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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::GoapEnergy, including all inherited members.
| angle_table_ | core::energy_methods::GoapEnergy | private |
| atomic_interaction_cutoff() const override | core::energy_methods::GoapEnergy | 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 |
| calc_cosineang(Vector const &v1, Vector const &v2) const | core::energy_methods::GoapEnergy | inlineprivate |
| calc_phi(Vector const &v1, Vector const &v2, Vector const &v3) const | core::energy_methods::GoapEnergy | inlineprivate |
| calculate_dipoles(pose::Pose const &pose, conformation::Residue const &rsd1, GoapRsdTypeCOP rsdtype, Size const atm1, Vector &xn, Vector &xd) const | core::energy_methods::GoapEnergy | private |
| clone() const override | core::energy_methods::GoapEnergy | inlinevirtual |
| ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ContextIndependentTwoBodyEnergy | |
| continuous() const | core::energy_methods::GoapEnergy | inline |
| continuous_ | core::energy_methods::GoapEnergy | 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(core::scoring::EnergyMap const &) const override | core::energy_methods::GoapEnergy | 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 |
| distance_table_ | core::energy_methods::GoapEnergy | private |
| distbin(Real const dis) | core::energy_methods::GoapEnergy | inlineprivate |
| distbin_map(Size i) const | core::energy_methods::GoapEnergy | inline |
| distbin_map_ | core::energy_methods::GoapEnergy | private |
| 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 &, pose::Pose const &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &) const override | core::energy_methods::GoapEnergy | inlinevirtual |
| 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_res(Size const resno) const | core::energy_methods::GoapEnergy | inline |
| eval_res_ | core::energy_methods::GoapEnergy | mutableprivate |
| eval_residue_pair_derivatives(conformation::Residue const &, conformation::Residue const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData const &, pose::Pose const &, core::scoring::EnergyMap const &, utility::vector1< core::scoring::DerivVectorPair > &, utility::vector1< core::scoring::DerivVectorPair > &) const override | core::energy_methods::GoapEnergy | virtual |
| 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 override | core::scoring::methods::ShortRangeTwoBodyEnergy | 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 override | core::scoring::methods::ShortRangeTwoBodyEnergy | 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 override | core::scoring::methods::ShortRangeTwoBodyEnergy | 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_angle_score(Real const dist, Size const atype1, Size const atype2, Vector const &xn1, Vector const &xd1, Vector const &xn2, Vector const &xd2, Vector const &xyz1, Vector const &xyz2) const | core::energy_methods::GoapEnergy | private |
| get_distance_score(Real const dist, Size const atype1, Size const atype2) const | core::energy_methods::GoapEnergy | private |
| GoapEnergy(core::scoring::methods::EnergyMethodOptions const &options) | core::energy_methods::GoapEnergy | |
| GoapEnergy(GoapEnergy const &src) | core::energy_methods::GoapEnergy | |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::energy_methods::GoapEnergy | inlinevirtual |
| max_dis() const | core::energy_methods::GoapEnergy | inline |
| max_dis_ | core::energy_methods::GoapEnergy | private |
| method_type() const override | core::scoring::methods::ContextIndependentTwoBodyEnergy | virtual |
| MIN_SEQ_SEPARATIONS | core::energy_methods::GoapEnergy | private |
| minimize_in_whole_structure_context(pose::Pose const &) const override | core::energy_methods::GoapEnergy | inlinevirtual |
| N_ANGLE1_BINS | core::energy_methods::GoapEnergy | private |
| N_ANGLE2_BINS | core::energy_methods::GoapEnergy | private |
| N_ATMTYPES | core::energy_methods::GoapEnergy | private |
| N_DISTANCE_BINS | core::energy_methods::GoapEnergy | private |
| parent typedef | core::energy_methods::GoapEnergy | |
| 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 |
| read_angle_definitions(std::string const &connection_file) | core::energy_methods::GoapEnergy | private |
| read_Goap_parameters() | core::energy_methods::GoapEnergy | private |
| read_potential_values(std::string const &distance_file, std::string const &angle_file) | core::energy_methods::GoapEnergy | private |
| 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 &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const override | core::energy_methods::GoapEnergy | 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 |
| rsdtypemap_ | core::energy_methods::GoapEnergy | mutableprivate |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| set_default() | core::energy_methods::GoapEnergy | private |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| setup_for_derivatives(pose::Pose &, core::scoring::ScoreFunction const &) const override | core::energy_methods::GoapEnergy | 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 override | core::energy_methods::GoapEnergy | 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::GoapEnergy | 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::energy_methods::GoapEnergy | inlinevirtual |
| xd(Size const resno, Size const atmno) const | core::energy_methods::GoapEnergy | inline |
| xd_ | core::energy_methods::GoapEnergy | mutableprivate |
| xn(Size const resno, Size const atmno) const | core::energy_methods::GoapEnergy | inline |
| xn_ | core::energy_methods::GoapEnergy | mutableprivate |
| ~ContextIndependentTwoBodyEnergy() override | core::scoring::methods::ContextIndependentTwoBodyEnergy | |
| ~GoapEnergy() override | core::energy_methods::GoapEnergy | |
| ~ShortRangeTwoBodyEnergy() override | core::scoring::methods::ShortRangeTwoBodyEnergy | |
| ~TwoBodyEnergy() override | core::scoring::methods::TwoBodyEnergy |
1.8.7