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

#include <RNA_LowResolutionPotential.hh>

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

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
 
bool check_for_base_neighbor (conformation::Residue const &rsd1, Vector const &heavy_atom_j, Real &atom_cutoff_weight) const
 
void setup_precise_zeta_cutoffs (chemical::AA const &na_rad, std::string const &hoogsteen_cutoff_atom, std::string const &sugar_cutoff_atom)
 
void get_zeta_cutoff (conformation::Residue const &res_i, Real &zeta_hoogsteen_cutoff, Real &zeta_sugar_cutoff) const
 

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 o2star_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_
 

Detailed Description

Definition at line 55 of file RNA_LowResolutionPotential.hh.

Constructor & Destructor Documentation

core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential ( )

Definition at line 77 of file RNA_LowResolutionPotential.cc.

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

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

Definition at line 2192 of file RNA_LowResolutionPotential.cc.

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

Definition at line 2254 of file RNA_LowResolutionPotential.cc.

References base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, 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
private

Definition at line 1340 of file RNA_LowResolutionPotential.cc.

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

Definition at line 2318 of file RNA_LowResolutionPotential.cc.

References 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

Definition at line 1131 of file RNA_LowResolutionPotential.cc.

References core::id::AtomID::atomno(), core::scoring::rna::chi1_torsion_atom_index(), core::graph::Node::const_edge_list_end(), 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

Definition at line 1793 of file RNA_LowResolutionPotential.cc.

References atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), backbone_backbone_distance_cutoff_, core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), core::graph::Edge::get_node(), get_rna_backbone_backbone_score(), interpolate_, num_RNA_backbone_oxygen_atoms_, o2star_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

Definition at line 1496 of file RNA_LowResolutionPotential.cc.

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::scoring::rna::chi1_torsion_atom_index(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), core::graph::Edge::get_node(), get_rna_base_backbone_xy(), interpolate_, 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

Definition at line 2008 of file RNA_LowResolutionPotential.cc.

References atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), core::graph::Node::const_edge_list_end(), 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

Definition at line 902 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1005 of file RNA_LowResolutionPotential.cc.

References 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(), get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), get_zeta_cutoff(), core::scoring::rna::HOOGSTEEN, core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name3(), core::scoring::rna::NUM_EDGES(), core::scoring::rna::RNA_RawBaseBaseInfo::resize(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::rna::SUGAR, core::pose::Pose::total_residue(), and core::scoring::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

Definition at line 2177 of file RNA_LowResolutionPotential.cc.

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

Definition at line 2240 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1748 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1770 of file RNA_LowResolutionPotential.cc.

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

Definition at line 495 of file RNA_LowResolutionPotential.cc.

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

Definition at line 651 of file RNA_LowResolutionPotential.cc.

References backbone_backbone_bin_width_, backbone_backbone_num_bins_, 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

Definition at line 554 of file RNA_LowResolutionPotential.cc.

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_, core::scoring::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

Definition at line 338 of file RNA_LowResolutionPotential.cc.

References base_stack_rho_fade_zone_, basepair_xy_bin_width_, basepair_xy_num_bins_, basepair_xy_table_size_, basepair_xy_z_fade_zone_, core::scoring::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

Definition at line 681 of file RNA_LowResolutionPotential.cc.

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

Definition at line 446 of file RNA_LowResolutionPotential.cc.

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

Definition at line 523 of file RNA_LowResolutionPotential.cc.

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
private

Definition at line 987 of file RNA_LowResolutionPotential.cc.

References core::scoring::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

Definition at line 2153 of file RNA_LowResolutionPotential.cc.

References check_atom_numbers_for_backbone_oxygens(), 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, core::chemical::ChemicalManager::residue_type_set(), and core::chemical::RNA.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 969 of file RNA_LowResolutionPotential.cc.

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

Definition at line 196 of file RNA_LowResolutionPotential.cc.

References rna_axis_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 292 of file RNA_LowResolutionPotential.cc.

References protocols::abinitio::filename(), and rna_backbone_backbone_potential_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 280 of file RNA_LowResolutionPotential.cc.

References rna_backbone_backbone_weight_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 233 of file RNA_LowResolutionPotential.cc.

References o2p_index_within_special_backbone_atoms_, o2star_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

Definition at line 252 of file RNA_LowResolutionPotential.cc.

References protocols::abinitio::filename(), and rna_base_backbone_xy_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 167 of file RNA_LowResolutionPotential.cc.

References protocols::abinitio::filename(), and rna_basepair_xy_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 322 of file RNA_LowResolutionPotential.cc.

References rna_repulsive_weight_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 214 of file RNA_LowResolutionPotential.cc.

References rna_stagger_.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 162 of file RNA_LowResolutionPotential.hh.

References more_precise_base_pair_classification_.

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

Definition at line 1662 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1673 of file RNA_LowResolutionPotential.cc.

References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, backbone_backbone_distance_cutoff_, get_rna_backbone_backbone_score(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), num_RNA_backbone_oxygen_atoms_, o2star_index_within_special_backbone_atoms_, rna_backbone_backbone_weight_, RNA_backbone_oxygen_atoms_, rna_verbose_, core::conformation::Residue::seqpos(), 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

Definition at line 1382 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1397 of file RNA_LowResolutionPotential.cc.

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(), get_rna_base_backbone_xy(), 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, 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

Definition at line 1918 of file RNA_LowResolutionPotential.cc.

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

Definition at line 1929 of file RNA_LowResolutionPotential.cc.

References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, get_rna_repulsive_score(), 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(), 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

Definition at line 923 of file RNA_LowResolutionPotential.cc.

References core::scoring::rna::convert_acgu_to_1234(), core::conformation::ResidueFactory::create_residue(), core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::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

Definition at line 725 of file RNA_LowResolutionPotential.cc.

References base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, core::graph::Node::const_edge_list_end(), 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(), get_zeta_cutoff(), 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(), 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::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_BaseBaseEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), and update_rna_base_pair_list().

void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list ( pose::Pose &  pose) const

Definition at line 884 of file RNA_LowResolutionPotential.cc.

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

Definition at line 712 of file RNA_LowResolutionPotential.cc.

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

Definition at line 302 of file RNA_LowResolutionPotential.hh.

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

Definition at line 330 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_axis_score().

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

Definition at line 331 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_axis_score(), and RNA_LowResolutionPotential().

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

Definition at line 349 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_backbone_backbone_score().

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

Definition at line 350 of file RNA_LowResolutionPotential.hh.

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

Definition at line 351 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_backbone_backbone_score(), and RNA_LowResolutionPotential().

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

Definition at line 344 of file RNA_LowResolutionPotential.hh.

Referenced by check_for_base_neighbor().

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

Definition at line 337 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

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

Definition at line 347 of file RNA_LowResolutionPotential.hh.

Referenced by check_for_base_neighbor().

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

Definition at line 341 of file RNA_LowResolutionPotential.hh.

Referenced by 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

Definition at line 338 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

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

Definition at line 343 of file RNA_LowResolutionPotential.hh.

Referenced by 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

Definition at line 346 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_base_backbone_xy().

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

Definition at line 339 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().

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

Definition at line 342 of file RNA_LowResolutionPotential.hh.

Referenced by 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

Definition at line 345 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_base_backbone_xy().

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

Definition at line 324 of file RNA_LowResolutionPotential.hh.

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

Definition at line 323 of file RNA_LowResolutionPotential.hh.

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

Definition at line 326 of file RNA_LowResolutionPotential.hh.

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

Definition at line 325 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_stack_score().

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

Definition at line 328 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy(), and get_rna_stack_score().

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

Definition at line 327 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_stack_score().

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

Definition at line 318 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

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

Definition at line 319 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

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

Definition at line 320 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().

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

Definition at line 321 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy().

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

Definition at line 374 of file RNA_LowResolutionPotential.hh.

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

Definition at line 366 of file RNA_LowResolutionPotential.hh.

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

Definition at line 365 of file RNA_LowResolutionPotential.hh.

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

Definition at line 370 of file RNA_LowResolutionPotential.hh.

Referenced by get_zeta_cutoff(), and more_precise_base_pair_classification().

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

Definition at line 359 of file RNA_LowResolutionPotential.hh.

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

Definition at line 358 of file RNA_LowResolutionPotential.hh.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 360 of file RNA_LowResolutionPotential.hh.

Referenced by RNA_LowResolutionPotential().

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

Definition at line 363 of file RNA_LowResolutionPotential.hh.

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::o2star_index_within_special_backbone_atoms_
private

Definition at line 362 of file RNA_LowResolutionPotential.hh.

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

Definition at line 299 of file RNA_LowResolutionPotential.hh.

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

Definition at line 307 of file RNA_LowResolutionPotential.hh.

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

Definition at line 306 of file RNA_LowResolutionPotential.hh.

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

Definition at line 301 of file RNA_LowResolutionPotential.hh.

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

Definition at line 304 of file RNA_LowResolutionPotential.hh.

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

Definition at line 317 of file RNA_LowResolutionPotential.hh.

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

Definition at line 315 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_basepair_xy().

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

Definition at line 316 of file RNA_LowResolutionPotential.hh.

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

Definition at line 297 of file RNA_LowResolutionPotential.hh.

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

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

Definition at line 356 of file RNA_LowResolutionPotential.hh.

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

Definition at line 355 of file RNA_LowResolutionPotential.hh.

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

Definition at line 353 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_repulsive_score().

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

Definition at line 354 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_repulsive_score().

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

Definition at line 309 of file RNA_LowResolutionPotential.hh.

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

Definition at line 298 of file RNA_LowResolutionPotential.hh.

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

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

Definition at line 368 of file RNA_LowResolutionPotential.hh.

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

Definition at line 334 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_stagger_score().

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

Definition at line 335 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_stagger_score().

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

Definition at line 333 of file RNA_LowResolutionPotential.hh.

Referenced by get_rna_stagger_score(), and RNA_LowResolutionPotential().

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

Definition at line 311 of file RNA_LowResolutionPotential.hh.

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

Definition at line 312 of file RNA_LowResolutionPotential.hh.

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:
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