| ApproximateBuriedUnsatPenalty()=delete | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | |
| ApproximateBuriedUnsatPenalty(core::scoring::methods::EnergyMethodOptions const &options) | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | |
| assume_const_backbone_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| atomic_interaction_cutoff() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &p) const | core::scoring::methods::TwoBodyEnergy | virtual |
| backbone_backbone_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
| backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
| bump_energy_backbone(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const | core::scoring::methods::TwoBodyEnergy | virtual |
| bump_energy_full(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const | core::scoring::methods::TwoBodyEnergy | virtual |
| burial_atomic_depth_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| burial_probe_radius_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| burial_resolution_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| clone() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| ContextDependentTwoBodyEnergy(EnergyMethodCreatorOP creator) | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| cor_opt_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| defines_intrares_dof_derivatives(pose::Pose const &p) const | core::scoring::methods::TwoBodyEnergy | virtual |
| defines_intrares_energy(scoring::EnergyMap const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| defines_intrares_energy_for_residue(conformation::Residue const &res) const | core::scoring::methods::TwoBodyEnergy | virtual |
| defines_score_for_residue_pair(conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const | core::scoring::methods::TwoBodyEnergy | virtual |
| divides_backbone_and_sidechain_energetics() const | core::scoring::methods::ShortRangeTwoBodyEnergy | virtual |
| 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_intrares_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::TwoBodyEnergy | virtual |
| eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &emap) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| eval_intrares_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
| eval_intraresidue_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::TwoBodyEnergy | virtual |
| eval_residue_pair_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const | core::scoring::methods::TwoBodyEnergy | virtual |
| evaluate_rotamer_background_energies(conformation::RotamerSetBase const &, conformation::Residue const &, pose::Pose const &, scoring::ScoreFunction const &, scoring::EnergyMap const &, utility::vector1< core::PackerEnergy > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| evaluate_rotamer_background_energy_maps(conformation::RotamerSetBase const &, conformation::Residue const &, pose::Pose const &, scoring::ScoreFunction const &, scoring::EnergyMap const &, utility::vector1< scoring::EnergyMap > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| evaluate_rotamer_intrares_energies(conformation::RotamerSetBase const &set, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, utility::vector1< scoring::EnergyMap > &emaps) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| evaluate_rotamer_pair_energies(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_after_minimizing(pose::Pose &pose) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| finalize_total_energy(pose::Pose &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &total_energy) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| get_energies_cache(pose::Pose const &pose) const | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| hbond_bonus_opt_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
| hbond_energy_threshold_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| IDLE enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| method_type() const override | core::scoring::methods::ContextDependentTwoBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| MINIMIZING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| Mode enum name | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| mode_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
| oversat_penalty_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| PACKING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| parent typedef | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
| requires_a_setup_for_derivatives_for_residue_pair_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| requires_a_setup_for_scoring_for_residue_pair_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
| residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &emap) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| residue_pair_energy_ext(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| scorefxn_bb_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| scorefxn_hbond_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| scorefxn_sc_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| SCORING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
| 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_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::TwoBodyEnergy | virtual |
| setup_for_derivatives_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
| setup_for_minimizing(pose::Pose &, scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, basic::datacache::BasicDataCache &residue_data_cache, ResSingleMinimizationData &res_data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
| setup_for_minimizing_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
| setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, scoring::ScoreFunction const &sfxn) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| setup_for_scoring(pose::Pose &, scoring::ScoreFunction const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
| setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const | core::scoring::methods::TwoBodyEnergy | 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_for_scoring_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
| ShortRangeTwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ShortRangeTwoBodyEnergy | |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| sidechain_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
| TwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::TwoBodyEnergy | |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| use_extended_intrares_energy_interface() const | core::scoring::methods::TwoBodyEnergy | virtual |
| use_extended_residue_pair_energy_interface() const | core::scoring::methods::TwoBodyEnergy | virtual |
| version() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
| ~ContextDependentTwoBodyEnergy() override | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| ~ShortRangeTwoBodyEnergy() override | core::scoring::methods::ShortRangeTwoBodyEnergy | |
| ~TwoBodyEnergy() override | core::scoring::methods::TwoBodyEnergy | |
1.8.7