| ::BuriedUnsatPenaltySymmetricTests class | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | friend |
| ::BuriedUnsatPenaltyTests class | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | friend |
| add_to_list_of_partners_of_changed_nodes(graph::BuriedUnsatPenaltyGraphCOP curstate_graph, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > &changed_node_partners) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| atomic_interaction_cutoff() const | core::scoring::methods::WholeStructureEnergy | inlinevirtual |
| BuriedUnsatPenalty(core::scoring::methods::EnergyMethodOptions const &options) | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| 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::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| calculate_penalty_once_almost_from_scratch_using_reference_graph(utility::vector1< core::conformation::ResidueCOP > const &resvect, graph::BuriedUnsatPenaltyGraph const &reference_graph, core::Size const symm_multiplier) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| calculate_penalty_once_from_scratch(core::pose::Pose const &pose) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| clean_up_residuearrayannealableenergy_after_packing(core::pose::Pose &pose) override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| clone() const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| commit_considered_substitution() override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| compute_penalty(core::Size const unsat_acceptor_count, core::Size const unsat_donor_count, core::Size const unsat_acceptor_and_donor_count, core::Size const oversat_acceptor_count, core::Size const oversat_donor_count, core::Size const oversat_acceptor_and_donor_count) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| curstate_graph_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| decrement_counts(core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< graph::BuriedUnsatPenaltyNodeDataCOP > const &old_data, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| disabled_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | 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(core::pose::Pose &pose) const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| finalize_total_energy(core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &totals) const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| graph_options_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| hbond_options_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| increment_counts(core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| initialize_curstate_graph(core::pose::Pose const &pose) | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| initialize_curstate_graph(utility::vector1< core::conformation::ResidueCOP > const &resvect) | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| method_type() const override | core::scoring::methods::WholeStructureEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| nres_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| num_symmetric_copies_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| oversat_acceptor_and_donor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| oversat_acceptor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| oversat_donor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| parent typedef | core::scoring::methods::WholeStructureEnergy | |
| parent1 typedef | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| parent2 typedef | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| prevent_pruning_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| provide_pymol_commands_to_show_groups(std::ostream &out, core::pose::Pose const &pose) const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| report() const | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| 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_types() const | core::scoring::methods::EnergyMethod | inline |
| set_prevent_pruning(bool const setting) | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | 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::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_minimizing(core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap) const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | 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 |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| symmetric_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| unsat_acceptor_and_donor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| unsat_acceptor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| unsat_donor_count_lastaccepted_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | mutableprivate |
| unsat_graph_ | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | private |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| version() const override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | virtual |
| WholeStructureEnergy(EnergyMethodCreatorOP) | core::scoring::methods::WholeStructureEnergy | |
| ~BuriedUnsatPenalty() override | core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty | |
| ~ResidueArrayAnnealableEnergy() | core::scoring::annealing::ResidueArrayAnnealableEnergy | virtual |
| ~WholeStructureEnergy() override | core::scoring::methods::WholeStructureEnergy | inline |
1.8.7