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core::pack::interaction_graph::DensePDInteractionGraph Member List

This is the complete list of members for core::pack::interaction_graph::DensePDInteractionGraph, including all inherited members.

aa_submatrix_energies_retrievable() const core::pack::interaction_graph::DensePDInteractionGraphvirtual
aatype_for_node_state(int node_ind, int node_state) const core::pack::interaction_graph::DensePDInteractionGraphvirtual
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_two_body_energies_for_edge(int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
add_to_two_body_energies_for_edge(int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
any_vertex_state_unassigned() const core::pack::interaction_graph::InteractionGraphBase
blanket_assign_state_0()core::pack::interaction_graph::DensePDInteractionGraphvirtual
clear_two_body_energy_for_edge(int node1, int node2, int state_node1, int state_node2)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
commit_considered_substitution()core::pack::interaction_graph::DensePDInteractionGraphvirtual
COMMIT_LIMIT_BETWEEN_UPDATEScore::pack::interaction_graph::DensePDInteractionGraphprivatestatic
consider_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node)core::pack::interaction_graph::DensePDInteractionGraphvirtual
count_connected_components_and_initialize_vertex_groups()core::pack::interaction_graph::InteractionGraphBase
count_dynamic_memory() const core::pack::interaction_graph::DensePDInteractionGraphvirtual
count_static_memory() const core::pack::interaction_graph::DensePDInteractionGraphvirtual
create_new_edge(int index1, int index2)core::pack::interaction_graph::DensePDInteractionGraphprotectedvirtual
create_new_node(int node_index, int num_states)core::pack::interaction_graph::DensePDInteractionGraphprotectedvirtual
declare_edge_energies_final(int node1, int node2)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphvirtual
DensePDInteractionGraph(int num_nodes)core::pack::interaction_graph::DensePDInteractionGraph
DensePDInteractionGraph()core::pack::interaction_graph::DensePDInteractionGraphprivate
DensePDInteractionGraph(DensePDInteractionGraph const &)core::pack::interaction_graph::DensePDInteractionGraphprivate
drop_all_edges_for_node(int node)core::pack::interaction_graph::InteractionGraphBase
drop_edge(std::list< EdgeBase * >::iterator edge)core::pack::interaction_graph::InteractionGraphBaseprotected
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
FixedBBInteractionGraph(int num_nodes)core::pack::interaction_graph::FixedBBInteractionGraphinline
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::DensePDInteractionGraphvirtual
get_dpd_edge(int node1, int node2) const core::pack::interaction_graph::DensePDInteractionGraphinlineprotected
get_dpd_edge(int node1, int node2)core::pack::interaction_graph::DensePDInteractionGraphinlineprotected
get_dpd_node(int index) const core::pack::interaction_graph::DensePDInteractionGraphinlineprotected
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::InteractionGraphBaseinline
get_edge_list_begin() const core::pack::interaction_graph::InteractionGraphBaseinline
get_edge_list_end() const core::pack::interaction_graph::InteractionGraphBaseinline
get_edge_memory_usage() const core::pack::interaction_graph::DensePDInteractionGraphvirtual
get_edge_weight(int node1, int node2) const core::pack::interaction_graph::InteractionGraphBase
get_energy_current_state_assignment()core::pack::interaction_graph::DensePDInteractionGraphvirtual
get_energy_sum_for_vertex_group(int group_id)core::pack::interaction_graph::DensePDInteractionGraphvirtual
get_fixedbb_edge(int node1, int node2) const core::pack::interaction_graph::FixedBBInteractionGraphinlineprotected
get_fixedbb_edge(int node1, int node2)core::pack::interaction_graph::FixedBBInteractionGraphinlineprotected
get_fixedbb_node(int node_index) const core::pack::interaction_graph::FixedBBInteractionGraphinlineprotected
get_fixedbb_node(int node_index)core::pack::interaction_graph::FixedBBInteractionGraphinlineprotected
get_node(int index) const core::pack::interaction_graph::InteractionGraphBaseinline
get_node_state_offset(int index) const core::pack::interaction_graph::InteractionGraphBaseinlineprotected
get_num_aatypes() const core::pack::interaction_graph::DensePDInteractionGraphinlinevirtual
get_num_edges() const core::pack::interaction_graph::InteractionGraphBaseinline
get_num_nodes() const core::pack::interaction_graph::InteractionGraphBaseinline
get_num_nodes_v() const core::pack::interaction_graph::InteractionGraphBaseinlinevirtual
get_num_states_for_node(int node) const core::pack::interaction_graph::InteractionGraphBase
get_num_total_states() const core::pack::interaction_graph::InteractionGraphBaseinline
get_one_body_energy_for_node_state(int node, int state)core::pack::interaction_graph::DensePDInteractionGraphvirtual
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::FixedBBInteractionGraphvirtual
get_vertex_member_of_energy_sum_group(int node_index, int group_id)core::pack::interaction_graph::InteractionGraphBaseinline
getTotalMemoryUsage() const core::pack::interaction_graph::InteractionGraphBasevirtual
increment_edge_list_iterator() const core::pack::interaction_graph::InteractionGraphBase
initialize(rotamer_set::RotamerSetsBase const &rot_sets)core::pack::interaction_graph::DensePDInteractionGraphvirtual
InteractionGraphBase(int num_nodes)core::pack::interaction_graph::InteractionGraphBase
mine(EdgeBase const *edge) const core::pack::interaction_graph::InteractionGraphBaseinlineprotected
node_considering_alt_state_core::pack::interaction_graph::DensePDInteractionGraphprivate
note_vertex_reached(int node_index)core::pack::interaction_graph::InteractionGraphBase
num_commits_since_last_update_core::pack::interaction_graph::DensePDInteractionGraphprivate
operator=(DensePDInteractionGraph const &)core::pack::interaction_graph::DensePDInteractionGraphprivate
output_connectivity(std::ostream &os) const core::pack::interaction_graph::InteractionGraphBase
output_dimacs(std::ostream &os) const core::pack::interaction_graph::InteractionGraphBase
PrecomputedPairEnergiesInteractionGraph(int num_nodes)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphinline
prepare_for_simulated_annealing()core::pack::interaction_graph::InteractionGraphBasevirtual
print() const core::pack::interaction_graph::InteractionGraphBaseinlinevirtual
print_current_state_assignment() const core::pack::interaction_graph::DensePDInteractionGraphvirtual
print_vertex_groups()core::pack::interaction_graph::InteractionGraphBase
print_vertices() const core::pack::interaction_graph::InteractionGraphBase
reset_edge_list_iterator_for_node(int node_index) const core::pack::interaction_graph::InteractionGraphBase
set_edge_weight(int node1, int node2, Real edge_weight)core::pack::interaction_graph::InteractionGraphBase
set_errorfull_deltaE_threshold(core::PackerEnergy)core::pack::interaction_graph::DensePDInteractionGraphinlinevirtual
set_network_state(ObjexxFCL::FArray1_int &node_states)core::pack::interaction_graph::DensePDInteractionGraphvirtual
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_sparse_aa_info_for_edge(int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info)core::pack::interaction_graph::FixedBBInteractionGraph
set_state_for_node(int node_ind, int new_state)core::pack::interaction_graph::DensePDInteractionGraphvirtual
set_two_body_energy_for_edge(int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
set_vertex_member_of_group(int vertex, int group)core::pack::interaction_graph::InteractionGraphBase
swap_edge_energies(int node1, int node2, ObjexxFCL::FArray2D< core::PackerEnergy > &new_edge_table)core::pack::interaction_graph::DensePDInteractionGraph
total_energy_alternate_state_assignment_core::pack::interaction_graph::DensePDInteractionGraphprivate
total_energy_current_state_assignment_core::pack::interaction_graph::DensePDInteractionGraphprivate
update_internal_energy_totals()core::pack::interaction_graph::DensePDInteractionGraphprotected
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
~FixedBBInteractionGraph()core::pack::interaction_graph::FixedBBInteractionGraphinlinevirtual
~InteractionGraphBase()core::pack::interaction_graph::InteractionGraphBasevirtual
~PrecomputedPairEnergiesInteractionGraph()core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphinlinevirtual