Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_repulsive_score ( Distance const &  r, Size const &  atom_num_j_bin, Real &  deriv = dummy_deriv  ) const

private

References rna_repulsive_distance_cutoff_, rna_repulsive_max_penalty_, rna_repulsive_screen_scale_, and rna_repulsive_weight_.

Referenced by eval_atom_derivative_rna_repulsive(), and rna_repulsive_pair_energy_one_way().

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 base_stack_max_height_, base_stack_min_height_, base_stack_radius_, base_stack_rho_fade_zone_, base_stack_z_fade_zone_, fade_, and core::scoring::rna::get_fade_correction().

Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_stagger_score ( Distance const  height, Real &  deriv = dummy_deriv  ) const

private

References interpolate_, core::scoring::interpolate_value_and_deriv(), rna_stagger_, stagger_bin_width_, stagger_distance_cutoff_, and stagger_num_bins_.

Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

void core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff	(	conformation::Residue const &	res_i,
		Real &	zeta_hoogsteen_cutoff,
		Real &	zeta_sugar_cutoff
	)		const

References core::chemical::rna::convert_acgu_to_1234(), more_precise_base_pair_classification_, core::conformation::Residue::name1(), zeta_hoogsteen_cutoff_precise_, and zeta_sugar_cutoff_precise_.

Referenced by eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations ( )

private

References check_atom_numbers_for_backbone_oxygens(), core::chemical::FA_RNA, fill_atom_numbers_for_backbone_oxygens(), core::chemical::ChemicalManager::get_instance(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and core::chemical::ChemicalManager::residue_type_set().

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_more_precise_base_pair_cutoffs ( )

private

References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, setup_precise_zeta_cutoffs(), zeta_hoogsteen_cutoff_precise_, and zeta_sugar_cutoff_precise_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_axis ( )

private

References rna_axis_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone ( )

private

References utility::io::izstream::close(), utility::exit(), filename(), basic::database::full_name(), r1, r2, rna_backbone_backbone_potential_, skip, and core::scoring::tr.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone_weights ( )

private

References rna_backbone_backbone_weight_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_RNA_backbone_oxygen_atoms ( )

private

References o2p_index_within_special_backbone_atoms_, o2prime_index_within_special_backbone_atoms_, and RNA_backbone_oxygen_atoms_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_base_backbone_xy ( )

private

References utility::io::izstream::close(), utility::exit(), filename(), basic::database::full_name(), rna_base_backbone_xy_, skip, and core::scoring::tr.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_basepair_xy ( )

private

References utility::io::izstream::close(), utility::exit(), filename(), basic::database::full_name(), rna_basepair_xy_, skip, and core::scoring::tr.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_repulsive_weights ( )

private

References rna_repulsive_weight_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_stagger ( )

private

References rna_stagger_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification ( bool const &  value )

inline

References more_precise_base_pair_classification_.

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

References rna_backbone_backbone_pair_energy_one_way().

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

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

private

References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, backbone_backbone_distance_cutoff_, core::chemical::element::F, get_rna_backbone_backbone_score(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), numeric::xyzVector< class >::length(), core::conformation::Residue::name1(), num_RNA_backbone_oxygen_atoms_, o2prime_index_within_special_backbone_atoms_, rna_backbone_backbone_weight_, RNA_backbone_oxygen_atoms_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::tr, and core::conformation::Residue::xyz().

Referenced by rna_backbone_backbone_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

References rna_base_backbone_pair_energy_one_way().

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

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

private

References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, base_backbone_distance_cutoff_, base_backbone_rho_cutoff_, base_backbone_z_cutoff_, check_for_base_neighbor(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), dot_product(), core::chemical::element::F, get_rna_base_backbone_xy(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name3(), num_RNA_backbone_oxygen_atoms_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::total_score, core::scoring::tr, and core::conformation::Residue::xyz().

Referenced by rna_base_backbone_pair_energy().

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

References rna_repulsive_pair_energy_one_way().

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

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

private

References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, core::chemical::element::F, get_rna_repulsive_score(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name3(), num_RNA_backbone_oxygen_atoms_, o2p_index_within_special_backbone_atoms_, rna_repulse_all_, rna_repulsive_distance_cutoff_, rna_repulsive_weight_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::tr, and core::conformation::Residue::xyz().

Referenced by rna_repulsive_pair_energy().

void core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs ( chemical::AA const &  na_rad, std::string const &  hoogsteen_cutoff_atom, std::string const &  sugar_cutoff_atom  )

private

References numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), core::chemical::rna::convert_acgu_to_1234(), numeric::conversions::degrees(), dot_product(), core::chemical::FA_RNA, zeta_hoogsteen_cutoff_precise_, and zeta_sugar_cutoff_precise_.

Referenced by initialize_more_precise_base_pair_cutoffs().

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

(

pose::Pose &

pose

)

const

References numeric::arccos(), base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), core::graph::Node::const_edge_list_end(), numeric::conversions::degrees(), dot_product(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::chemical::element::F, core::graph::Edge::get_node(), get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), get_zeta_cutoff(), core::chemical::rna::HOOGSTEEN, core::chemical::element::I, core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_RawBaseBaseInfo::resize(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), rna_verbose_, core::chemical::rna::SUGAR, core::pose::Pose::total_residue(), core::scoring::tr, core::scoring::rna::RNA_CentroidInfo::update(), and core::chemical::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().

Member Data Documentation

utility::vector1< Size > core::scoring::rna::RNA_LowResolutionPotential::atom_numbers_for_backbone_score_calculations_

private

Referenced by check_atom_numbers_for_backbone_oxygens(), eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), eval_atom_derivative_rna_repulsive(), fill_atom_numbers_for_backbone_oxygens(), find_backbone_oxygen_atom(), rna_backbone_backbone_pair_energy_one_way(), rna_base_backbone_pair_energy_one_way(), and rna_repulsive_pair_energy_one_way().

Real const core::scoring::rna::RNA_LowResolutionPotential::axis_bin_width_

private

Referenced by get_rna_axis_score().

Size const core::scoring::rna::RNA_LowResolutionPotential::axis_num_bins_

private

Referenced by get_rna_axis_score(), and RNA_LowResolutionPotential().

Real const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_bin_width_

private

Referenced by get_rna_backbone_backbone_score().

Real const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_distance_cutoff_

private

Referenced by eval_atom_derivative_rna_backbone_backbone(), and rna_backbone_backbone_pair_energy_one_way().

Size const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_num_bins_

private

Referenced by get_rna_backbone_backbone_score(), and RNA_LowResolutionPotential().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_atom_dist_cutoff_

private

Referenced by check_for_base_neighbor().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_bin_width_

private

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

bool const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_check_atom_neighbor_

private

Referenced by check_for_base_neighbor().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff_

private

Referenced by base_backbone_distance_cutoff(), eval_atom_derivative_rna_base_backbone(), and rna_base_backbone_pair_energy_one_way().

Size const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_num_bins_

private

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff_

private

Referenced by base_backbone_rho_cutoff(), eval_atom_derivative_rna_base_backbone(), get_rna_base_backbone_xy(), and rna_base_backbone_pair_energy_one_way().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_fade_zone_

private

Referenced by get_rna_base_backbone_xy().

Size const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_table_size_

private

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff_

private

Referenced by base_backbone_z_cutoff(), eval_atom_derivative_rna_base_backbone(), get_rna_base_backbone_xy(), and rna_base_backbone_pair_energy_one_way().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_fade_zone_

private

Referenced by get_rna_base_backbone_xy().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_max_height_

private

Referenced by check_clear_for_stacking(), eval_rna_base_pair_energy_one_way(), get_rna_stack_score(), and update_rna_base_base_interactions().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_min_height_

private

Referenced by check_clear_for_stacking(), eval_rna_base_pair_energy_one_way(), get_rna_stack_score(), and update_rna_base_base_interactions().

Real const core::scoring::rna::RNA_LowResolutionPotential::base_stack_radius2_

private

Referenced by check_clear_for_stacking(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_radius_

private

Referenced by get_rna_stack_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_rho_fade_zone_

private

Referenced by get_rna_basepair_xy(), and get_rna_stack_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_z_fade_zone_

private

Referenced by get_rna_stack_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_bin_width_

private

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

Size const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_num_bins_

private

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

Size const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_table_size_

private

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

Distance const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_z_fade_zone_

private

Referenced by get_rna_basepair_xy().

core::Real core::scoring::rna::RNA_LowResolutionPotential::dummy_deriv = 0.0

static

bool const core::scoring::rna::RNA_LowResolutionPotential::fade_

private

Referenced by get_rna_base_backbone_xy(), get_rna_basepair_xy(), and get_rna_stack_score().

bool const core::scoring::rna::RNA_LowResolutionPotential::interpolate_

private

Referenced by eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), get_rna_axis_score(), get_rna_backbone_backbone_score(), get_rna_base_backbone_xy(), get_rna_basepair_xy(), and get_rna_stagger_score().

bool core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification_

private

Referenced by get_zeta_cutoff(), and more_precise_base_pair_classification().

Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_backbone_oxygen_atoms_

private

Referenced by check_atom_numbers_for_backbone_oxygens(), eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), eval_atom_derivative_rna_repulsive(), fill_atom_numbers_for_backbone_oxygens(), find_backbone_oxygen_atom(), rna_backbone_backbone_pair_energy_one_way(), rna_base_backbone_pair_energy_one_way(), RNA_LowResolutionPotential(), and rna_repulsive_pair_energy_one_way().

Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_base_pair_orientations_

private

Referenced by RNA_LowResolutionPotential().

Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_res_types_

private

Referenced by RNA_LowResolutionPotential().

Size core::scoring::rna::RNA_LowResolutionPotential::o2p_index_within_special_backbone_atoms_

private

Referenced by eval_atom_derivative_rna_repulsive(), initialize_RNA_backbone_oxygen_atoms(), and rna_repulsive_pair_energy_one_way().

Size core::scoring::rna::RNA_LowResolutionPotential::o2prime_index_within_special_backbone_atoms_

private

Referenced by eval_atom_derivative_rna_backbone_backbone(), initialize_RNA_backbone_oxygen_atoms(), and rna_backbone_backbone_pair_energy_one_way().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_axis_

private

Referenced by get_rna_axis_score(), initialize_rna_axis(), and RNA_LowResolutionPotential().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_potential_

private

Referenced by get_rna_backbone_backbone_score(), initialize_rna_backbone_backbone(), and RNA_LowResolutionPotential().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_weight_

private

Referenced by eval_atom_derivative_rna_backbone_backbone(), get_rna_backbone_backbone_score(), initialize_rna_backbone_backbone_weights(), and rna_backbone_backbone_pair_energy_one_way().

utility::vector1< std::string > core::scoring::rna::RNA_LowResolutionPotential::RNA_backbone_oxygen_atoms_

private

Referenced by check_atom_numbers_for_backbone_oxygens(), fill_atom_numbers_for_backbone_oxygens(), initialize_RNA_backbone_oxygen_atoms(), and rna_backbone_backbone_pair_energy_one_way().

ObjexxFCL::FArray4D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_xy_

private

Referenced by get_rna_base_backbone_xy(), initialize_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

Real const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_radius_cutoff2_

private

Referenced by check_forming_base_pair(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().

Distance const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_radius_cutoff_

private

Referenced by get_rna_basepair_xy().

Distance const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_stagger_cutoff_

private

Referenced by check_forming_base_pair(), eval_rna_base_pair_energy_one_way(), get_rna_basepair_xy(), and update_rna_base_base_interactions().

ObjexxFCL::FArray5D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_xy_

private

Referenced by get_rna_basepair_xy(), initialize_rna_basepair_xy(), and RNA_LowResolutionPotential().

Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulse_all_

private

Referenced by eval_atom_derivative_rna_repulsive(), and rna_repulsive_pair_energy_one_way().

Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_distance_cutoff_

private

Referenced by eval_atom_derivative_rna_repulsive(), get_rna_repulsive_score(), and rna_repulsive_pair_energy_one_way().

Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_max_penalty_

private

Referenced by get_rna_repulsive_score().

Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_screen_scale_

private

Referenced by get_rna_repulsive_score().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_weight_

private

Referenced by eval_atom_derivative_rna_repulsive(), get_rna_repulsive_score(), initialize_rna_repulsive_weights(), RNA_LowResolutionPotential(), and rna_repulsive_pair_energy_one_way().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_stagger_

private

Referenced by get_rna_stagger_score(), initialize_rna_stagger(), and RNA_LowResolutionPotential().

bool const core::scoring::rna::RNA_LowResolutionPotential::rna_verbose_

private

Referenced by eval_rna_base_pair_energy_one_way(), rna_backbone_backbone_pair_energy_one_way(), rna_base_backbone_pair_energy_one_way(), rna_repulsive_pair_energy_one_way(), and update_rna_base_base_interactions().

Distance const core::scoring::rna::RNA_LowResolutionPotential::stagger_bin_width_

private

Referenced by get_rna_stagger_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::stagger_distance_cutoff_

private

Referenced by get_rna_stagger_score().

Size const core::scoring::rna::RNA_LowResolutionPotential::stagger_num_bins_

private

Referenced by get_rna_stagger_score(), and RNA_LowResolutionPotential().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::zeta_hoogsteen_cutoff_precise_

private

Referenced by get_zeta_cutoff(), initialize_more_precise_base_pair_cutoffs(), and setup_precise_zeta_cutoffs().

ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::zeta_sugar_cutoff_precise_

private

Referenced by get_zeta_cutoff(), initialize_more_precise_base_pair_cutoffs(), and setup_precise_zeta_cutoffs().

---

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