| atomic_interaction_cutoff() const | core::scoring::methods::WholeStructureEnergy | inlinevirtual |
| calculate_energy(utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &rotamer_ids, core::Size const substitution_position=0) const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| clean_up_residuearrayannealableenergy_after_packing(core::pose::Pose &pose) | core::scoring::annealing::ResidueArrayAnnealableEnergy | virtual |
| clone() const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| commit_considered_substitution() override | core::energy_methods::MHCEpitopeEnergy | virtual |
| considered_total_ | core::energy_methods::MHCEpitopeEnergy | mutableprivate |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| difference_btw_cached_and_full_rescore(utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > const &masks, utility::vector1< core::Real > const &cst_weights) const | core::energy_methods::MHCEpitopeEnergy | private |
| disabled_ | core::energy_methods::MHCEpitopeEnergy | mutableprivate |
| 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 |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_after_minimizing(pose::Pose &pose) const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| finalize_total_energy(core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| full_rescore(utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > const &masks, utility::vector1< core::Real > const &cst_weights, bool cache, bool native) const | core::energy_methods::MHCEpitopeEnergy | private |
| get_helpers_from_pose(core::pose::Pose const &pose, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > &masks, utility::vector1< core::Real > &cst_weights) const | core::energy_methods::MHCEpitopeEnergy | private |
| indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| method_type() const override | core::scoring::methods::WholeStructureEnergy | virtual |
| MHCEpitopeEnergy(core::scoring::methods::EnergyMethodOptions const &options) | core::energy_methods::MHCEpitopeEnergy | |
| MHCEpitopeEnergy(MHCEpitopeEnergy const &src) | core::energy_methods::MHCEpitopeEnergy | |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| pad | core::energy_methods::MHCEpitopeEnergy | private |
| parent typedef | core::scoring::methods::WholeStructureEnergy | |
| parent1 typedef | core::energy_methods::MHCEpitopeEnergy | |
| parent2 typedef | core::energy_methods::MHCEpitopeEnergy | |
| 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 |
| report() const | core::energy_methods::MHCEpitopeEnergy | |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| ResidueArrayAnnealableEnergy() | core::scoring::annealing::ResidueArrayAnnealableEnergy | |
| ResidueArrayAnnealableEnergy(ResidueArrayAnnealableEnergy const &src) | core::scoring::annealing::ResidueArrayAnnealableEnergy | |
| score_caches_ | core::energy_methods::MHCEpitopeEnergy | private |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| set_up_residuearrayannealableenergy_for_packing(core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn) override | core::energy_methods::MHCEpitopeEnergy | virtual |
| setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_minimizing(pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap) const override | core::energy_methods::MHCEpitopeEnergy | 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, basic::datacache::BasicDataCache &residue_data_cache) const | core::scoring::methods::EnergyMethod | virtual |
| setup_helper_cop(core::Size const index) const | core::energy_methods::MHCEpitopeEnergy | inlineprivate |
| setup_helper_count() const | core::energy_methods::MHCEpitopeEnergy | inlineprivate |
| setup_helper_masks_for_packing_ | core::energy_methods::MHCEpitopeEnergy | private |
| setup_helper_weights_for_packing_ | core::energy_methods::MHCEpitopeEnergy | private |
| setup_helpers_ | core::energy_methods::MHCEpitopeEnergy | private |
| setup_helpers_for_packing_ | core::energy_methods::MHCEpitopeEnergy | private |
| setup_symmetry(core::pose::Pose const &pose) const | core::energy_methods::MHCEpitopeEnergy | private |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| symm_ | core::energy_methods::MHCEpitopeEnergy | mutableprivate |
| symm_multipliers_ | core::energy_methods::MHCEpitopeEnergy | mutableprivate |
| total_ | core::energy_methods::MHCEpitopeEnergy | mutableprivate |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| update_score(utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position, utility::vector1< core::Real > const &cst_weights) const | core::energy_methods::MHCEpitopeEnergy | private |
| version() const override | core::energy_methods::MHCEpitopeEnergy | virtual |
| WholeStructureEnergy(EnergyMethodCreatorOP) | core::scoring::methods::WholeStructureEnergy | |
| ~MHCEpitopeEnergy() override | core::energy_methods::MHCEpitopeEnergy | |
| ~ResidueArrayAnnealableEnergy() | core::scoring::annealing::ResidueArrayAnnealableEnergy | virtual |
| ~WholeStructureEnergy() override | core::scoring::methods::WholeStructureEnergy | inline |
1.8.7