| add_sugar_ring_closure_constraints(conformation::Residue const &rsd, core::scoring::constraints::ConstraintSet &cst_set) const | core::energy_methods::RNA_SugarCloseEnergy | |
| angle_sd1_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| angle_sd2_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| angle_sd_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| bond_sd_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| c4prime_o4prime_c1prime_angle_harm_func_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| c4prime_o4prime_c1prime_angle_north_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| c4prime_o4prime_c1prime_angle_south_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| c4prime_o4prime_c1prime_bond_angle_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| clone() const override | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| ContextIndependentOneBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ContextIndependentOneBodyEnergy | |
| defines_dof_derivatives(pose::Pose const &p) const | core::scoring::methods::OneBodyEnergy | virtual |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| defines_score_for_residue(conformation::Residue const &) const | core::scoring::methods::OneBodyEnergy | virtual |
| EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
| eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap const &weights, Vector &F1, Vector &F2) const override | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| eval_residue_derivatives(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const | core::scoring::methods::OneBodyEnergy | virtual |
| eval_residue_dof_derivative(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const | core::scoring::methods::OneBodyEnergy | virtual |
| fade_delta_north_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| fade_delta_south_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| 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 |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| method_type() const override | core::scoring::methods::ContextIndependentOneBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| o4prime_c1prime_bond_length_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_bond_north_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_bond_south_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_c2prime_angle_harm_func_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_c2prime_angle_north_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_c2prime_angle_south_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_c2prime_bond_angle_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_dist_harm_func_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_first_base_angle_harm_func_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_first_base_bond_angle_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_n1_9_angle_north_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_n1_9_angle_south_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| o4prime_c1prime_sd_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| OneBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::OneBodyEnergy | |
| parent typedef | core::energy_methods::RNA_SugarCloseEnergy | |
| 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_derivatives_for_residue_opportunity(pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| residue_energy(conformation::Residue const &rsd, core::scoring::EnergyMap &emap) const | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| residue_energy(conformation::Residue const &rsd, pose::Pose const &, core::scoring::EnergyMap &emap) const override | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| residue_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const | core::scoring::methods::OneBodyEnergy | virtual |
| rna_fitted_torsion_info_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| rna_sugar_close_constraints_ | core::energy_methods::RNA_SugarCloseEnergy | mutableprivate |
| RNA_SugarCloseEnergy() | core::energy_methods::RNA_SugarCloseEnergy | |
| scale_rna_torsion_sd_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| scale_rna_torsion_tether_ | core::energy_methods::RNA_SugarCloseEnergy | 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, core::scoring::ScoreFunction const &) const override | core::energy_methods::RNA_SugarCloseEnergy | virtual |
| setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const | core::scoring::methods::OneBodyEnergy | virtual |
| setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, basic::datacache::BasicDataCache &, ResSingleMinimizationData &) const | core::scoring::methods::OneBodyEnergy | 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, ResSingleMinimizationData &min_data) const | core::scoring::methods::OneBodyEnergy | virtual |
| core::scoring::methods::EnergyMethod::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_sugar_ring_closure_constraints(pose::Pose &pose) const | core::energy_methods::RNA_SugarCloseEnergy | |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| use_extended_residue_energy_interface() const | core::scoring::methods::OneBodyEnergy | virtual |
| use_phenix_sugar_close_ | core::energy_methods::RNA_SugarCloseEnergy | private |
| version() const override | core::energy_methods::RNA_SugarCloseEnergy | privatevirtual |
| ~OneBodyEnergy() override | core::scoring::methods::OneBodyEnergy | |
| ~RNA_SugarCloseEnergy() override | core::energy_methods::RNA_SugarCloseEnergy | |
1.8.7