| all_nmer_pssms_ | core::scoring::methods::NMerPSSMEnergy | private |
| atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| clone() const override | core::scoring::methods::NMerPSSMEnergy | 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 |
| 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_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::NMerPSSMEnergy | 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_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 |
| gate_pssm_scores(bool const ) | core::scoring::methods::NMerPSSMEnergy | |
| gate_pssm_scores_ | core::scoring::methods::NMerPSSMEnergy | private |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::scoring::methods::NMerPSSMEnergy | virtual |
| initialize_from_options() | core::scoring::methods::NMerPSSMEnergy | private |
| method_type() const override | core::scoring::methods::ContextIndependentOneBodyEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const override | core::scoring::methods::NMerPSSMEnergy | inlinevirtual |
| n_pssms() const | core::scoring::methods::NMerPSSMEnergy | |
| nmer_cterm_ | core::scoring::methods::NMerPSSMEnergy | private |
| nmer_length(core::Size const ) | core::scoring::methods::NMerPSSMEnergy | |
| nmer_length_ | core::scoring::methods::NMerPSSMEnergy | private |
| nmer_pssm_scorecut(core::Real const ) | core::scoring::methods::NMerPSSMEnergy | |
| nmer_pssm_scorecut_ | core::scoring::methods::NMerPSSMEnergy | private |
| NMerPSSMEnergy() | core::scoring::methods::NMerPSSMEnergy | |
| NMerPSSMEnergy(utility::vector1< std::map< core::chemical::AA, utility::vector1< core::Real > > > const &all_nmer_pssms_in) | core::scoring::methods::NMerPSSMEnergy | |
| NMerPSSMEnergy(core::Size const nmer_length, bool const gate_pssm_scores, core::Real const nmer_pssm_scorecut, utility::vector1< std::string > const &pssm_fname_vec) | core::scoring::methods::NMerPSSMEnergy | |
| OneBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::OneBodyEnergy | |
| operator==(NMerPSSMEnergy const &) const | core::scoring::methods::NMerPSSMEnergy | virtual |
| parent typedef | core::scoring::methods::NMerPSSMEnergy | |
| 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 |
| pssm_energy_at_frame_seqpos(core::Size const, core::chemical::AA const, core::Size const ) const | core::scoring::methods::NMerPSSMEnergy | |
| read_nmer_pssm(std::string) | core::scoring::methods::NMerPSSMEnergy | |
| read_nmer_pssm_fname_vector(utility::vector1< std::string > const &) | core::scoring::methods::NMerPSSMEnergy | |
| read_nmer_pssm_list(std::string) | core::scoring::methods::NMerPSSMEnergy | |
| read_nmer_pssms_from_options() | core::scoring::methods::NMerPSSMEnergy | 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_during_minimization(pose::Pose const &pose) const | core::scoring::methods::OneBodyEnergy | virtual |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| residue_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const override | core::scoring::methods::NMerPSSMEnergy | 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, basic::datacache::BasicDataCache &res_data_cache) 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 &, basic::datacache::BasicDataCache &, 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_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 &, 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 |
| 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 |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| 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 |
| version() const override | core::scoring::methods::NMerPSSMEnergy | privatevirtual |
| ~NMerPSSMEnergy() override | core::scoring::methods::NMerPSSMEnergy | |
| ~OneBodyEnergy() override | core::scoring::methods::OneBodyEnergy | |
1.8.7