|
Rosetta
|
This is the complete list of members for core::scoring::lkball::LK_DomeEnergy, including all inherited members.
| ::LK_DomeEnergyTests class | core::scoring::lkball::LK_DomeEnergy | friend |
| accumulate_single_atom_contributions(Size const atom1, Size const, Size atom1_n_attached_waters, Size atom1_start_water, WaterCoords const &atom1_waters, WaterOcclusions const &atom1_occlusions, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_water, EnergyMap &emap) const | core::scoring::lkball::LK_DomeEnergy | |
| atomic_interaction_cutoff() const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| atomistic_energy(core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const | core::scoring::methods::EnergyMethod | virtual |
| atomistic_pair_energy(core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const | core::scoring::methods::EnergyMethod | 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 |
| ball_overlap_width_A2_ | core::scoring::lkball::LK_DomeEnergy | private |
| 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 |
| clone() const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| ContextDependentTwoBodyEnergy(EnergyMethodCreatorOP creator) | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| d2_low_ | core::scoring::lkball::LK_DomeEnergy | private |
| debug_disable_count_pair_ | core::scoring::lkball::LK_DomeEnergy | mutable |
| debug_dome_waters_ | core::scoring::lkball::LK_DomeEnergy | mutableprivate |
| 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(EnergyMap const &weights) const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| 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 override | core::scoring::lkball::LK_DomeEnergy | virtual |
| divides_backbone_and_sidechain_energetics() const | core::scoring::methods::ShortRangeTwoBodyEnergy | virtual |
| dlk_frac_sigmoid(Real distance) const | core::scoring::lkball::LK_DomeEnergy | |
| dmy_lk_fraction(Real distance) const | core::scoring::lkball::LK_DomeEnergy | |
| dome_water_dist2(Vector const &base_atom_xyz, Vector const &water, Vector const &other_atom_xyz, Real &water_atom_distance, Vector &wadj_water) const | core::scoring::lkball::LK_DomeEnergy | |
| dump_dome_bridge_waters_ | core::scoring::lkball::LK_DomeEnergy | mutable |
| dump_dome_waters_ | core::scoring::lkball::LK_DomeEnergy | mutable |
| 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_d_lk_fraction_dr_over_r(Real const d2_delta, Real const width) const | core::scoring::lkball::LK_DomeEnergy | |
| 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, ScoreFunction const &sfxn, EnergyMap &emap) const override | core::scoring::lkball::LK_DomeEnergy | 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_lk_fraction(Real const d2_delta, Real const width) const | core::scoring::lkball::LK_DomeEnergy | |
| 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 override | core::scoring::lkball::LK_DomeEnergy | 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 |
| fill_occlusions_1way(conformation::Residue const &rsd1, LKD_ResidueInfo &rsd1_info, conformation::Residue const &rsd2) const | core::scoring::lkball::LK_DomeEnergy | |
| fill_static_occlusions(pose::Pose &pose) const | core::scoring::lkball::LK_DomeEnergy | |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_after_minimizing(pose::Pose &pose) const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const | core::scoring::methods::EnergyMethod | virtual |
| get_avail(Real occl) const | core::scoring::lkball::LK_DomeEnergy | |
| get_dome_water(Vector const &base_atom_xyz, Vector const &water, Vector const &other_atom_xyz, Real &water_atom_distance, Vector &wadj_water) const | core::scoring::lkball::LK_DomeEnergy | |
| get_lkb_bridge2_fractional_1way(Size n_atom1_waters, Size atom1_start_water, Size n_atom2_waters, Size atom2_start_water, WaterCoords const &atom1_waters, WaterCoords const &atom2_waters, WaterOcclusions const &atom1_occlusions) const | core::scoring::lkball::LK_DomeEnergy | |
| get_lkd_bridge_fractional_1way(Vector const &atom1_xyz, Size n_atom1_waters, Size atom1_start_water, Size n_atom2_waters, Size atom2_start_water, WaterCoords const &atom1_waters, WaterCoords const &atom2_waters, WaterOcclusions const &atom1_occlusions) const | core::scoring::lkball::LK_DomeEnergy | |
| get_lkd_frac_dome_dist(Real dw_dist, Real atom2_type) const | core::scoring::lkball::LK_DomeEnergy | |
| get_sol_value(chemical::AtomType const &at, Size nattached_waters) const | core::scoring::lkball::LK_DomeEnergy | |
| h2o_radius_ | core::scoring::lkball::LK_DomeEnergy | private |
| has_atomistic_energies() const | core::scoring::methods::EnergyMethod | virtual |
| has_atomistic_pairwise_energies() const | core::scoring::methods::EnergyMethod | virtual |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::scoring::lkball::LK_DomeEnergy | inlinevirtual |
| lk_ball() const | core::scoring::lkball::LK_DomeEnergy | |
| lk_ball_ | core::scoring::lkball::LK_DomeEnergy | private |
| LK_DomeEnergy(core::scoring::methods::EnergyMethodOptions const &options) | core::scoring::lkball::LK_DomeEnergy | |
| lk_frac_sigmoid(Real distance) const | core::scoring::lkball::LK_DomeEnergy | |
| max_angle_cos_ | core::scoring::lkball::LK_DomeEnergy | private |
| max_angle_sin_ | core::scoring::lkball::LK_DomeEnergy | private |
| method_type() const override | core::scoring::methods::ContextDependentTwoBodyEnergy | virtual |
| min_angle_cos_ | core::scoring::lkball::LK_DomeEnergy | private |
| min_angle_sin_ | core::scoring::lkball::LK_DomeEnergy | private |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| minimizing_ | core::scoring::lkball::LK_DomeEnergy | mutableprivate |
| my_lk_fraction(Real distance) const | core::scoring::lkball::LK_DomeEnergy | |
| my_setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, basic::datacache::BasicDataCache &residue_data_cache) const | core::scoring::lkball::LK_DomeEnergy | |
| occlusion_max() const | core::scoring::lkball::LK_DomeEnergy | |
| occlusion_max_ | core::scoring::lkball::LK_DomeEnergy | private |
| occlusion_min() const | core::scoring::lkball::LK_DomeEnergy | |
| occlusion_min_ | core::scoring::lkball::LK_DomeEnergy | private |
| overlap_width_A2_ | core::scoring::lkball::LK_DomeEnergy | private |
| packing_ | core::scoring::lkball::LK_DomeEnergy | mutableprivate |
| parent typedef | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| poly_params_ | core::scoring::lkball::LK_DomeEnergy | private |
| 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 |
| ramp_width_A2_ | core::scoring::lkball::LK_DomeEnergy | private |
| requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &) const override | core::scoring::lkball::LK_DomeEnergy | 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 &) const override | core::scoring::lkball::LK_DomeEnergy | 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, ScoreFunction const &sfxn, EnergyMap &emap) const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| residue_pair_energy(conformation::Residue const &rsd1, LKD_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKD_ResidueInfo const &rsd2_info, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::lkball::LK_DomeEnergy | |
| 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 |
| score_types_ | core::scoring::methods::EnergyMethod | private |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| setup_d2_bounds() | core::scoring::lkball::LK_DomeEnergy | |
| 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 &, ScoreFunction const &, ResSingleMinimizationData &, basic::datacache::BasicDataCache &residue_data_cache) const override | core::scoring::lkball::LK_DomeEnergy | 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 override | core::scoring::lkball::LK_DomeEnergy | 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 &, ScoreFunction const &, kinematics::MinimizerMapBase const &, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData &pair_data) const override | core::scoring::lkball::LK_DomeEnergy | virtual |
| setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const override | core::scoring::lkball::LK_DomeEnergy | 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 &, scoring::ScoreFunction const &) const override | core::scoring::lkball::LK_DomeEnergy | 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 |
| 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::TwoBodyEnergy | |
| 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 |
| setup_poly_params() | core::scoring::lkball::LK_DomeEnergy | |
| 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 |
| single_water_atom_fractions(Vector const &base_atom_xyz, Vector const &water_xyz, Vector const &other_atom_xyz, Size other_atom_type_index, Real &lk_dome_iso_frac, Real &lk_dome_frac) const | core::scoring::lkball::LK_DomeEnergy | |
| single_water_water_bridge2_fraction_1way(Vector const &water_xyz, Vector const &other_water_xyz) const | core::scoring::lkball::LK_DomeEnergy | |
| single_water_water_fraction_1way(Vector const &base_atom_xyz, Vector const &water_xyz, Vector const &other_water_xyz) const | core::scoring::lkball::LK_DomeEnergy | |
| sum_deriv_contributions_for_heavyatom_pair(Real const d2, Size const heavyatom1, conformation::Residue const &rsd1, LKD_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKD_ResidueInfo const &rsd2_info, pose::Pose const &, EnergyMap const &weights, Real const cp_weight, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const | core::scoring::lkball::LK_DomeEnergy | |
| sum_deriv_contributions_for_heavyatom_pair_one_way(Size const heavyatom1, conformation::Residue const &rsd1, LKD_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKD_ResidueInfo const &rsd2_info, EnergyMap const &weights, Real const weight_factor, Real const d2, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const | core::scoring::lkball::LK_DomeEnergy | |
| TwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::TwoBodyEnergy | |
| update_cached_lkb_resinfo(conformation::Residue const &rsd, basic::datacache::BasicDataCache &residue_data_cache, bool compute_derivs, bool clear_occlusions) const | core::scoring::lkball::LK_DomeEnergy | |
| 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::scoring::lkball::LK_DomeEnergy | virtual |
| w_dist() const | core::scoring::lkball::LK_DomeEnergy | |
| w_dist_ | core::scoring::lkball::LK_DomeEnergy | private |
| water_adjust() const | core::scoring::lkball::LK_DomeEnergy | |
| water_adjust_ | core::scoring::lkball::LK_DomeEnergy | private |
| water_atom_interaction_cutoff() const | core::scoring::lkball::LK_DomeEnergy | |
| water_atom_interaction_cutoff2() const | core::scoring::lkball::LK_DomeEnergy | |
| water_water_bridge_cutoff2() const | core::scoring::lkball::LK_DomeEnergy | |
| ~ContextDependentTwoBodyEnergy() override | core::scoring::methods::ContextDependentTwoBodyEnergy | |
| ~ShortRangeTwoBodyEnergy() override | core::scoring::methods::ShortRangeTwoBodyEnergy | |
| ~TwoBodyEnergy() override | core::scoring::methods::TwoBodyEnergy |
1.9.1