| aa_offsets_for_edges_ | core::pack::interaction_graph::PDNode | private |
| aatype_for_state(int state) const | core::pack::interaction_graph::PDNode | virtual |
| acknowledge_neighbors_state_substitution(int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info) | core::pack::interaction_graph::PDNode | inline |
| add_edge(EdgeBase *edge_ptr) | core::pack::interaction_graph::NodeBase | |
| add_to_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &energies) override | core::pack::interaction_graph::PDNode | virtual |
| add_to_one_body_energy(int state, core::PackerEnergy energy) override | core::pack::interaction_graph::PDNode | virtual |
| alt_state_sparse_mat_info_ | core::pack::interaction_graph::PDNode | private |
| alternate_state_ | core::pack::interaction_graph::PDNode | private |
| alternate_state_is_being_considered_ | core::pack::interaction_graph::PDNode | private |
| alternate_state_one_body_energy_ | core::pack::interaction_graph::PDNode | private |
| alternate_state_total_energy_ | core::pack::interaction_graph::PDNode | private |
| alternate_state_two_body_energies_ | core::pack::interaction_graph::PDNode | private |
| assign_state(int new_state) | core::pack::interaction_graph::PDNode | |
| assign_zero_state() override | core::pack::interaction_graph::PDNode | virtual |
| calc_deltaEpd(int alternate_state) | core::pack::interaction_graph::PDNode | protected |
| commit_considered_substitution() | core::pack::interaction_graph::PDNode | |
| considering_alternate_state() const | core::pack::interaction_graph::PDNode | inlineprotected |
| count_dynamic_memory() const override | core::pack::interaction_graph::PDNode | virtual |
| count_static_memory() const override | core::pack::interaction_graph::PDNode | virtual |
| curr_state_one_body_energy_ | core::pack::interaction_graph::PDNode | private |
| curr_state_sparse_mat_info_ | core::pack::interaction_graph::PDNode | private |
| curr_state_total_energy_ | core::pack::interaction_graph::PDNode | private |
| curr_state_two_body_energies_ | core::pack::interaction_graph::PDNode | private |
| current_state_ | core::pack::interaction_graph::PDNode | private |
| depth_first_connected_component_counting() | core::pack::interaction_graph::NodeBase | |
| drop_all_edges() | core::pack::interaction_graph::NodeBase | |
| drop_edge(std::list< EdgeBase * >::iterator edge_iterator) | core::pack::interaction_graph::NodeBase | |
| edge_list_begin() | core::pack::interaction_graph::NodeBase | |
| edge_list_end() | core::pack::interaction_graph::NodeBase | |
| edge_matrix_ptrs_ | core::pack::interaction_graph::PDNode | private |
| find_edge(int other_node_index) const | core::pack::interaction_graph::NodeBase | |
| FixedBBNode(InteractionGraphBase *owner, int node_id, int num_states) | core::pack::interaction_graph::FixedBBNode | inline |
| get_adjacent_node(int index) const | core::pack::interaction_graph::NodeBase | inline |
| get_adjacent_node(int index) | core::pack::interaction_graph::NodeBase | inline |
| get_alt_pd_energy_total() const | core::pack::interaction_graph::PDNode | inlineprotected |
| get_alternate_state() const | core::pack::interaction_graph::PDNode | inlineprotected |
| get_curr_pd_energy_total() const | core::pack::interaction_graph::PDNode | inlineprotected |
| get_current_state() const | core::pack::interaction_graph::PDNode | |
| get_edge_vector_up_to_date() const | core::pack::interaction_graph::NodeBase | inlineprotected |
| get_incident_edge(int index) const | core::pack::interaction_graph::NodeBase | inline |
| get_incident_edge(int index) | core::pack::interaction_graph::NodeBase | inline |
| get_incident_pd_edge(int index) const | core::pack::interaction_graph::PDNode | inlineprivate |
| get_incident_pd_edge(int index) | core::pack::interaction_graph::PDNode | inlineprivate |
| get_index_of_adjacent_node(int index) const | core::pack::interaction_graph::NodeBase | inline |
| get_node_index() const | core::pack::interaction_graph::NodeBase | inline |
| get_num_edges_to_larger_indexed_nodes() const | core::pack::interaction_graph::NodeBase | inline |
| get_num_edges_to_smaller_indexed_nodes() const | core::pack::interaction_graph::NodeBase | inline |
| get_num_incident_edges() const | core::pack::interaction_graph::NodeBase | inline |
| get_num_states() const | core::pack::interaction_graph::NodeBase | |
| get_num_states_for_aa_type(int aa_type) const | core::pack::interaction_graph::PDNode | |
| get_num_states_for_aa_types() const | core::pack::interaction_graph::PDNode | |
| get_one_body_energy(int state) const override | core::pack::interaction_graph::PDNode | virtual |
| get_one_body_energy_current_state() const | core::pack::interaction_graph::PDNode | |
| get_owner() const | core::pack::interaction_graph::NodeBase | inlineprotected |
| get_owner() | core::pack::interaction_graph::NodeBase | inlineprotected |
| get_pdig_owner() const | core::pack::interaction_graph::PDNode | inlineprivate |
| get_pdig_owner() | core::pack::interaction_graph::PDNode | inlineprivate |
| get_sparse_mat_info_for_curr_state() const | core::pack::interaction_graph::PDNode | |
| get_sparse_mat_info_for_state(int state) const | core::pack::interaction_graph::PDNode | |
| get_weighted_energy_with_higher_indexed_nodes(ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) const | core::pack::interaction_graph::PDNode | |
| neighbors_curr_state_ | core::pack::interaction_graph::PDNode | private |
| neighbors_curr_state_sparse_info_ | core::pack::interaction_graph::PDNode | private |
| NodeBase(InteractionGraphBase *, int node_id, int num_states) | core::pack::interaction_graph::NodeBase | |
| num_aa_types_ | core::pack::interaction_graph::PDNode | private |
| num_states_for_aa_type_for_higher_indexed_neighbor_ | core::pack::interaction_graph::PDNode | private |
| num_states_for_aatype_ | core::pack::interaction_graph::PDNode | private |
| one_body_energies_ | core::pack::interaction_graph::PDNode | private |
| operator=(PDNode const &) | core::pack::interaction_graph::PDNode | private |
| PDNode(InteractionGraphBase *owner, int node_id, int num_states) | core::pack::interaction_graph::PDNode | |
| PDNode() | core::pack::interaction_graph::PDNode | private |
| PDNode(PDNode const &) | core::pack::interaction_graph::PDNode | private |
| PrecomputedPairEnergiesNode(InteractionGraphBase *owner, int node_id, int num_states) | core::pack::interaction_graph::PrecomputedPairEnergiesNode | inline |
| prepare_for_simulated_annealing() override | core::pack::interaction_graph::PDNode | virtual |
| print() const override | core::pack::interaction_graph::PDNode | virtual |
| print_internal_energies() const | core::pack::interaction_graph::PDNode | |
| project_deltaE_for_substitution(int alternate_state, core::PackerEnergy &prev_node_energy) | core::pack::interaction_graph::PDNode | inline |
| project_deltaE_for_substitution(int alternate_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::PDNode | |
| set_alt_aa_offsets_from_edge(int edge_index, ObjexxFCL::FArray2D_int const &offsets) | core::pack::interaction_graph::PDNode | private |
| set_alternate_state(int alt) | core::pack::interaction_graph::PDNode | inlineprotected |
| set_amino_acid_types(std::vector< int > const &) | core::pack::interaction_graph::PDNode | virtual |
| sparse_mat_info_for_state_ | core::pack::interaction_graph::PDNode | private |
| state_unassigned() const override | core::pack::interaction_graph::PDNode | inlinevirtual |
| update_edge_vector() | core::pack::interaction_graph::NodeBase | protected |
| update_internal_energy_sums() | core::pack::interaction_graph::PDNode | |
| update_internal_vectors() | core::pack::interaction_graph::PDNode | protected |
| update_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &energies) | core::pack::interaction_graph::PDNode | virtual |
| update_one_body_energy(int state, core::PackerEnergy energy) override | core::pack::interaction_graph::PDNode | virtual |
| zero_one_body_energies() override | core::pack::interaction_graph::PDNode | virtual |
| ~FixedBBNode() override | core::pack::interaction_graph::FixedBBNode | inline |
| ~NodeBase() | core::pack::interaction_graph::NodeBase | virtual |
| ~PDNode() override | core::pack::interaction_graph::PDNode | |
| ~PrecomputedPairEnergiesNode() override | core::pack::interaction_graph::PrecomputedPairEnergiesNode | inline |
1.8.7