| add_background_edge(int first_class_node_index, int bg_node_index) | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| AdditionalBackgroundNodesInteractionGraph(int num_nodes) | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| alt_state_being_considered_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| BackgroundEdgeList typedef | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| BackgroundEdgeListConstIter typedef | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| BackgroundEdgeListIter typedef | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| BackgroundNodeVector typedef | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| bg_node_2_resid(Size node_index) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| bgenumeration_2_resid_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| blanket_assign_state_0() override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| calculate_alt_state_npd_hbond_score() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| calculate_npd_hbond_deltaE() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| calculated_npd_hbond_deltaE_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| clean_up_bgtfc_edges_marked_for_deletion() | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| commit_considered_substitution() override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| COMMIT_LIMIT_BETWEEN_UPDATES | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | privatestatic |
| consider_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| count_dynamic_memory() const override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| count_static_memory() const override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| create_background_edge(int fc_node_index, int bg_node_index) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protectedvirtual |
| create_background_node(int node_index) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protectedvirtual |
| create_new_edge(int index1, int index2) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protected |
| create_new_node(int node_index, int num_states) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protected |
| decide_procrastinate_npd_hbond_computations(Real const pd_deltaE, Real const threshold) const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| deltaE_for_substitution_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| deltaE_threshold_for_avoiding_npd_hbond_calcs_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| drop_background_edge(BackgroundEdgeListIter iter) | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| find_background_edge(int first_class_node_index, int bg_node_index) const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| get_background_node(int index) const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inlineprotected |
| get_bg_edge_list_begin() const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inlineprotected |
| get_bg_edge_list_end() const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inlineprotected |
| get_edge_memory_usage() const override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| get_energy_current_state_assignment() override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| get_energy_sum_for_vertex_group(Size group_id) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | virtual |
| get_network_state() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| get_npd_hbond_bg_node(int index) const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| get_npd_hbond_bg_node(int index) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| get_npd_hbond_node(int index) const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| get_npd_hbond_node(int index) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| get_npd_hbond_score() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| get_num_background_nodes() const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inline |
| get_num_bg_edges() const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inlineprotected |
| getTotalMemoryUsage() const override | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| hbond_database() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| hbond_database_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| hbond_options() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| hbond_options_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| hbonding_to_res_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| hbonding_to_res_vector() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| hbonds_queue_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| initialize(pack_basic::RotamerSetsBase const &rot_sets) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| last_considered_substitution_accepted_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| neighbor_graph_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| node_considering_alt_state_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hb_weight(scoring::hbonds::HBEvalType eval_type, bool intra_res) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| npd_hbond_energy_alternate_state_assignment_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hbond_energy_current_state_assignment_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hbond_score_min_last_100_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hbond_score_min_recent_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hbond_score_weights_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| npd_hbond_set() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| npd_hbond_set_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| NPDHBondInteractionGraph(int num_nodes) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| NPDHBondInteractionGraph()=delete | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| NPDHBondInteractionGraph(NPDHBondInteractionGraph< V, E, G > const &)=delete | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| num_commits_since_last_update_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| num_npd_hbond_comps_later_made_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | privatestatic |
| num_npd_hbond_comps_procrastinated_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | privatestatic |
| num_residues_assigned_as_background_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| num_state_substitutions_considered_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | privatestatic |
| num_substitutions_since_npd_hbond_min_update_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| num_total_residues_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| observed_sufficient_npd_hbond_E_to_predict_min_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| operator=(NPDHBondInteractionGraph< V, E, G > const &)=delete | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| packer_neighbor_graph() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| packer_task() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| packer_task_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| parent typedef | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| pose() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| pose_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| prepare_graph_for_simulated_annealing() override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| prepared_for_simulated_annealing_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| print() const override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| print_internal_energies_for_current_state_assignment() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| print_npd_hbond_avoidance_stats() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | static |
| reset_from_previous_delta_npd_hbond_comp() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| reset_npd_hbond_avoidance_stats() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | static |
| resid_2_bgenumeration_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| return_hbond_to_queue(NPDHBondOP const &hbond) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| rotamer_sets() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| rotamer_sets_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| scorefxn() const | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | inline |
| scorefxn_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| set_errorfull_deltaE_threshold(core::PackerEnergy deltaE) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_network_state(ObjexxFCL::FArray1_int &node_states) override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_num_background_nodes(int num_bg_nodes) | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| set_num_background_residues(Size num_background_residues) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_num_residues_in_protein(Size num_res) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_observed_sufficient_boolean_true() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_packer_neighbor_graph(utility::graph::Graph const &neighbor_graph) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_packer_task(task::PackerTask const &task) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_pose(pose::Pose const &pose) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_residue_as_background_residue(int residue) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_rotamer_sets(rotamer_set::RotamerSets const &rotsets) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| set_score_function(scoring::ScoreFunction const &scorefxn) | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| total_energy_alternate_state_assignment_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| total_energy_current_state_assignment_ | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | private |
| track_npd_hbond_E_min() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protected |
| unused_hbond() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
| update_internal_energy_totals_npd_hbond() | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | protected |
| ~AdditionalBackgroundNodesInteractionGraph() override | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| ~NPDHBondInteractionGraph() override | core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > | |
1.8.7