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Rosetta Core
2014.16.56682
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Rosetta Core
2014.16.56682
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This is the complete list of members for core::scoring::methods::LK_BallEnergy, including all inherited members.
| accumulate_single_atom_contributions(Size const atom1, Size const atom1_type_index, Vectors const &atom1_waters, utility::vector1< Real > const &atom1_wts, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const | core::scoring::methods::LK_BallEnergy | |
| atom_type_is_charged_ | core::scoring::methods::LK_BallEnergy | private |
| atomic_interaction_cutoff() const | core::scoring::methods::LK_BallEnergy | 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 |
| calculate_lk_ball_atom_energies(Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const | core::scoring::methods::LK_BallEnergy | |
| calculate_lk_ball_atom_energies_cp(Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, etable::count_pair::CPCrossoverBehavior const &cp_crossover, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const | core::scoring::methods::LK_BallEnergy | |
| calculate_lk_desolvation_of_single_atom_by_residue(Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2) | core::scoring::methods::LK_BallEnergy | |
| calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2) | core::scoring::methods::LK_BallEnergy | |
| clone() const | core::scoring::methods::LK_BallEnergy | virtual |
| ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ContextIndependentTwoBodyEnergy | |
| d2_low_ | core::scoring::methods::LK_BallEnergy | 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(EnergyMap const &) const | core::scoring::methods::LK_BallEnergy | 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 |
| dsolv1_ | core::scoring::methods::LK_BallEnergy | private |
| EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
| EnergyMethod(EnergyMethod const &src) | core::scoring::methods::EnergyMethod | |
| etable_ | core::scoring::methods::LK_BallEnergy | private |
| etable_bins_per_A2_ | core::scoring::methods::LK_BallEnergy | private |
| 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) const | core::scoring::methods::LK_BallEnergy | |
| eval_desolvation_derivs_no_count_pair(Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv) | core::scoring::methods::LK_BallEnergy | |
| 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 &, ScoreFunction const &, EnergyMap &) const | core::scoring::methods::LK_BallEnergy | 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_lk_ball_fraction_deriv(Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, bool const evaluate_deriv, Vector &f1, Vector &f2) const | core::scoring::methods::LK_BallEnergy | |
| eval_lk_fraction(Real const d2_delta) const | core::scoring::methods::LK_BallEnergy | |
| 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::LK_BallEnergy | 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 | core::scoring::methods::LK_BallEnergy | 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::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 | core::scoring::methods::LK_BallEnergy | virtual |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) 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_lk_fractional_contribution(Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, Size &closest_water, Real &closest_water_dis2) const | core::scoring::methods::LK_BallEnergy | |
| get_lk_fractional_contribution(Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters) const | core::scoring::methods::LK_BallEnergy | |
| get_lk_fractional_contribution_for_single_water(Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const | core::scoring::methods::LK_BallEnergy | |
| indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const | core::scoring::methods::LK_BallEnergy | virtual |
| lk_ball_prefactor_ | core::scoring::methods::LK_BallEnergy | private |
| LK_BallEnergy(EnergyMethodOptions const &options) | core::scoring::methods::LK_BallEnergy | |
| LK_BallEnergy(LK_BallEnergy const &src) | core::scoring::methods::LK_BallEnergy | |
| method_type() const | core::scoring::methods::ContextIndependentTwoBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::LK_BallEnergy | virtual |
| parent typedef | core::scoring::methods::LK_BallEnergy | |
| prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const | core::scoring::methods::LK_BallEnergy | virtual |
| ramp_width_A2_ | core::scoring::methods::LK_BallEnergy | privatestatic |
| requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &) const | core::scoring::methods::LK_BallEnergy | 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(pose::Pose const &) const | core::scoring::methods::LK_BallEnergy | 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 &, EnergyMap &emap) const | core::scoring::methods::LK_BallEnergy | virtual |
| residue_pair_energy(conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap &emap) const | core::scoring::methods::LK_BallEnergy | |
| residue_pair_energy_ext(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &pairdata, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const | core::scoring::methods::LK_BallEnergy | virtual |
| ResidueType typedef | core::scoring::methods::LK_BallEnergy | |
| safe_max_dis2_ | core::scoring::methods::LK_BallEnergy | private |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| setup_d2_bounds() | core::scoring::methods::LK_BallEnergy | |
| setup_for_derivatives(pose::Pose &pose, ScoreFunction const &scfxn) const | core::scoring::methods::LK_BallEnergy | virtual |
| setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const | core::scoring::methods::LK_BallEnergy | 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 &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData &resdata) const | core::scoring::methods::LK_BallEnergy | virtual |
| setup_for_minimizing_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData const &res1data, ResSingleMinimizationData const &res2data, ResPairMinimizationData &pairdata) const | core::scoring::methods::LK_BallEnergy | virtual |
| setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const | core::scoring::methods::LK_BallEnergy | virtual |
| setup_for_scoring(pose::Pose &pose, ScoreFunction const &) const | core::scoring::methods::LK_BallEnergy | virtual |
| setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &sfxn, ResSingleMinimizationData &resdata) const | core::scoring::methods::LK_BallEnergy | 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 | |
| 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 |
| Sizes typedef | core::scoring::methods::LK_BallEnergy | |
| solv1_ | core::scoring::methods::LK_BallEnergy | private |
| solv2_ | core::scoring::methods::LK_BallEnergy | private |
| sum_deriv_contributions_for_atom_pair(Size const atom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const atom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &pose, scoring::EnergyMap const &weights, Real const cp_weight, Vector &F1, Vector &F2) const | core::scoring::methods::LK_BallEnergy | |
| sum_deriv_contributions_for_atom_pair_one_way(Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, utility::vector1< Real > const &atom1_wts, Size const atom2, conformation::Residue const &rsd2, scoring::EnergyMap const &weights, Real const weight_factor, Real const d2, Vector &F1, Vector &F2) const | core::scoring::methods::LK_BallEnergy | |
| TwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::TwoBodyEnergy | |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::LK_BallEnergy | virtual |
| use_extended_intrares_energy_interface() const | core::scoring::methods::TwoBodyEnergy | virtual |
| use_extended_residue_pair_energy_interface() const | core::scoring::methods::LK_BallEnergy | virtual |
| use_intra_dna_cp_crossover_4_ | core::scoring::methods::LK_BallEnergy | private |
| Vectors typedef | core::scoring::methods::LK_BallEnergy | |
| version() const | core::scoring::methods::LK_BallEnergy | privatevirtual |
| ~ContextIndependentTwoBodyEnergy() | core::scoring::methods::ContextIndependentTwoBodyEnergy | virtual |
| ~EnergyMethod() | core::scoring::methods::EnergyMethod | virtual |
| ~ShortRangeTwoBodyEnergy() | core::scoring::methods::ShortRangeTwoBodyEnergy | virtual |
| ~TwoBodyEnergy() | core::scoring::methods::TwoBodyEnergy | virtual |
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