| acknowledge_neighbors_substitution_surface() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| add_background_edge(BackgroundToFirstClassEdge< V, E, G > *edge) | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| alt_state_total_hASA_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| assign_state_surface(int state) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| assign_zero_state() override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| average_residue_hASA() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| average_residue_hASA(chemical::AA residue_type, Size num_nbs) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| BackgroundEdgeList typedef | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| BackgroundEdgeListIter typedef | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| BackgroundEdgeVector typedef | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| BackgroundEdgeVectorIter typedef | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| BackgroundNodeVector typedef | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| bg_neighbor_map | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| BURIED_RESIDUE_NO_HSASA_CUTOFF | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| calculate_amount_total_hydrophobic_ASA() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| calculated_surface_deltaE_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| commit_considered_substitution_surface() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| count_dynamic_memory() const override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| count_static_memory() const override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| curr_state_total_hASA_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| decide_procrastinate_surface_computations(Real const pd_deltaE, Real const threshold) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| deltaE_for_substitution_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| detect_neighborship_with_node(int node_id, bool first_class) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| drop_background_edge(BackgroundEdgeListIter edge) | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| fc_neighbor_map | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| FirstClassNode(G *owner, int node_id, int num_states) | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| get_adjacent_background_node(int index) const | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_adjacent_background_node(int index) | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_alt_hASA() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_alt_state_hASA_for_node_and_nbs() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_bg_edge_vector_up_to_date_() const | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_curr_state_surface_energy() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_current_hASA() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_edge_to_bg_node(int index) const | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_edge_to_bg_node(int index) | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_edge_to_surface_bg_node(int index) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | inlineprotected |
| get_hASA_for_node_and_nbs() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_incident_surface_edge(int index) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | inlineprotected |
| get_index_of_adjacent_background_node(int index) const | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_num_edges_to_background_nodes() const | core::pack::interaction_graph::FirstClassNode< V, E, G > | inlineprotected |
| get_rotamer(int state) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_surface_deltaE_for_neighbors_state_substitution(SurfaceNode< V, E, G > *node_considering_substitution, int changing_nodes_curr_state, int changing_nodes_alt_state) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| get_surface_owner() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | inlineprotected |
| get_surface_score_difference() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| getMemoryUsageInBytes() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | virtual |
| hASA_energy(Real patch_area) const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| have_prepared_for_simA_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| init_hASA_variables() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| initialize_num_neighbors_counting_self() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| INTERACTION_RADIUS | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| is_below_buried_residue_no_hsasa_cutoff() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| is_below_buried_residue_no_hsasa_cutoff(bool value) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| is_below_buried_residue_no_hsasa_cutoff_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| is_surface_exposed() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| MAX_PATCH_SURFACE_AREA | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| MAX_SURFACE_ENERGY | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| num_neighbors_counting_self() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| num_neighbors_counting_self_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | mutableprivate |
| num_state_substitutions_considered_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| num_substitutions_since_surface_min_update_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| num_surface_comps_later_made_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| num_surface_comps_procrastinated_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| observed_sufficient_surface_E_to_predict_min_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| operator=(SurfaceNode< V, E, G > const &) | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| parent typedef | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| prepare_for_simulated_annealing() override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| print() const override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| print_surface_avoidance_stats() | core::pack::interaction_graph::SurfaceNode< V, E, G > | static |
| project_deltaE_for_substitution_surface(int alternate_state, core::PackerEnergy &prev_energy_for_node, float deltaE_thresh_for_avoiding_surface_calcs) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| project_surface_deltaE() | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| reset_alt_state_total_hASA() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| reset_surface_avoidance_stats() | core::pack::interaction_graph::SurfaceNode< V, E, G > | static |
| rotamer_set_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| rotamers_vector_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| set_observed_sufficient_boolean_true() | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| set_rotamers(rotamer_set::RotamerSetCOP rotamers) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| state_unassigned() const override | core::pack::interaction_graph::SurfaceNode< V, E, G > | inline |
| surface_energy_weight_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| surface_exposed(bool value) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| surface_exposed_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| SURFACE_EXPOSED_CUTOFF | core::pack::interaction_graph::SurfaceNode< V, E, G > | privatestatic |
| surface_score_min_last_100_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| surface_score_min_recent_ | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| SurfaceNode(G *owner, int node_index, int num_states) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| SurfaceNode() | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| SurfaceNode(SurfaceNode< V, E, G > const &) | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| track_surface_E_min() | core::pack::interaction_graph::SurfaceNode< V, E, G > | private |
| update_bg_edge_vector() | core::pack::interaction_graph::FirstClassNode< V, E, G > | protected |
| verify_patch_areas_correct(int node_id, int previous_state, Real previous_state_hASA) | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
| wt_residue_for_node() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | inline |
| wt_seqpos_for_node() const | core::pack::interaction_graph::SurfaceNode< V, E, G > | inline |
| ~FirstClassNode() override | core::pack::interaction_graph::FirstClassNode< V, E, G > | |
| ~SurfaceNode() override | core::pack::interaction_graph::SurfaceNode< V, E, G > | |
1.8.7