| 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_bg_bg_exhpobeolap_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| alt_state_being_considered_ | core::pack::interaction_graph::HPatchInteractionGraph< 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_bg_atom_atom_overlaps_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bg_bg_respairs_w_hphobe_olap_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bg_exp_hphobe_djs_offsets_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bg_n_exp_hphobes_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bg_node_2_resid(Size node_index) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| bg_nodes_near_rotsub_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bg_nodes_near_rotsub_bool_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| bgenumeration_2_resid_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| blanket_assign_state_0() override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| calculate_alt_state_hpatch_score() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| calculate_hpatch_deltaE() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| calculated_hpatch_deltaE_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| carbon_atom | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| clean_up_bgtfc_edges_marked_for_deletion() | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| commit_considered_substitution() override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| COMMIT_LIMIT_BETWEEN_UPDATES | core::pack::interaction_graph::HPatchInteractionGraph< 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::HPatchInteractionGraph< V, E, G > | |
| count_dynamic_memory() const override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| count_static_memory() const override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| create_background_edge(int fc_node_index, int bg_node_index) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protectedvirtual |
| create_background_node(int node_index) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protectedvirtual |
| create_new_edge(int index1, int index2) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protected |
| create_new_node(int node_index, int num_states) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protected |
| curr_bg_bg_exhpobeolap_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| decide_procrastinate_hpatch_computations(Real const pd_deltaE, Real const threshold) const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| deltaE_for_substitution_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| deltaE_threshold_for_avoiding_hpatch_calcs_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| detect_background_residue_and_first_class_residue_overlap() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| djs_id_2_hphobe_index_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| djs_rep_node_index_2_cc_index_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| drop_background_edge(BackgroundEdgeListIter iter) | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| ep_sasa_for_djs_node_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| fc_exp_hphobe_djs_offsets_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| fc_n_exp_hphobes_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| fc_nodes_near_rotsub_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| fc_nodes_near_rotsub_bool_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| find_background_edge(int first_class_node_index, int bg_node_index) const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | protected |
| get_all_sasas(utility::vector1< Real > &node_sasas, utility::vector1< Real > &bgnode_sasas) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| get_background_node(int index) const | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | inlineprotected |
| get_bg_bg_atom_atom_overlaps(Size node1_index, Size node2_index) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| 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::HPatchInteractionGraph< V, E, G > | |
| get_energy_current_state_assignment() override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| get_energy_sum_for_vertex_group(Size group_id) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | virtual |
| get_hpatch_bg_node(int index) const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| get_hpatch_node(int index) const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| get_hpatch_score() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| get_network_state() const | core::pack::interaction_graph::HPatchInteractionGraph< 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 > | |
| hpatch_energy_alternate_state_assignment_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| hpatch_energy_current_state_assignment_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| hpatch_score_min_last_100_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| hpatch_score_min_recent_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| hpatch_score_weight_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| HPatchInteractionGraph(int num_nodes) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| HPatchInteractionGraph() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| HPatchInteractionGraph(HPatchInteractionGraph< V, E, G > const &) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| init_SASA_radii_from_database() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| initialize(pack_basic::RotamerSetsBase const &rot_sets) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| initialize_bg_bg_atom_atom_overlaps() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| initialize_bg_bg_overlaps() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| initialized_SASA_radii | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| node_considering_alt_state_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| num_commits_since_last_update_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| num_hpatch_comps_later_made_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| num_hpatch_comps_procrastinated_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| num_residues_assigned_as_background_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| num_state_substitutions_considered_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| num_substitutions_since_hpatch_min_update_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| num_total_residues_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| observed_sufficient_hpatch_E_to_predict_min_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| operator=(HPatchInteractionGraph< V, E, G > const &) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| packer_task() const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| packer_task_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| parent typedef | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| pose() const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| pose_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| prepare_graph_for_simulated_annealing() override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| prepared_for_simulated_annealing_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| print() const override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| print_hpatch_avoidance_stats() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | static |
| print_internal_energies_for_current_state_assignment() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| radii_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| register_bg_node_affected_by_rotsub(int bg_node_ind) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| register_fc_node_affected_by_rotsub(int fc_node_ind) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| register_fc_node_in_state0() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| reps_for_nonzero_rank_ccs_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| reset_from_previous_deltaHpatch_comp() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| reset_hpatch_avoidance_stats() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | static |
| resid_2_bgenumeration_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| rotamer_sets() const | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| rotamer_sets_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| sasa_for_cc_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| set_background_residue_rotamer_dots(Size residue, conformation::Residue const &rotamer) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_errorfull_deltaE_threshold(core::PackerEnergy deltaE) override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_network_state(ObjexxFCL::FArray1_int &node_states) override | core::pack::interaction_graph::HPatchInteractionGraph< 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::HPatchInteractionGraph< V, E, G > | |
| set_num_residues_in_protein(Size num_res) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_observed_sufficient_boolean_true() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_packer_task(task::PackerTask const &task) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_pose(pose::Pose const &pose) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_residue_as_background_residue(int residue) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_rotamer_dots_for_node_state(Size node_index, Size state, conformation::Residue const &rotamer) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_rotamer_sets(rotamer_set::RotamerSets const &rotsets) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| set_score_weight(Real weight) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | inline |
| some_node_in_state_0_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| sulfur_atom | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | privatestatic |
| total_energy_alternate_state_assignment_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| total_energy_current_state_assignment_ | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | private |
| track_hpatch_E_min() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protected |
| update_disjoint_sets_using_cache(conformation::Residue const &rsd, InvRotamerDots const &invdots, utility::vector1< Size > const &exp_hphobes, Size residue_djs_offset, utility::vector1< utility::vector1< bool > > const &atom_atom_self_overlap, utility::graph::DisjointSets &ds) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| update_disjoint_sets_using_cache(conformation::Residue const &rsd1, InvRotamerDots const &invdots1, utility::vector1< Size > const &exp_hphobes1, Size djs_offset_1, conformation::Residue const &rsd2, InvRotamerDots const &invdots2, utility::vector1< Size > const &exp_hphobes2, Size djs_offset_2, utility::vector1< utility::vector1< bool > > const &atom_atom_overlaps, utility::graph::DisjointSets &ds) | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
| update_internal_energy_totals_hpatch() | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | protected |
| ~AdditionalBackgroundNodesInteractionGraph() override | core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > | |
| ~HPatchInteractionGraph() override | core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > | |
1.8.7