| aa_submatrix_energies_retrievable() const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| aatype_for_node_state(int node_ind, int node_state) const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| add_edge(int node1, int node2) | core::pack::interaction_graph::PDInteractionGraph | virtual |
| add_longrange_twobody_energies_multithreaded(std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::methods::LongRangeTwoBodyEnergyCOP lr_energy, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| 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 | |
| add_to_two_body_energies_for_edge(int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array, bool const use_threadsafe_method=false) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| add_to_two_body_energies_for_edge(int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| 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 | core::pack::interaction_graph::PDInteractionGraph | virtual |
| clash_threshold_ | core::pack::hbonds::HBondGraphInitializerIG | private |
| 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 |
| clear_two_body_energy_for_edge(int node1, int node2, int state_node1, int state_node2) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| commit_considered_substitution() override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| commit_considered_substitution(ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) | core::pack::interaction_graph::PDInteractionGraph | virtual |
| consider_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| consider_substitution(int node_ind, int new_state, core::PackerEnergy &deltaE_unweighted, core::PackerEnergy &prevE_unweighted, core::PackerEnergy &deltaE_weighted, core::PackerEnergy &prevE_weighted, ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) | core::pack::interaction_graph::PDInteractionGraph | virtual |
| count_connected_components_and_initialize_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| count_dynamic_memory() const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| count_static_memory() const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| create_new_edge(int index1, int index2) override | core::pack::hbonds::HBondGraphInitializerIG | inlinevirtual |
| create_new_node(int node_index, int num_states) override | core::pack::interaction_graph::PDInteractionGraph | protectedvirtual |
| declare_all_edge_energies_final() | core::pack::interaction_graph::InteractionGraphBase | virtual |
| declare_edge_energies_final(int node1, int node2, bool const use_threadsafe_lookup=false) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | 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 | |
| eval_rot_pair(unsigned int const global_rot1, unsigned int const global_rot2, PackerEnergy const two_body_energy) | core::pack::hbonds::HBondGraphInitializerIG | |
| finalize_hbond_graph() | core::pack::hbonds::HBondGraphInitializerIG | |
| 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_symmetric_hbonds(conformation::symmetry::SymmetryInfo const &symm_info, pose::Pose const &pose, Real hb_threshold) | core::pack::hbonds::HBondGraphInitializerIG | |
| FixedBBInteractionGraph(int num_nodes) | core::pack::interaction_graph::FixedBBInteractionGraph | inline |
| force_aa_neighbors_for_edge(int node1, int node2, int node1aa, int node2aa) | core::pack::interaction_graph::FixedBBInteractionGraph | |
| force_all_aa_neighbors_for_edge(int node1, int node2) | core::pack::interaction_graph::FixedBBInteractionGraph | |
| future_edges_ | core::pack::hbonds::HBondGraphInitializerIG | private |
| get_aa_submatrix_energies_for_edge(int node1, int node2, int node1aa, int node2aa) const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| 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 | core::pack::interaction_graph::PDInteractionGraph | virtual |
| get_edge_weight(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
| get_energy_current_state_assignment() override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| get_energy_PD_current_state_assignment() | core::pack::interaction_graph::PDInteractionGraph | protected |
| get_energy_sum_for_vertex_group(int group_id) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| get_fixedbb_edge(int node1, int node2) const | core::pack::interaction_graph::FixedBBInteractionGraph | inlineprotected |
| get_fixedbb_edge(int node1, int node2) | core::pack::interaction_graph::FixedBBInteractionGraph | inlineprotected |
| get_fixedbb_node(int node_index) const | core::pack::interaction_graph::FixedBBInteractionGraph | inlineprotected |
| get_fixedbb_node(int node_index) | core::pack::interaction_graph::FixedBBInteractionGraph | inlineprotected |
| get_ind_res(pose::Pose const &pose, Size const res_i, conformation::symmetry::SymmetryInfo const &symm_info, std::map< char, std::pair< Size, Size > > &chain_bounds) const | core::pack::hbonds::HBondGraphInitializerIG | private |
| 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_aatypes() const override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| get_num_edges() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_num_nodes() const override | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| get_num_states_for_node(int node) const override | core::pack::interaction_graph::InteractionGraphBase | virtual |
| get_num_total_states() const override | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| get_one_body_energy_for_node_state(int node, int state) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| get_pd_edge(int node1, int node2) const | core::pack::interaction_graph::PDInteractionGraph | inlineprotected |
| get_pd_edge(int node1, int node2) | core::pack::interaction_graph::PDInteractionGraph | inlineprotected |
| get_pd_node(int index) const | core::pack::interaction_graph::PDInteractionGraph | inlineprotected |
| get_sparse_aa_info_for_edge(int node1, int node2, int node1aa, int node2aa) | core::pack::interaction_graph::FixedBBInteractionGraph | |
| get_two_body_energy_for_edge(int, int, int, int) const override | core::pack::hbonds::HBondGraphInitializerIG | inlinevirtual |
| get_vertex_member_of_energy_sum_group(int node_index, int group_id) | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_weighted_energy(ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) const | core::pack::interaction_graph::PDInteractionGraph | |
| getMemoryUsageInBytes() const | core::pack::interaction_graph::PDInteractionGraph | protectedvirtual |
| getTotalMemoryUsage() const | core::pack::interaction_graph::InteractionGraphBase | virtual |
| hbond_graph_ | core::pack::hbonds::HBondGraphInitializerIG | private |
| hbond_threshold_ | core::pack::hbonds::HBondGraphInitializerIG | private |
| HBondGraphInitializerIG(scoring::hbonds::graph::HBondGraphOP hbond_graph, rotamer_set::RotamerSetsCOP rotamer_sets, float hbond_threshold, float clash_threshold) | core::pack::hbonds::HBondGraphInitializerIG | |
| increment_edge_list_iterator() const | core::pack::interaction_graph::InteractionGraphBase | |
| initialize(pack_basic::RotamerSetsBase const &rot_sets) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| InteractionGraphBase(int num_nodes) | core::pack::interaction_graph::InteractionGraphBase | |
| mine(EdgeBase const *edge) const | core::pack::interaction_graph::InteractionGraphBase | inlineprotected |
| note_vertex_reached(int node_index) | core::pack::interaction_graph::InteractionGraphBase | |
| output_connectivity(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| output_dimacs(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| PDInteractionGraph(int num_nodes) | core::pack::interaction_graph::PDInteractionGraph | |
| PrecomputedPairEnergiesInteractionGraph(int num_nodes) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | inline |
| 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 | core::pack::interaction_graph::PDInteractionGraph | virtual |
| print_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| print_vertices() const | core::pack::interaction_graph::InteractionGraphBase | |
| reset_edge_list_iterator_for_node(int node_index) const | core::pack::interaction_graph::InteractionGraphBase | |
| rotamer_sets() | core::pack::hbonds::HBondGraphInitializerIG | inline |
| rotamer_sets_ | core::pack::hbonds::HBondGraphInitializerIG | private |
| set_edge_weight(int node1, int node2, Real edge_weight) | core::pack::interaction_graph::InteractionGraphBase | |
| set_errorfull_deltaE_threshold(core::PackerEnergy) override | core::pack::interaction_graph::PDInteractionGraph | inlinevirtual |
| set_network_state(ObjexxFCL::FArray1_int &node_states) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| set_network_state(ObjexxFCL::FArray1_int &node_states, ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) | core::pack::interaction_graph::PDInteractionGraph | |
| 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_sparse_aa_info_for_edge(int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info) | core::pack::interaction_graph::FixedBBInteractionGraph | |
| set_state_for_node(int node_ind, int new_state) override | core::pack::interaction_graph::PDInteractionGraph | virtual |
| set_two_body_energy_for_edge(int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| set_twobody_energies_multithreaded(std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap) | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | |
| set_vertex_member_of_group(int vertex, int group) | core::pack::interaction_graph::InteractionGraphBase | |
| update_internal_energy_totals() | core::pack::interaction_graph::PDInteractionGraph | protected |
| 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 | |
| ~FixedBBInteractionGraph() override | core::pack::interaction_graph::FixedBBInteractionGraph | inline |
| ~HBondGraphInitializerIG() override | core::pack::hbonds::HBondGraphInitializerIG | |
| ~InteractionGraphBase() override | core::pack::interaction_graph::InteractionGraphBase | |
| ~PrecomputedPairEnergiesInteractionGraph() override | core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph | inline |
1.8.7