| aa_neighbors_for_edges_ | core::pack::interaction_graph::LinearMemNode | private |
| ACCEPTANCE_REJECTION_HISTORY_LENGTH | core::pack::interaction_graph::LinearMemNode | privatestatic |
| ACCEPTED | core::pack::interaction_graph::LinearMemNode | privatestatic |
| accepted_history_head_ | core::pack::interaction_graph::LinearMemNode | private |
| accepted_rejected_substitution_history_ | core::pack::interaction_graph::LinearMemNode | private |
| acknowledge_last_substititon_not_committed() | core::pack::interaction_graph::LinearMemNode | |
| acknowledge_neighbors_partial_state_substitution(int edge_to_altered_neighbor, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info, int other_state_recent_history_index) | core::pack::interaction_graph::LinearMemNode | |
| 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, int other_node_recent_history_index) | core::pack::interaction_graph::LinearMemNode | inline |
| add_edge(EdgeBase *edge_ptr) | core::pack::interaction_graph::NodeBase | |
| add_to_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &energy1b) override | core::pack::interaction_graph::OnTheFlyNode | virtual |
| add_to_one_body_energy(int state, core::PackerEnergy energy) override | core::pack::interaction_graph::OnTheFlyNode | virtual |
| already_prepped_for_simA_ | core::pack::interaction_graph::LinearMemNode | private |
| alt_state_sparse_mat_info_ | core::pack::interaction_graph::LinearMemNode | private |
| alternate_state_ | core::pack::interaction_graph::LinearMemNode | private |
| alternate_state_is_being_considered_ | core::pack::interaction_graph::LinearMemNode | private |
| alternate_state_one_body_energy_ | core::pack::interaction_graph::LinearMemNode | private |
| alternate_state_total_energy_ | core::pack::interaction_graph::LinearMemNode | private |
| alternate_state_two_body_energies_ | core::pack::interaction_graph::LinearMemNode | private |
| assign_state(int new_state) | core::pack::interaction_graph::LinearMemNode | |
| assign_zero_state() override | core::pack::interaction_graph::LinearMemNode | virtual |
| bb_bounding_sphere() const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| BoundingSphere typedef | core::pack::interaction_graph::OnTheFlyNode | |
| calc_deltaEpd(int alternate_state) | core::pack::interaction_graph::LinearMemNode | protected |
| commit_considered_substitution() | core::pack::interaction_graph::LinearMemNode | |
| complete_state_assignment() | core::pack::interaction_graph::LinearMemNode | |
| compute_pair_energy_for_alternate_state(int edge_making_energy_request) | core::pack::interaction_graph::LinearMemNode | |
| compute_pair_energy_for_current_state(int edge_making_energy_request) | core::pack::interaction_graph::LinearMemNode | |
| compute_rotamer_pair_energy(int edge_making_energy_request, int state_this, int state_other) const | core::pack::interaction_graph::OnTheFlyNode | |
| considering_alternate_state() const | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| count_dynamic_memory() const override | core::pack::interaction_graph::LinearMemNode | virtual |
| count_static_memory() const override | core::pack::interaction_graph::LinearMemNode | virtual |
| curr_state_one_body_energy_ | core::pack::interaction_graph::LinearMemNode | private |
| curr_state_sparse_mat_info_ | core::pack::interaction_graph::LinearMemNode | private |
| curr_state_total_energy_ | core::pack::interaction_graph::LinearMemNode | private |
| curr_state_two_body_energies_ | core::pack::interaction_graph::LinearMemNode | private |
| current_state_ | core::pack::interaction_graph::LinearMemNode | private |
| depth_first_connected_component_counting() | core::pack::interaction_graph::NodeBase | |
| distinguish_backbone_and_sidechain() const | core::pack::interaction_graph::OnTheFlyNode | inline |
| distinguish_backbone_and_sidechain(bool setting) | core::pack::interaction_graph::OnTheFlyNode | |
| 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 | |
| filled_substitution_history_ | core::pack::interaction_graph::LinearMemNode | 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_linmem_node(int index) const | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_adjacent_linmem_node(int index) | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_adjacent_node(int index) const | core::pack::interaction_graph::NodeBase | inline |
| get_adjacent_node(int index) | core::pack::interaction_graph::NodeBase | inline |
| get_adjacent_otf_node(int index) | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_adjacent_otf_node(int index) const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_alt_pd_energy_total() const | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| get_alternate_state() const | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| get_curr_pd_energy_total() const | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| get_curr_state_recent_state_id() const | core::pack::interaction_graph::LinearMemNode | inline |
| get_current_rotamer() | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| get_current_state() const | core::pack::interaction_graph::LinearMemNode | inline |
| 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_linmem_edge(int index) const | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_incident_linmem_edge(int index) | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_incident_otf_edge(int edge) | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_incident_otf_edge(int edge) const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_index_of_adjacent_node(int index) const | core::pack::interaction_graph::NodeBase | inline |
| get_linmem_ig_owner() const | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_linmem_ig_owner() | core::pack::interaction_graph::LinearMemNode | inlineprivate |
| get_node_index() const | core::pack::interaction_graph::NodeBase | inline |
| get_num_aa_types() const | core::pack::interaction_graph::OnTheFlyNode | 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) | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_num_states_for_aa_types() | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_num_states_for_aa_types() const | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_on_the_fly_owner() | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_on_the_fly_owner() const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_one_body_energy(int state) const | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_one_body_energy_current_state() const | core::pack::interaction_graph::LinearMemNode | inline |
| get_owner() const | core::pack::interaction_graph::NodeBase | inlineprotected |
| get_owner() | core::pack::interaction_graph::NodeBase | inlineprotected |
| get_recent_history_size() const | core::pack::interaction_graph::LinearMemNode | |
| get_rotamer(int state) const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| get_sparse_mat_info_for_curr_state() const | core::pack::interaction_graph::LinearMemNode | inline |
| get_sparse_mat_info_for_state(int state) const | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_state_offset_for_aatype(int aatype) const | core::pack::interaction_graph::OnTheFlyNode | inline |
| get_totalE() const | core::pack::interaction_graph::LinearMemNode | inlinevirtual |
| LinearMemNode(InteractionGraphBase *owner, int node_id, int num_states) | core::pack::interaction_graph::LinearMemNode | |
| neighbors_curr_state_ | core::pack::interaction_graph::LinearMemNode | private |
| neighbors_curr_state_sparse_info_ | core::pack::interaction_graph::LinearMemNode | private |
| neighbors_state_recent_history_index_ | core::pack::interaction_graph::LinearMemNode | private |
| NodeBase(InteractionGraphBase *, int node_id, int num_states) | core::pack::interaction_graph::NodeBase | |
| num_recently_accepted_ | core::pack::interaction_graph::LinearMemNode | private |
| OnTheFlyNode(InteractionGraphBase *owner, int node_id, int num_states) | core::pack::interaction_graph::OnTheFlyNode | |
| partial_assign_state(int new_state) | core::pack::interaction_graph::LinearMemNode | |
| prepare_for_simulated_annealing() override | core::pack::interaction_graph::LinearMemNode | virtual |
| print() const override | core::pack::interaction_graph::LinearMemNode | virtual |
| print_internal_energies() const | core::pack::interaction_graph::LinearMemNode | |
| project_deltaE_for_substitution(int alternate_state, core::PackerEnergy &prev_node_energy) | core::pack::interaction_graph::LinearMemNode | |
| REJECTED | core::pack::interaction_graph::LinearMemNode | privatestatic |
| rhq_ | core::pack::interaction_graph::LinearMemNode | private |
| sc_bounding_sphere(int state) const | core::pack::interaction_graph::OnTheFlyNode | inlineprotected |
| set_alternate_state(int alt) | core::pack::interaction_graph::LinearMemNode | inlineprotected |
| set_one_body_energy(int state, core::PackerEnergy energy) | core::pack::interaction_graph::OnTheFlyNode | virtual |
| set_recent_history_size(int num_states_to_maintain_in_recent_history) | core::pack::interaction_graph::LinearMemNode | |
| set_rotamers(rotamer_set::RotamerSetCOP rotamers) | core::pack::interaction_graph::OnTheFlyNode | |
| state_unassigned() const override | core::pack::interaction_graph::LinearMemNode | inlinevirtual |
| THRESHOLD_ACCEPTANCE_RATE_FOR_RPE_STORAGE | core::pack::interaction_graph::LinearMemNode | privatestatic |
| update_edge_vector() | core::pack::interaction_graph::NodeBase | protected |
| update_internal_energy_sums() | core::pack::interaction_graph::LinearMemNode | |
| update_internal_vectors() | core::pack::interaction_graph::LinearMemNode | private |
| update_one_body_energy(int state, core::PackerEnergy energy) override | core::pack::interaction_graph::OnTheFlyNode | virtual |
| update_recent_history(int state) | core::pack::interaction_graph::LinearMemNode | private |
| zero_one_body_energies() override | core::pack::interaction_graph::OnTheFlyNode | virtual |
| zero_one_body_energy(int state) | core::pack::interaction_graph::OnTheFlyNode | virtual |
| ~FixedBBNode() override | core::pack::interaction_graph::FixedBBNode | inline |
| ~LinearMemNode() override | core::pack::interaction_graph::LinearMemNode | |
| ~NodeBase() | core::pack::interaction_graph::NodeBase | virtual |
| ~OnTheFlyNode() override | core::pack::interaction_graph::OnTheFlyNode | |
1.8.7