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Rosetta
2021.16
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Rosetta
2021.16
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This is the complete list of members for core::energy_methods::CartesianBondedEnergy, including all inherited members.
| atomic_interaction_cutoff() const | core::energy_methods::CartesianBondedEnergy | virtual |
| 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 |
| CartesianBondedEnergy()=delete | core::energy_methods::CartesianBondedEnergy | |
| CartesianBondedEnergy(core::scoring::methods::EnergyMethodOptions const &options) | core::energy_methods::CartesianBondedEnergy | |
| CartesianBondedEnergy(CartesianBondedEnergy const &src) | core::energy_methods::CartesianBondedEnergy | |
| clone() const override | core::energy_methods::CartesianBondedEnergy | virtual |
| ContextIndependentLRTwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| db_ | core::energy_methods::CartesianBondedEnergy | private |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| defines_intrares_dof_derivatives(pose::Pose const &) const override | core::energy_methods::CartesianBondedEnergy | inlinevirtual |
| defines_intrares_energy(core::scoring::EnergyMap const &) const override | core::energy_methods::CartesianBondedEnergy | inlinevirtual |
| defines_intrares_energy_for_residue(conformation::Residue const &res) const | core::scoring::methods::TwoBodyEnergy | virtual |
| defines_residue_pair_energy(pose::Pose const &pose, Size res1, Size res2) const override | core::energy_methods::CartesianBondedEnergy | 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 |
| 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_interresidue_angle_derivs_two_from_rsd1(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_angle_derivs_two_from_rsd2(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_angle_energies_two_from_rsd1(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_angle_energies_two_from_rsd2(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_bond_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_bond_length_derivs(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_improper_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &res1params, ResidueCartBondedParameters const &res2params, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_improper_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_ring_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_interresidue_ring_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_intrares_derivatives(conformation::Residue const &rsd, core::scoring::ResSingleMinimizationData const &res_data_cache, pose::Pose const &pose, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &atom_derivs) const override | core::energy_methods::CartesianBondedEnergy | virtual |
| eval_intrares_energy(conformation::Residue const &, pose::Pose const &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &) const override | core::energy_methods::CartesianBondedEnergy | 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, core::scoring::ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap const &weights) const override | core::energy_methods::CartesianBondedEnergy | virtual |
| eval_residue_pair_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData const &min_data, pose::Pose const &, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const override | core::energy_methods::CartesianBondedEnergy | virtual |
| eval_residue_pair_derivatives_sorted(conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData const &min_data, pose::Pose const &, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | |
| eval_residue_pair_energies(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, Real phi2, Real psi2, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_score(Real val, Real K, Real val0) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_angle_derivatives(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_angle_energies(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_derivatives(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real phi, Real psi, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_energy(conformation::Residue const &rsd, ResidueCartBondedParameters const &rsdparams, Real phi, Real psi, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_improper_derivatives(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_improper_energies(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_length_derivatives(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_length_energies(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_ring_derivatives(conformation::Residue const &rsd, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_ring_energies(conformation::Residue const &rsd, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_torsion_derivatives(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r_atom_derivs) const | core::energy_methods::CartesianBondedEnergy | private |
| eval_singleres_torsion_energies(conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, pose::Pose const &pose, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | private |
| evaluate_rotamer_background_energies(conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const | core::scoring::methods::TwoBodyEnergy | virtual |
| evaluate_rotamer_background_energy_maps(conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const | core::scoring::methods::TwoBodyEnergy | virtual |
| evaluate_rotamer_intrares_energies(conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const | core::scoring::methods::TwoBodyEnergy | virtual |
| evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const | core::scoring::methods::TwoBodyEnergy | virtual |
| evaluate_rotamer_pair_energies(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const | core::scoring::methods::TwoBodyEnergy | virtual |
| 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 |
| get_db(Real k_len, Real k_ang, Real k_tors, Real k_tors_prot, Real k_tors_improper) | core::energy_methods::CartesianBondedEnergy | privatestatic |
| idealize_proline_nvs(pose::Pose &pose) const | core::energy_methods::CartesianBondedEnergy | |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::energy_methods::CartesianBondedEnergy | virtual |
| linear_bonded_potential_ | core::energy_methods::CartesianBondedEnergy | private |
| long_range_type() const override | core::energy_methods::CartesianBondedEnergy | virtual |
| LongRangeTwoBodyEnergy(EnergyMethodCreatorOP creator) | core::scoring::methods::LongRangeTwoBodyEnergy | |
| method_type() const override | core::scoring::methods::ContextIndependentLRTwoBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const override | core::energy_methods::CartesianBondedEnergy | inlinevirtual |
| parent typedef | core::energy_methods::CartesianBondedEnergy | |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| pro_nv_ | core::energy_methods::CartesianBondedEnergy | private |
| 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::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, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const override | core::energy_methods::CartesianBondedEnergy | 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 |
| residue_pair_energy_sorted(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, core::scoring::ScoreFunction const &sf, core::scoring::EnergyMap &emap) const | core::energy_methods::CartesianBondedEnergy | 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 &sfxn) const override | core::energy_methods::CartesianBondedEnergy | 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 &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const | core::scoring::methods::EnergyMethod | 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 | 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 &pose, core::scoring::ScoreFunction const &) const override | core::energy_methods::CartesianBondedEnergy | 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 |
| 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 |
| skip_cutpoints_ | core::energy_methods::CartesianBondedEnergy | private |
| 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::energy_methods::CartesianBondedEnergy | privatevirtual |
| ~CartesianBondedEnergy() override | core::energy_methods::CartesianBondedEnergy | |
| ~ContextIndependentLRTwoBodyEnergy() override | core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| ~LongRangeTwoBodyEnergy() override | core::scoring::methods::LongRangeTwoBodyEnergy | |
| ~TwoBodyEnergy() override | core::scoring::methods::TwoBodyEnergy |
1.8.7