| aa_submatrix_energies_retrievable() const | core::pack::interaction_graph::FixedBBInteractionGraph | virtual |
| aatype_for_node_state(int node_ind, int node_state) const | core::pack::interaction_graph::FixedBBInteractionGraph | virtual |
| 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 | |
| add_to_one_body_energy_for_node_state(int node_ind, int state, core::PackerEnergy one_body_energy) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| any_vertex_state_unassigned() const | core::pack::interaction_graph::InteractionGraphBase | |
| blanket_assign_state_0() | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| commit_considered_substitution() | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| COMMIT_LIMIT_BETWEEN_UPDATES | core::pack::interaction_graph::LinearMemoryInteractionGraph | privatestatic |
| consider_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| count_connected_components_and_initialize_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| count_dynamic_memory() const | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| count_static_memory() const | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| create_new_edge(int index1, int index2) | core::pack::interaction_graph::LinearMemoryInteractionGraph | protectedvirtual |
| create_new_node(int node_index, int num_states) | core::pack::interaction_graph::LinearMemoryInteractionGraph | protectedvirtual |
| distinguish_backbone_and_sidechain_for_node(int node) const | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| distinguish_backbone_and_sidechain_for_node(int node, bool setting) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| 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 | |
| find_edge(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
| find_edge(int node1, int node2) | core::pack::interaction_graph::InteractionGraphBase | |
| first_time_prepping_for_simA_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| 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 | |
| get_aa_submatrix_energies_for_edge(int node1, int node2, int node1aa, int node2aa) const | core::pack::interaction_graph::FixedBBInteractionGraph | virtual |
| get_edge() const | core::pack::interaction_graph::InteractionGraphBase | |
| get_edge_exists(int node1, int node2) | 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() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_edge_memory_usage() const | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| get_edge_weight(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
| get_energy_current_state_assignment() | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| get_energy_PD_current_state_assignment() | core::pack::interaction_graph::LinearMemoryInteractionGraph | protected |
| get_energy_sum_for_vertex_group(int group_id) | core::pack::interaction_graph::LinearMemoryInteractionGraph | 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_linmem_node(int index) const | core::pack::interaction_graph::LinearMemoryInteractionGraph | inlineprotected |
| get_linmem_node(int index) | core::pack::interaction_graph::LinearMemoryInteractionGraph | 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_aatypes() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inlinevirtual |
| get_num_edges() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_num_nodes() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_num_nodes_v() const | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| get_num_rpe_calculations_count() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| get_num_states_for_node(int node) const | core::pack::interaction_graph::InteractionGraphBase | |
| get_num_total_states() const | core::pack::interaction_graph::InteractionGraphBase | inline |
| get_on_the_fly_node(int node_index) | core::pack::interaction_graph::OnTheFlyInteractionGraph | inlineprotected |
| get_on_the_fly_node(int node_index) const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inlineprotected |
| get_one_body_energy_for_node_state(int node, int state) | core::pack::interaction_graph::OnTheFlyInteractionGraph | virtual |
| get_recent_history_size() const | core::pack::interaction_graph::LinearMemoryInteractionGraph | |
| 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 node1, int node2, int state_node1, int state_node2) const | core::pack::interaction_graph::FixedBBInteractionGraph | virtual |
| 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 |
| have_not_committed_last_substitution_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| increment_edge_list_iterator() const | core::pack::interaction_graph::InteractionGraphBase | |
| initialize(rotamer_set::RotamerSetsBase const &rot_sets) | core::pack::interaction_graph::OnTheFlyInteractionGraph | virtual |
| InteractionGraphBase(int num_nodes) | core::pack::interaction_graph::InteractionGraphBase | |
| LinearMemoryInteractionGraph(int numNodes) | core::pack::interaction_graph::LinearMemoryInteractionGraph | |
| LinearMemoryInteractionGraph() | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| LinearMemoryInteractionGraph(LinearMemoryInteractionGraph const &) | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| mine(EdgeBase const *edge) const | core::pack::interaction_graph::InteractionGraphBase | inlineprotected |
| node_considering_alt_state_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| non_const_pose() | core::pack::interaction_graph::OnTheFlyInteractionGraph | inline |
| note_long_range_interactions_exist_for_edge(int node1, int node2) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| note_rpe_calculated() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inline |
| note_short_range_interactions_exist_for_edge(int node1, int node2) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| note_vertex_reached(int node_index) | core::pack::interaction_graph::InteractionGraphBase | |
| num_commits_since_last_update_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| OnTheFlyInteractionGraph(int num_nodes) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| operator=(LinearMemoryInteractionGraph const &) | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| output_connectivity(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| output_dimacs(std::ostream &os) const | core::pack::interaction_graph::InteractionGraphBase | |
| pose() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inline |
| Pose typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| PoseOP typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| prepare_for_simulated_annealing() | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| print() const | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
| print_current_state_assignment() const | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| print_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
| print_vertices() const | core::pack::interaction_graph::InteractionGraphBase | |
| recent_history_size_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| reset_edge_list_iterator_for_node(int node_index) const | core::pack::interaction_graph::InteractionGraphBase | |
| reset_rpe_calculations_count() | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| score_function() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inline |
| ScoreFunction typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| ScoreFunctionOP typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_edge_weight(int node1, int node2, Real edge_weight) | core::pack::interaction_graph::InteractionGraphBase | |
| set_errorfull_deltaE_threshold(core::PackerEnergy deltaE) | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| set_network_state(ObjexxFCL::FArray1_int &node_states) | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| 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_one_body_energy_for_node_state(int node_ind, int state, core::PackerEnergy one_body_energy) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_pose(Pose const &) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_ProCorrection_values_for_edge(int node1, int node2, int node_not_neccessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_recent_history_size(Size recent_history_size) | core::pack::interaction_graph::LinearMemoryInteractionGraph | |
| set_recent_history_sizes() | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| set_score_function(ScoreFunction const &) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_sparse_aa_info_for_edge(int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| set_state_for_node(int node_ind, int new_state) | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| set_vertex_member_of_group(int vertex, int group) | core::pack::interaction_graph::InteractionGraphBase | |
| total_energy_alternate_state_assignment_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| total_energy_current_state_assignment_ | core::pack::interaction_graph::LinearMemoryInteractionGraph | private |
| update_internal_energy_totals() | core::pack::interaction_graph::LinearMemoryInteractionGraph | 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 | |
| zero_one_body_energy_for_node_state(int node_ind, int state) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
| ~FixedBBInteractionGraph() | core::pack::interaction_graph::FixedBBInteractionGraph | inlinevirtual |
| ~InteractionGraphBase() | core::pack::interaction_graph::InteractionGraphBase | virtual |
| ~LinearMemoryInteractionGraph() | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
| ~OnTheFlyInteractionGraph() | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
1.8.7