| aa_encoder_ | core::scoring::methods::NMerSVMEnergy | private |
| add_encoded_termini(std::string const, core::Size const, utility::vector1< core::Real > &) const | core::scoring::methods::NMerSVMEnergy | |
| add_pssm_features(std::string const, core::Size const, utility::vector1< core::Real > &) const | core::scoring::methods::NMerSVMEnergy | |
| all_nmer_svms_ | core::scoring::methods::NMerSVMEnergy | private |
| clone() const | core::scoring::methods::NMerSVMEnergy | virtual |
| ContextIndependentOneBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ContextIndependentOneBodyEnergy | |
| defines_dof_derivatives(pose::Pose const &p) const | core::scoring::methods::OneBodyEnergy | virtual |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| defines_score_for_residue(conformation::Residue const &) const | core::scoring::methods::OneBodyEnergy | virtual |
| encode_aa_string(std::string const ) const | core::scoring::methods::NMerSVMEnergy | |
| encode_nmer(std::string const, core::Size const, core::Size const ) const | core::scoring::methods::NMerSVMEnergy | |
| encode_wtd_avg_aa_string(std::string const, utility::vector1< core::Real > const ) const | core::scoring::methods::NMerSVMEnergy | |
| EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
| EnergyMethod(EnergyMethod const &src) | 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_dof_derivative(id::DOF_ID const &dof_id, id::TorsionID const &tor_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const | core::scoring::methods::NMerSVMEnergy | virtual |
| eval_residue_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::OneBodyEnergy | virtual |
| eval_residue_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::OneBodyEnergy | 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 |
| gate_svm_scores(bool const ) | core::scoring::methods::NMerSVMEnergy | |
| gate_svm_scores_ | core::scoring::methods::NMerSVMEnergy | private |
| get_residue_energy_by_svm(core::pose::Pose const &, core::Size const &, core::Real &, utility::vector1< core::Real > &) const | core::scoring::methods::NMerSVMEnergy | |
| get_svm_nodes(utility::vector1< core::Real > const ) const | core::scoring::methods::NMerSVMEnergy | |
| indicate_required_context_graphs(utility::vector1< bool > &) const | core::scoring::methods::NMerSVMEnergy | virtual |
| initialize_from_options() | core::scoring::methods::NMerSVMEnergy | private |
| method_type() const | core::scoring::methods::ContextIndependentOneBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::NMerSVMEnergy | inlinevirtual |
| n_svms() const | core::scoring::methods::NMerSVMEnergy | |
| nmer_cterm_ | core::scoring::methods::NMerSVMEnergy | private |
| nmer_length(core::Size const ) | core::scoring::methods::NMerSVMEnergy | |
| nmer_length() const | core::scoring::methods::NMerSVMEnergy | |
| nmer_length_ | core::scoring::methods::NMerSVMEnergy | private |
| nmer_pssm_ | core::scoring::methods::NMerSVMEnergy | private |
| nmer_svm_scorecut(core::Real const ) | core::scoring::methods::NMerSVMEnergy | |
| nmer_svm_scorecut_ | core::scoring::methods::NMerSVMEnergy | private |
| NMerSVMEnergy() | core::scoring::methods::NMerSVMEnergy | |
| NMerSVMEnergy(utility::vector1< std::string > const &svm_fnames) | core::scoring::methods::NMerSVMEnergy | |
| OneBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::OneBodyEnergy | |
| parent typedef | core::scoring::methods::NMerSVMEnergy | |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| read_aa_encoding_matrix(std::string const ) | core::scoring::methods::NMerSVMEnergy | |
| read_nmer_svm(std::string const ) | core::scoring::methods::NMerSVMEnergy | |
| read_nmer_svm_list(std::string const ) | core::scoring::methods::NMerSVMEnergy | |
| read_nmer_svms_from_options() | core::scoring::methods::NMerSVMEnergy | private |
| requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity(pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| residue_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const | core::scoring::methods::NMerSVMEnergy | virtual |
| residue_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const | core::scoring::methods::OneBodyEnergy | virtual |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| 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) const | core::scoring::methods::OneBodyEnergy | 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 &, ScoreFunction const &, kinematics::MinimizerMapBase const &, ResSingleMinimizationData &) const | core::scoring::methods::OneBodyEnergy | virtual |
| setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_scoring(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const | core::scoring::methods::OneBodyEnergy | virtual |
| term_length(core::Size const ) | core::scoring::methods::NMerSVMEnergy | |
| term_length() const | core::scoring::methods::NMerSVMEnergy | |
| term_length_ | core::scoring::methods::NMerSVMEnergy | private |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| use_extended_residue_energy_interface() const | core::scoring::methods::OneBodyEnergy | virtual |
| use_pssm_features(bool const ) | core::scoring::methods::NMerSVMEnergy | |
| use_pssm_features_ | core::scoring::methods::NMerSVMEnergy | private |
| version() const | core::scoring::methods::NMerSVMEnergy | privatevirtual |
| ~EnergyMethod() | core::scoring::methods::EnergyMethod | virtual |
| ~NMerSVMEnergy() | core::scoring::methods::NMerSVMEnergy | virtual |
| ~OneBodyEnergy() | core::scoring::methods::OneBodyEnergy | virtual |
1.8.7