| __pad0__ | core::scoring::rna::RNA_LowResolutionPotential | |
| atom_numbers_for_backbone_score_calculations_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| atomic_interaction_cutoff() const | core::scoring::methods::WholeStructureEnergy | inlinevirtual |
| axis_bin_width_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| axis_num_bins_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| backbone_backbone_bin_width_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| backbone_backbone_distance_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| backbone_backbone_num_bins_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_atom_dist_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_bin_width_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_check_atom_neighbor_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_distance_cutoff() const | core::scoring::rna::RNA_LowResolutionPotential | inline |
| base_backbone_distance_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_num_bins_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_rho_cutoff() const | core::scoring::rna::RNA_LowResolutionPotential | inline |
| base_backbone_rho_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_rho_fade_zone_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_table_size_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_z_cutoff() const | core::scoring::rna::RNA_LowResolutionPotential | inline |
| base_backbone_z_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_backbone_z_fade_zone_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_max_height_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_min_height_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_radius2_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_radius_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_rho_fade_zone_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| base_stack_z_fade_zone_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| basepair_xy_bin_width_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| basepair_xy_num_bins_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| basepair_xy_table_size_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| basepair_xy_z_fade_zone_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| check_atom_numbers_for_backbone_oxygens(core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| check_clear_for_stacking(pose::Pose &pose, Size const &i, int const &sign) const | core::scoring::rna::RNA_LowResolutionPotential | |
| check_for_base_neighbor(conformation::Residue const &rsd1, Vector const &heavy_atom_j, Real &atom_cutoff_weight) const | core::scoring::rna::RNA_LowResolutionPotential | |
| check_forming_base_pair(pose::Pose &pose, Size const &i, Size const &j) const | core::scoring::rna::RNA_LowResolutionPotential | |
| clone() const override | core::scoring::rna::RNA_LowResolutionPotential | inlinevirtual |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| dummy_deriv | core::scoring::rna::RNA_LowResolutionPotential | static |
| EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
| eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const | core::scoring::methods::EnergyMethod | virtual |
| eval_atom_derivative_base_base(id::AtomID const &atom_id, pose::Pose const &pose, scoring::EnergyMap const &weights, Vector &F1, Vector &F2) const | 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 | 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 | core::scoring::rna::RNA_LowResolutionPotential | |
| eval_atom_derivative_rna_repulsive(id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const | core::scoring::rna::RNA_LowResolutionPotential | |
| eval_rna_base_pair_energy(pose::rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid1, Vector const ¢roid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const | core::scoring::rna::RNA_LowResolutionPotential | |
| eval_rna_base_pair_energy_one_way(pose::rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &res_i, conformation::Residue const &res_j, Vector const ¢roid1, Vector const ¢roid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| fade_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| fill_atom_numbers_for_backbone_oxygens(core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa) | core::scoring::rna::RNA_LowResolutionPotential | private |
| finalize(pose::Pose &pose) const | core::scoring::rna::RNA_LowResolutionPotential | |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_after_minimizing(pose::Pose &pose) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const | core::scoring::methods::EnergyMethod | virtual |
| find_backbone_oxygen_atom(ObjexxFCL::FArray2D< Size > const &atom_number_for_backbone_score_calculations, Size const &i, Size const &atom_num_i) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| find_backbone_oxygen_atom(Size const &atom_num_i) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_base_backbone(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const &m) const | core::scoring::rna::RNA_LowResolutionPotential | |
| get_base_backbone(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid_i, kinematics::Stub const &stub_i, core::Size const &m) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_rna_axis_score(Real const cos_theta, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_rna_backbone_backbone_score(Distance const &r, Size const &atom_num_j_bin, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_rna_backbone_backbone_xy(Distance const x, Distance const y, conformation::Residue const &res_i, Size const &atom_num_j_bin) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| 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=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| 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=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_rna_repulsive_score(Distance const &r, Size const &atom_num_j_bin, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_rna_stack_score(Distance const x, Distance const y, Distance const z, Real &deriv_x=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | |
| get_rna_stagger_score(Distance const height, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| get_zeta_cutoff(conformation::Residue const &res_i, Real &zeta_hoogsteen_cutoff, Real &zeta_sugar_cutoff) const | core::scoring::rna::RNA_LowResolutionPotential | |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::scoring::rna::RNA_LowResolutionPotential | inlinevirtual |
| initialize_atom_numbers_for_backbone_score_calculations() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_more_precise_base_pair_cutoffs() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_axis() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_backbone_backbone() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_backbone_backbone_weights() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_RNA_backbone_oxygen_atoms() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_base_backbone_xy() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_basepair_xy() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_repulsive_weights() | core::scoring::rna::RNA_LowResolutionPotential | private |
| initialize_rna_stagger() | core::scoring::rna::RNA_LowResolutionPotential | private |
| interpolate_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| method_type() const override | core::scoring::methods::WholeStructureEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| more_precise_base_pair_classification(bool const &value) | core::scoring::rna::RNA_LowResolutionPotential | inline |
| more_precise_base_pair_classification_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| num_RNA_backbone_oxygen_atoms_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| num_RNA_base_pair_orientations_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| num_RNA_res_types_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| o2p_index_within_special_backbone_atoms_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| o2prime_index_within_special_backbone_atoms_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| parent typedef | core::scoring::methods::WholeStructureEnergy | |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | core::scoring::methods::EnergyMethod | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| rna_axis_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_backbone_backbone_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const | core::scoring::rna::RNA_LowResolutionPotential | |
| rna_backbone_backbone_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_backbone_backbone_potential_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_backbone_backbone_weight_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| RNA_backbone_oxygen_atoms_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_base_backbone_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid1, Vector const ¢roid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const | core::scoring::rna::RNA_LowResolutionPotential | |
| rna_base_backbone_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid1, core::kinematics::Stub const &stub1) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_base_backbone_xy_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_base_pair_xy_filename_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_basepair_radius_cutoff2_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_basepair_radius_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_basepair_stagger_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_basepair_xy_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| RNA_LowResolutionPotential() | core::scoring::rna::RNA_LowResolutionPotential | |
| RNA_LowResolutionPotential(std::string const &filename) | core::scoring::rna::RNA_LowResolutionPotential | |
| rna_repulse_all_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_repulsive_distance_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_repulsive_max_penalty_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_repulsive_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const | core::scoring::rna::RNA_LowResolutionPotential | |
| rna_repulsive_pair_energy_one_way(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_repulsive_screen_scale_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_repulsive_weight_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_stagger_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| rna_verbose_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_scoring(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const | core::scoring::methods::EnergyMethod | virtual |
| setup_precise_zeta_cutoffs(chemical::AA const &na_rad, std::string const &hoogsteen_cutoff_atom, std::string const &sugar_cutoff_atom) | core::scoring::rna::RNA_LowResolutionPotential | private |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| stagger_bin_width_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| stagger_distance_cutoff_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| stagger_num_bins_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| update_rna_base_base_interactions(pose::Pose &pose) const | core::scoring::rna::RNA_LowResolutionPotential | |
| update_rna_base_pair_list(pose::Pose &pose) const | core::scoring::rna::RNA_LowResolutionPotential | |
| update_rna_centroid_info(pose::Pose &pose) const | core::scoring::rna::RNA_LowResolutionPotential | |
| version() const override | core::scoring::rna::RNA_LowResolutionPotential | inlinevirtual |
| WholeStructureEnergy(EnergyMethodCreatorOP) | core::scoring::methods::WholeStructureEnergy | |
| zeta_hoogsteen_cutoff_precise_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| zeta_sugar_cutoff_precise_ | core::scoring::rna::RNA_LowResolutionPotential | private |
| ~WholeStructureEnergy() override | core::scoring::methods::WholeStructureEnergy | inline |
1.8.7