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 | |
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::LinearMemoryInteractionGraph | virtual |
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 |
commit_considered_substitution() override | 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) override | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
count_connected_components_and_initialize_vertex_groups() | core::pack::interaction_graph::InteractionGraphBase | |
count_dynamic_memory() const override | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
count_static_memory() const override | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
create_new_edge(int index1, int index2) override | core::pack::interaction_graph::LinearMemoryInteractionGraph | protectedvirtual |
create_new_node(int node_index, int num_states) override | core::pack::interaction_graph::LinearMemoryInteractionGraph | protectedvirtual |
declare_all_edge_energies_final() | core::pack::interaction_graph::InteractionGraphBase | virtual |
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, 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 | |
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) 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::LinearMemoryInteractionGraph | virtual |
get_edge_weight(int node1, int node2) const | core::pack::interaction_graph::InteractionGraphBase | |
get_energy_current_state_assignment() override | 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) override | 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 override | core::pack::interaction_graph::OnTheFlyInteractionGraph | inlinevirtual |
get_num_edges() const | core::pack::interaction_graph::InteractionGraphBase | inline |
get_num_nodes() const override | 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 override | core::pack::interaction_graph::InteractionGraphBase | virtual |
get_num_total_states() const override | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
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) override | 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(pack_basic::RotamerSetsBase const &rot_sets) override | 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 typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
pose() const | core::pack::interaction_graph::OnTheFlyInteractionGraph | inline |
PoseOP typedef | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
prepare_graph_for_simulated_annealing() override | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
print() const | core::pack::interaction_graph::InteractionGraphBase | inlinevirtual |
print_current_state_assignment() const override | 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) override | core::pack::interaction_graph::LinearMemoryInteractionGraph | virtual |
set_GlyCorrection_values_for_edge(int node1, int node2, int node_not_neccessarily_glycine, int state, core::PackerEnergy bb_regbb_E, core::PackerEnergy bb_glybb_E, core::PackerEnergy sc_regbb_E, core::PackerEnergy sc_glybb_E) | core::pack::interaction_graph::OnTheFlyInteractionGraph | |
set_network_state(ObjexxFCL::FArray1_int &node_states) override | 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_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_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_regbb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_regbb_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) override | 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 | |
~AnnealableGraphBase() override | core::pack::interaction_graph::AnnealableGraphBase | |
~FixedBBInteractionGraph() override | core::pack::interaction_graph::FixedBBInteractionGraph | inline |
~InteractionGraphBase() override | core::pack::interaction_graph::InteractionGraphBase | |
~LinearMemoryInteractionGraph() override | core::pack::interaction_graph::LinearMemoryInteractionGraph | |
~OnTheFlyInteractionGraph() override | core::pack::interaction_graph::OnTheFlyInteractionGraph | |