| add_edge(int node1, int node2) | core::pack::interaction_graph::InteractionGraphBase | |
| add_to_nodes_one_body_energy(int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies) | core::pack::interaction_graph::InteractionGraphBase | |
| add_to_nodes_one_body_energy(int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies) | core::pack::interaction_graph::InteractionGraphBase | |
| add_to_nodes_one_body_energy(int node_ind, int state_id, core::PackerEnergy const one_body_energy) | core::pack::interaction_graph::InteractionGraphBase | |
| add_to_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies) | core::pack::interaction_graph::InteractionGraphBase | |
| AnnealableGraphBase() | core::pack::interaction_graph::AnnealableGraphBase | |
| AnnealableGraphBase(AnnealableGraphBase const &src) | core::pack::interaction_graph::AnnealableGraphBase | |
| any_vertex_state_unassigned() const override | core::pack::interaction_graph::InteractionGraphBase | virtual |
| blanket_assign_state_0() override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| BOTH_SC_AND_BB enum value | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| cast_flexbb_edge(EdgeBase const *edge) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| cast_flexbb_edge(EdgeBase *edge) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| cast_minimalist_flexbb_edge(EdgeBase const *edge) const | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| cast_minimalist_flexbb_edge(EdgeBase *edge) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| cast_otfflexbb_edge(EdgeBase const *edge) const | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| cast_otfflexbb_edge(EdgeBase *edge) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| clean_up_after_packing(core::pose::Pose &pose) | core::pack::interaction_graph::AnnealableGraphBase | virtual |
| clean_up_edges_marked_for_deletion() | core::pack::interaction_graph::InteractionGraphBase | protected |
| commit_considered_backbone_move(ObjexxFCL::FArray1_int &rotamer_on_node) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | privatevirtual |
| commit_considered_substitution() override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| complete_deltaE_prediction_for_bbmove(core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protected |
| consider_backbone_move(int bb_id, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_flexseg_energy, bool &valid_motion, int &num_nodes_changing_state) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| consider_bbmove_w_state_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| consider_substitution(int node_ind, int new_state, PackerEnergy &delta_energy, PackerEnergy &prev_energy_for_node) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| count_connected_components_and_initialize_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| count_dynamic_memory() const override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protectedvirtual |
| count_static_memory() const override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protectedvirtual |
| create_new_edge(int index1, int index2) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protectedvirtual |
| create_new_node(int node_index, int num_states) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protectedvirtual |
| debug_note_accepted_substitution() | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| debug_note_considered_substitution(core::conformation::Residue const &alt_rotamer, int index) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| debug_note_projected_deltaE_of_considered_substitution(PackerEnergy deltaE, PackerEnergy node_alt_total, bool require_match=true) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| debug_note_rejected_substitution() | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| declare_all_edge_energies_final() | core::pack::interaction_graph::InteractionGraphBase | virtual |
| drop_all_edges_for_node(int node) | core::pack::interaction_graph::InteractionGraphBase | |
| drop_edge(std::list< EdgeBase * >::iterator edge) | core::pack::interaction_graph::InteractionGraphBase | protected |
| edge_list_iterator_at_end() const | core::pack::interaction_graph::InteractionGraphBase | |
| EdgeBase typedef | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| find_edge(int node1, int node2, bool const use_threadsafe_lookup=false) const | core::pack::interaction_graph::InteractionGraphBase | |
| find_edge(int node1, int node2, bool const use_threadsafe_lookup=false) | core::pack::interaction_graph::InteractionGraphBase | |
| find_flexbb_edge(int node1, int node2) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| find_flexbb_edge(int node1, int node2) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| find_minimalist_flexbb_edge(int node1, int node2) const | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| find_minimalist_flexbb_edge(int node1, int node2) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| find_otfflexbb_edge(int node1, int node2) const | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| find_otfflexbb_edge(int node1, int node2) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| FlexbbInteractionGraph(int num_nodes) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| flexseg_considering_alt_bb() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| flexseg_for_moltenres(int moltenres) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| flexseg_members(int flexseg) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inline |
| get_accessible_states(Subsitution move_mode, utility::vector1< core::Size > &rotlist) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_backbone_currently_assigned(int bbid) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_backbone_list(utility::vector1< core::Size > &bblist) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_bb_for_state(int node, int state) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_edge() const | core::pack::interaction_graph::InteractionGraphBase | |
| get_edge_exists(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
| get_edge_list_begin() | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_edge_list_begin() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_edge_list_end() | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_edge_list_end() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_edge_memory_usage() const override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| get_edge_weight(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
| get_energy_current_state_assignment() override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| get_energy_sum_for_vertex_group(int group_id) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| get_enforce_bb_contiguity() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_flexbb_node(int index) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| get_flexbb_node(int index) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| get_flexseg_bb_offset(int flexseg_id) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inline |
| get_flexseg_for_bb(int bb) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inline |
| get_minimalistflexbb_node(int index) const | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| get_minimalistflexbb_node(int index) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | inlineprotected |
| get_node(int index) const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_node_state_offset(int index) const | core::pack::interaction_graph::InteractionGraphBase | inlineprotected |
| get_num_aa_types() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inline |
| get_num_edges() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_num_nodes() const override | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| get_num_nodes_changing_state() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protected |
| get_num_states_for_node(int node) const override | core::pack::interaction_graph::InteractionGraphBase | virtual |
| get_num_states_per_backbone_for_node(int node, int bb) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| get_num_total_states() const override | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| get_one_body_energy_for_node_state(int node, int state) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| get_otfflexbb_node(int index) const | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| get_otfflexbb_node(int index) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | inlineprotected |
| get_pose() const | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| get_scorefxn() const | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| get_vertex_member_of_energy_sum_group(int node_index, int group_id) | core::pack::interaction_graph::InteractionGraphBase | inline |
| getTotalMemoryUsage() const | core::pack::interaction_graph::InteractionGraphBase | virtual |
| increment_count_nodes_in_flexseg() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| increment_edge_list_iterator() const | core::pack::interaction_graph::InteractionGraphBase | |
| initialize(core::pack_basic::RotamerSetsBase const &rot_sets) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| InteractionGraphBase(int num_nodes) | core::pack::interaction_graph::InteractionGraphBase | |
| last_considered_backbone_sub_unresolved() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| last_considered_backbone_sub_valid() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| last_considered_substitution_kept_backbone_fixed() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| last_considered_substitution_moved_the_backbone() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| last_considered_substitution_unresolved() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| mine(EdgeBase const *edge) const | core::pack::interaction_graph::InteractionGraphBase | inlineprotected |
| MinimalistFlexbbInteractionGraph(int num_nodes) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | |
| node_considering_alt_state() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| nodes_from_same_flexseg(int node1, int node2) const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| note_bbjump_substitution() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| note_fixedbb_substitution() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| note_last_considered_substitution_resolved() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protected |
| note_long_range_interactions_exist_for_edge(int node1, int node2) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| note_vertex_reached(int node_index) | core::pack::interaction_graph::InteractionGraphBase | |
| OTFFlexbbInteractionGraph(int num_nodes) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| output_connectivity(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| output_dimacs(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| PackerEnergy typedef | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| parent typedef | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | |
| Pose typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| PoseCOP typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| PoseOP typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| prepare_graph_for_simulated_annealing() override | core::pack::interaction_graph::InteractionGraphBase | virtual |
| print() const | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| print_current_state_assignment() const override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| print_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| print_vertices() const | core::pack::interaction_graph::InteractionGraphBase | |
| project_deltaE_for_substitution(int alternate_state, PackerEnergy &prev_energy_for_node) | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | private |
| Real typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| reset_edge_list_iterator_for_node(int node_index) const | core::pack::interaction_graph::InteractionGraphBase | |
| reset_node_in_moving_flexseg_count() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protected |
| resolve_uncommitted_substitution() | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | protected |
| SC_ONLY enum value | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| ScoreFunction typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| ScoreFunctionCOP typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| ScoreFunctionOP typedef | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| set_edge_weight(int node1, int node2, Real edge_weight) | core::pack::interaction_graph::InteractionGraphBase | |
| set_enforce_bb_contiguity(bool) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protected |
| set_errorfull_deltaE_threshold(PackerEnergy deltaE) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| set_flexseg_considering_alt_bb(int setting) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| set_GlyCorrection_values_for_edge(int node1, int node2, int node_not_necessarily_glycine, int state, int other_bb, PackerEnergy bb_nonglybb_E, PackerEnergy bb_glybb_E, PackerEnergy sc_nonglybb_E, PackerEnergy sc_glybb_E) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| set_last_considered_backbone_sub_valid(bool setting) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| set_network_state(ObjexxFCL::FArray1_int &node_states) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| set_node_considering_alt_state(int setting) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| set_num_states_for_node(int node, int num_states) | core::pack::interaction_graph::InteractionGraphBase | |
| set_number_of_energy_sum_vertex_groups(int num_groups) | core::pack::interaction_graph::InteractionGraphBase | |
| set_onebody_energies_multithreaded(core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments) | core::pack::interaction_graph::InteractionGraphBase | |
| set_pose(Pose const &pose) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | virtual |
| set_ProCorrection_values_for_edge(int node1, int node2, int node_not_necessarily_proline, int state, int other_bb, PackerEnergy bb_nonprobb_E, PackerEnergy bb_probb_E, PackerEnergy sc_nonprobb_E, PackerEnergy sc_probb_E) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
| set_scorefxn(ScoreFunction const &sfxn) | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | virtual |
| set_state_for_node(int node_ind, int new_state) override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | virtual |
| set_total_energy_alternate_state_assignment(PackerEnergy setting) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| set_total_energy_current_state_assignment(PackerEnergy setting) | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protected |
| set_vertex_member_of_group(int vertex, int group) | core::pack::interaction_graph::InteractionGraphBase | |
| Subsitution enum name | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| total_energy_alternate_state_assignment() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| total_energy_current_state_assignment() const | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | inlineprotected |
| update_internal_energy_totals() | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | protectedvirtual |
| update_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b) | core::pack::interaction_graph::InteractionGraphBase | |
| vertex_already_reached(int node_index) | core::pack::interaction_graph::InteractionGraphBase | |
| zero_one_body_energies_for_node(int node) | core::pack::interaction_graph::InteractionGraphBase | |
| ~AnnealableGraphBase() override | core::pack::interaction_graph::AnnealableGraphBase | |
| ~FlexbbInteractionGraph() override | protocols::flexpack::interaction_graph::FlexbbInteractionGraph | |
| ~InteractionGraphBase() override | core::pack::interaction_graph::InteractionGraphBase | |
| ~MinimalistFlexbbInteractionGraph() override | protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph | |
| ~OTFFlexbbInteractionGraph() override | protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph | |
1.8.7