Bindings for core::pack::interaction_graph namespace

Classes
		builtins.object AnnealableGraphBase InteractionGraphBase FixedBBInteractionGraph OnTheFlyInteractionGraph DoubleLazyInteractionGraph LazyInteractionGraph LinearMemoryInteractionGraph PrecomputedPairEnergiesInteractionGraph DensePDInteractionGraph DoubleDensePDInteractionGraph FASTERInteractionGraph PDInteractionGraph SymmOnTheFlyInteractionGraph SymmLinearMemoryInteractionGraph SymmMinimalistInteractionGraph MultiplexedAnnealableGraph ResidueArrayAnnealingEvaluator DotSphere EdgeBase FixedBBEdge OnTheFlyEdge DoubleLazyEdge LazyEdge LinearMemEdge PrecomputedPairEnergiesEdge DensePDEdge DoubleDensePDEdge FASTEREdge PDEdge SymmOnTheFlyEdge SymmLinearMemEdge SymmMinimalistEdge InteractionGraphFactory InvRotamerDots NodeBase FixedBBNode OnTheFlyNode DoubleLazyNode LazyNode LinearMemNode PrecomputedPairEnergiesNode DensePDNode DoubleDensePDNode FASTERNode PDNode SymmOnTheFlyNode SymmLinearMemNode SymmMinimalistNode ResiduePairEvalType RotamerDots RotamerDotsCache SparseMatrixIndex exposed_hydrophobic_data history_queue_struct rosetta.core.graph.Edge(builtins.object) SimpleEdge rosetta.core.graph.Graph(builtins.object) SimpleInteractionGraph rosetta.core.graph.Node(builtins.object) SimpleNode rosetta.core.scoring.methods.ContextDependentOneBodyEnergy(rosetta.core.scoring.methods.OneBodyEnergy) HPatchEnergy SurfaceEnergy rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object) HPatchEnergyCreator SurfaceEnergyCreator rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t(builtins.object) RotamerDotsRadiusData rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t(builtins.object) SurfacePotential   class AnnealableGraphBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> NoneType   2. __init__(rosetta.core.pack.interaction_graph.AnnealableGraphBase, rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> bool   Is any state of any vertex unassigned?      Must be implemented by derived classes. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> NoneType   State initialization      Must be implemented by derived classes. commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> float   Accept a considered substitution (i.e. make the substitution permanent; commit it).      Must be implemented by derived classes. consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType   Consider switching node "node_ind" to state "new_state".      Must be implemented by derived classes.      The node index.      The state index that we are considering switching TO.      The change in energy that results from the switch under consideration, computed by this function.      The energy of this node prior to the substitutio, returned by this function. get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> float   Get the energy resulting from the current set of state assignments.      Must be implemented by derived classes. get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> int   Get the number of nodes in the graph.      Must be implemented by derived classes. get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase, node : int) -> int   Get the number of states for a node in the graph.      Must be implemented by derived classes. get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> int   Get the total number of states.      Must be implemented by derived classes. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> NoneType   Utility signal.      Must be implemented by derived classes. set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase, deltaE : float) -> NoneType   Set an error threshhold.      Must be implemented by derived classes. set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float   Explicit state modification for the network.      Must be implemented by derived classes. set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase, node_ind : int, new_state : int) -> float   Explicit state modification for a node.      Must be implemented by derived classes.   class DensePDEdge(PrecomputedPairEnergiesEdge)       Method resolution order: DensePDEdge PrecomputedPairEnergiesEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.DensePDEdge, node_ind : int, new_state : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.DensePDEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.DensePDEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int) -> NoneType add_to_two_body_energies(...) from builtins.PyCapsule add_to_two_body_energies(self : rosetta.core.pack.interaction_graph.DensePDEdge, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType add_to_two_body_energy(...) from builtins.PyCapsule add_to_two_body_energy(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int,  : float) -> NoneType clear_two_body_energy(...) from builtins.PyCapsule clear_two_body_energy(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DensePDEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DensePDEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.DensePDEdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.DensePDEdge) -> NoneType get_aa_submatrix_energies(...) from builtins.PyCapsule get_aa_submatrix_energies(rosetta.core.pack.interaction_graph.DensePDEdge) -> ObjexxFCL::FArray2D<float>   return all energies on this edge... get_alternate_state_energy(...) from builtins.PyCapsule get_alternate_state_energy(first_node_state : int, second_node_state : int, edge_energy_table : rosetta.ObjexxFCL.FArray2_float_t) -> float get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.DensePDEdge) -> float get_edge_table_ptr(...) from builtins.PyCapsule get_edge_table_ptr(rosetta.core.pack.interaction_graph.DensePDEdge) -> ObjexxFCL::FArray2A<float> get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.DensePDEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DensePDEdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.DensePDEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType set_two_body_energy(...) from builtins.PyCapsule set_two_body_energy(self : rosetta.core.pack.interaction_graph.DensePDEdge,  : int,  : int,  : float) -> NoneType swap_edge_energies(...) from builtins.PyCapsule swap_edge_energies(self : rosetta.core.pack.interaction_graph.DensePDEdge, new_edge_table : ObjexxFCL::FArray2D<float>) -> NoneType Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class DensePDInteractionGraph(PrecomputedPairEnergiesInteractionGraph)       Method resolution order: DensePDInteractionGraph PrecomputedPairEnergiesInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> bool   Override the InteractionGraphBase class's implementation of this function  to return 'true'. aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind : int, node_state : int) -> int blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> float   Accepts (commits) the state change previously considered in a call to  consider_substitution and returns the energy of the entire graph consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> int get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> int   returns the number of floats used in all edge two-body energy tables get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> float   removes all accumulated numerical drift and returns the  energy for the current state assignment. get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, group_id : int) -> float   a user may define subsets of the vertex set for which they would like to  know the internal energy sum. get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.DensePDInteractionGraph) -> NoneType   outputs the current state for each node, useful for debugging set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph,  : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind : int, new_state : int) -> float swap_edge_energies(...) from builtins.PyCapsule swap_edge_energies(self : rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node1 : int, node2 : int, new_edge_table : ObjexxFCL::FArray2D<float>) -> NoneType   Swap the contents of the edge pair-energy table with the contents in the new_edge_table Methods inherited from PrecomputedPairEnergiesInteractionGraph: add_to_two_body_energies_for_edge(...) from builtins.PyCapsule add_to_two_body_energies_for_edge(*args, **kwargs) Overloaded function.   1. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType   interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies   2. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies clear_two_body_energy_for_edge(...) from builtins.PyCapsule clear_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> NoneType   interface to PDEdge::clear_two_body_energy declare_edge_energies_final(...) from builtins.PyCapsule declare_edge_energies_final(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int) -> NoneType set_two_body_energy_for_edge(...) from builtins.PyCapsule set_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PDEdge::set_two_body_energy Methods inherited from FixedBBInteractionGraph: force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class DensePDNode(PrecomputedPairEnergiesNode)       Method resolution order: DensePDNode PrecomputedPairEnergiesNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.DensePDNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int) -> NoneType add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.DensePDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.DensePDNode, state : int, energy : float) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.DensePDNode, new_state : int) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DensePDNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DensePDNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.DensePDNode) -> int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.DensePDNode, state : int) -> float get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.DensePDNode) -> float prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.DensePDNode, alternate_state : int, prev_node_energy : float) -> float state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.DensePDNode) -> bool update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.DensePDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.DensePDNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.DensePDNode) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class DotSphere(builtins.object)     Represents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA.       For every atom in a protein, the vdW surface is patterned with dots. Each dot has to keep track of how many other residues are "covering" this dot. So, that's 1 character for each dot.  Each character is the count of the number of residues overlapping with this dot.  An assumption we're making here is that a single atom (or really, dot) will never be covered by more than 255 residues.   In this implementation of the LeGrand and Merz algorithm, we're going to be using 162 dots per atom. Turns out that you can distribute 162 dots evenly on the surface of a sphere.   This class is extremely simple. The RotamerDots class below does all the work of tying a particular residues atoms to DotSpheres. As a matter of fact, DotSphere doesn't even know what atom it's representing. It just has the one C-style array for the coverage count and that's it.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.DotSphere) -> NoneType   2. __init__(self : rosetta.core.pack.interaction_graph.DotSphere, rhs : rosetta.core.pack.interaction_graph.DotSphere) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.pack.interaction_graph.DotSphere, rhs : rosetta.core.pack.interaction_graph.DotSphere) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.pack.interaction_graph.DotSphere) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.DotSphere, rhs : rosetta.core.pack.interaction_graph.DotSphere) -> rosetta.core.pack.interaction_graph.DotSphere count_num_covered(...) from builtins.PyCapsule count_num_covered(rosetta.core.pack.interaction_graph.DotSphere) -> NoneType get_dot_covered(...) from builtins.PyCapsule get_dot_covered(self : rosetta.core.pack.interaction_graph.DotSphere, dot_index : int) -> bool get_num_covered(...) from builtins.PyCapsule get_num_covered(rosetta.core.pack.interaction_graph.DotSphere) -> int get_num_uncovered(...) from builtins.PyCapsule get_num_uncovered(rosetta.core.pack.interaction_graph.DotSphere) -> int get_total_dots(...) from builtins.PyCapsule get_total_dots(rosetta.core.pack.interaction_graph.DotSphere) -> int zero(...) from builtins.PyCapsule zero(rosetta.core.pack.interaction_graph.DotSphere) -> NoneType   class DoubleDensePDEdge(PrecomputedPairEnergiesEdge)       Method resolution order: DoubleDensePDEdge PrecomputedPairEnergiesEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge, node_ind : int, new_state : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int) -> NoneType add_to_two_body_energies(...) from builtins.PyCapsule add_to_two_body_energies(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType add_to_two_body_energy(...) from builtins.PyCapsule add_to_two_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int,  : float) -> NoneType clear_two_body_energy(...) from builtins.PyCapsule clear_two_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> NoneType get_alternate_state_energy(...) from builtins.PyCapsule get_alternate_state_energy(first_node_state : int, second_node_state : int, edge_energy_table : rosetta.ObjexxFCL.FArray2_float_t) -> float get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DoubleDensePDEdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType set_two_body_energy(...) from builtins.PyCapsule set_two_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDEdge,  : int,  : int,  : float) -> NoneType Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class DoubleDensePDInteractionGraph(PrecomputedPairEnergiesInteractionGraph)       Method resolution order: DoubleDensePDInteractionGraph PrecomputedPairEnergiesInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> float   Accepts (commits) the state change previously considered in a call to  consider_substitution and returns the energy of the entire graph consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> int get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> int   returns the number of floats used in all edge two-body energy tables get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> float   removes all accumulated numerical drift and returns the  energy for the current state assignment. get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, group_id : int) -> float   a user may define subsets of the vertex set for which they would like to  know the internal energy sum. get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) -> NoneType   outputs the current state for each node, useful for debugging set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph,  : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from PrecomputedPairEnergiesInteractionGraph: add_to_two_body_energies_for_edge(...) from builtins.PyCapsule add_to_two_body_energies_for_edge(*args, **kwargs) Overloaded function.   1. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType   interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies   2. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies clear_two_body_energy_for_edge(...) from builtins.PyCapsule clear_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> NoneType   interface to PDEdge::clear_two_body_energy declare_edge_energies_final(...) from builtins.PyCapsule declare_edge_energies_final(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int) -> NoneType set_two_body_energy_for_edge(...) from builtins.PyCapsule set_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PDEdge::set_two_body_energy Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class DoubleDensePDNode(PrecomputedPairEnergiesNode)       Method resolution order: DoubleDensePDNode PrecomputedPairEnergiesNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int) -> NoneType add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, state : int, energy : float) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, new_state : int) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, state : int) -> float get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> float prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, alternate_state : int, prev_node_energy : float) -> float state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> bool update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.DoubleDensePDNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.DoubleDensePDNode) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class DoubleLazyEdge(OnTheFlyEdge)       Method resolution order: DoubleLazyEdge OnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_change(...) from builtins.PyCapsule acknowledge_partial_state_change(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int, nodes_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType actual_twobody_memory_use(...) from builtins.PyCapsule actual_twobody_memory_use(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> int build_sc_only_rotamer(...) from builtins.PyCapsule build_sc_only_rotamer(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> bool count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> NoneType drop_aa_submatrix(...) from builtins.PyCapsule drop_aa_submatrix(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, submat_ind : int) -> int   For use by the DoubleLazyInteractionGraph only; if the DLIG is in "memory conservation"  mode, then it may request that its edges drop certain amino acid submatrices which have not been activated  for a "long time."  This function will cause an amino-acid submatrix to be dropped, and will return  the number of bytes that have been freed in the process. "const" but accesses mutable data force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> NoneType get_aa_submatrix_energies(...) from builtins.PyCapsule get_aa_submatrix_energies(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> float get_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1state : int, node2state : int) -> float get_two_body_energy_smi(...) from builtins.PyCapsule get_two_body_energy_smi(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1state : int, node2state : int, node1info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, node2info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> int potential_twobody_memory_use(...) from builtins.PyCapsule potential_twobody_memory_use(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> NoneType print_current_energy(...) from builtins.PyCapsule print_current_energy(rosetta.core.pack.interaction_graph.DoubleLazyEdge) -> NoneType set_edge_index(...) from builtins.PyCapsule set_edge_index(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, index : int) -> NoneType   For use by the DoubleLazyInteractionGraph only;  sets the edge index for this edge -- this is an arbitrary  index, but is used to so that the DLIG can communicate back  and forth with this edge. set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.DoubleLazyEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType Methods inherited from OnTheFlyEdge: eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind : int, state : int) -> float long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType set_ProCorrection_values(...) from builtins.PyCapsule set_ProCorrection_values(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class DoubleLazyInteractionGraph(OnTheFlyInteractionGraph)     The double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs.     Method resolution order: DoubleLazyInteractionGraph OnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, numNodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> bool   Override the FixedBBInteractionGraph class's implementation of this function  to return 'true'. aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind : int, node_state : int) -> int blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> int get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> int get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, group_id : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType note_submatrix_accessed(...) from builtins.PyCapsule note_submatrix_accessed(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, edge_index : int, submatrix_index : int) -> NoneType   For use only from the DoubleLazyEdge; the DLE will  report to the DLIG after it a rotamer pair energy submatrix  has been read from.  The DLIG keeps track of how recently each  submatrix has been accessed to ensure that, when it does ask  an edge to drop a submatrix, the submatrix being dropped  is the one that was accessed most distantly in the past. note_submatrix_added(...) from builtins.PyCapsule note_submatrix_added(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, edge_index : int, submatrix_index : int, submatrix_size : int) -> NoneType   For use only from the DoubleLazyEdge; the DLE will report  to the DLIG after it adds a submatrix of rotamer pair energies  (that is, all the RPEs for a particular pair of amino acids)  that it has done so; the DLIG monitors the access and the memory  usage of the various submatrices in the graph, and may, during  this function call, request that various edges (possibly the one  invoking this function!) drop some of their submatrices. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, deltaE : float) -> NoneType set_memory_max_for_rpes(...) from builtins.PyCapsule set_memory_max_for_rpes(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, setting : int) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from OnTheFlyInteractionGraph: add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, state : int) -> float non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_ProCorrection_values_for_edge(...) from builtins.PyCapsule set_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class DoubleLazyNode(OnTheFlyNode)       Method resolution order: DoubleLazyNode OnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aatype_for_state(...) from builtins.PyCapsule aatype_for_state(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, state : int) -> int acknowledge_neighbors_partial_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_substitution(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, edge_to_altered_neighbor : int, other_node_new_ : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, new_state : int) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType complete_state_assignment(...) from builtins.PyCapsule complete_state_assignment(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType compute_pair_energy_for_current_state(...) from builtins.PyCapsule compute_pair_energy_for_current_state(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, edge_making_energy_request : int) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> int get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> float get_sparse_mat_info_for_curr_state(...) from builtins.PyCapsule get_sparse_mat_info_for_curr_state(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_totalE(...) from builtins.PyCapsule get_totalE(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> float partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, new_state : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.DoubleLazyNode, alternate_state : int, prev_node_energy : float) -> float state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> bool update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.DoubleLazyNode) -> NoneType Methods inherited from OnTheFlyNode: add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, setting : bool) -> NoneType get_num_aa_types(...) from builtins.PyCapsule get_num_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int get_num_states_for_aa_type(...) from builtins.PyCapsule get_num_states_for_aa_type(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aa_type : int) -> int get_num_states_for_aa_types(...) from builtins.PyCapsule get_num_states_for_aa_types(*args, **kwargs) Overloaded function.   1. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> float get_sparse_mat_info_for_state(...) from builtins.PyCapsule get_sparse_mat_info_for_state(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_state_offset_for_aatype(...) from builtins.PyCapsule get_state_offset_for_aatype(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aatype : int) -> int set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, rotamers : core::pack::rotamer_set::RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class EdgeBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.EdgeBase, owner : core::pack::interaction_graph::InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.EdgeBase, weight : float) -> NoneType set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class FASTEREdge(PrecomputedPairEnergiesEdge)       Method resolution order: FASTEREdge PrecomputedPairEnergiesEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_assignment(...) from builtins.PyCapsule acknowledge_partial_state_assignment(self : rosetta.core.pack.interaction_graph.FASTEREdge, node : int, new_state : int) -> NoneType acknowledge_participation_in_perturbation(...) from builtins.PyCapsule acknowledge_participation_in_perturbation(rosetta.core.pack.interaction_graph.FASTEREdge) -> NoneType acknowledge_perturbed_state(...) from builtins.PyCapsule acknowledge_perturbed_state(self : rosetta.core.pack.interaction_graph.FASTEREdge, node : int, neighbors_context_state : int) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.FASTEREdge, node_ind : int, new_state : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.FASTEREdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.FASTEREdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int) -> NoneType add_to_two_body_energies(...) from builtins.PyCapsule add_to_two_body_energies(self : rosetta.core.pack.interaction_graph.FASTEREdge, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType add_to_two_body_energy(...) from builtins.PyCapsule add_to_two_body_energy(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int,  : float) -> NoneType clear_two_body_energy(...) from builtins.PyCapsule clear_two_body_energy(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.FASTEREdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.FASTEREdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.FASTEREdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.FASTEREdge) -> NoneType get_alternate_state_energy(...) from builtins.PyCapsule get_alternate_state_energy(first_node_state : int, second_node_state : int, edge_energy_table : rosetta.ObjexxFCL.FArray2_float_t) -> float get_curr_state_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_curr_state_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.FASTEREdge) -> float get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.FASTEREdge) -> float get_deltaE_for_neighbor_following_perturbation(...) from builtins.PyCapsule get_deltaE_for_neighbor_following_perturbation(self : rosetta.core.pack.interaction_graph.FASTEREdge, node_index : int) -> float get_deltaE_for_perturbation(...) from builtins.PyCapsule get_deltaE_for_perturbation(rosetta.core.pack.interaction_graph.FASTEREdge) -> float get_edge_table_ptr(...) from builtins.PyCapsule get_edge_table_ptr(rosetta.core.pack.interaction_graph.FASTEREdge) -> ObjexxFCL::FArray2A<float> get_energy_for_perturbed_state(...) from builtins.PyCapsule get_energy_for_perturbed_state(self : rosetta.core.pack.interaction_graph.FASTEREdge, node : int, nodes_perturbed_state : int) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int) -> bool get_two_body_energies_for_relaxed_states(...) from builtins.PyCapsule get_two_body_energies_for_relaxed_states(rosetta.core.pack.interaction_graph.FASTEREdge) -> float get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.FASTEREdge) -> int prepare_for_FASTER(...) from builtins.PyCapsule prepare_for_FASTER(rosetta.core.pack.interaction_graph.FASTEREdge) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.FASTEREdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.FASTEREdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : ObjexxFCL::FArray2<bool>) -> NoneType set_two_body_energy(...) from builtins.PyCapsule set_two_body_energy(self : rosetta.core.pack.interaction_graph.FASTEREdge,  : int,  : int,  : float) -> NoneType swap_edge_energies(...) from builtins.PyCapsule swap_edge_energies(self : rosetta.core.pack.interaction_graph.FASTEREdge, new_edge_table : ObjexxFCL::FArray2D<float>) -> NoneType Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class FASTERInteractionGraph(PrecomputedPairEnergiesInteractionGraph)       Method resolution order: FASTERInteractionGraph PrecomputedPairEnergiesInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign_BMEC(...) from builtins.PyCapsule assign_BMEC(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> float   Accepts (commits) the state change previously considered in a call to  consider_substitution and returns the energy of the entire graph commit_relaxation(...) from builtins.PyCapsule commit_relaxation(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> int get_current_network_state(...) from builtins.PyCapsule get_current_network_state(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, netstate : ObjexxFCL::FArray1<int>) -> NoneType get_current_state_for_node(...) from builtins.PyCapsule get_current_state_for_node(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind : int) -> int get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> int   returns the number of core::PackerEnergys used in all edge two-body energy tables get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> float   removes all accumulated numerical drift and returns the  energy for the current state assignment. get_energy_following_relaxation(...) from builtins.PyCapsule get_energy_following_relaxation(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, group_id : int) -> float   a user may define subsets of the vertex set for which they would like to  know the internal energy sum. get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node : int, state : int) -> float get_random_neighbor_for_node(...) from builtins.PyCapsule get_random_neighbor_for_node(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node : int) -> int initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType perturb_dBR_and_relax(...) from builtins.PyCapsule perturb_dBR_and_relax(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node1 : int, perturbed_state1 : int, node2 : int, perturbed_state2 : int) -> float perturb_sBR_and_relax(...) from builtins.PyCapsule perturb_sBR_and_relax(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node : int, perturbed_state : int) -> float prepare_for_FASTER(...) from builtins.PyCapsule prepare_for_FASTER(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType   outputs the current state for each node, useful for debugging probabilistically_commit_relaxation(...) from builtins.PyCapsule probabilistically_commit_relaxation(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, probability : float) -> NoneType reject_perturbation(...) from builtins.PyCapsule reject_perturbation(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType relax_in_current_context(...) from builtins.PyCapsule relax_in_current_context(rosetta.core.pack.interaction_graph.FASTERInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph,  : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind : int, new_state : int) -> float swap_edge_energies(...) from builtins.PyCapsule swap_edge_energies(self : rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node1 : int, node2 : int, new_edge_table : ObjexxFCL::FArray2D<float>) -> NoneType   Swap the contents of the edge pair-energy table with the contents in the new_edge_table Methods inherited from PrecomputedPairEnergiesInteractionGraph: add_to_two_body_energies_for_edge(...) from builtins.PyCapsule add_to_two_body_energies_for_edge(*args, **kwargs) Overloaded function.   1. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType   interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies   2. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies clear_two_body_energy_for_edge(...) from builtins.PyCapsule clear_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> NoneType   interface to PDEdge::clear_two_body_energy declare_edge_energies_final(...) from builtins.PyCapsule declare_edge_energies_final(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int) -> NoneType set_two_body_energy_for_edge(...) from builtins.PyCapsule set_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PDEdge::set_two_body_energy Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class FASTERNode(PrecomputedPairEnergiesNode)       Method resolution order: FASTERNode PrecomputedPairEnergiesNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_neighbors_partial_state_assignment(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_assignment(self : rosetta.core.pack.interaction_graph.FASTERNode, which_neighbor : int, neighbors_new_state : int) -> NoneType acknowledge_neighbors_perturbed_state(...) from builtins.PyCapsule acknowledge_neighbors_perturbed_state(self : rosetta.core.pack.interaction_graph.FASTERNode, which_neighbor : int, neighbors_perturbed_state : int) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.FASTERNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int) -> NoneType add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.FASTERNode, energies : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.FASTERNode, state : int, energy : float) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.FASTERNode, new_state : int) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType complete_partial_state_assignment(...) from builtins.PyCapsule complete_partial_state_assignment(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.FASTERNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.FASTERNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.FASTERNode) -> int get_deltaE_for_relaxed_state_following_perturbation(...) from builtins.PyCapsule get_deltaE_for_relaxed_state_following_perturbation(rosetta.core.pack.interaction_graph.FASTERNode) -> float get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.FASTERNode, state : int) -> float get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.FASTERNode) -> float get_one_body_energy_for_relaxed_state(...) from builtins.PyCapsule get_one_body_energy_for_relaxed_state(rosetta.core.pack.interaction_graph.FASTERNode) -> float get_random_neighbor(...) from builtins.PyCapsule get_random_neighbor(rosetta.core.pack.interaction_graph.FASTERNode) -> int get_relaxed_state(...) from builtins.PyCapsule get_relaxed_state(rosetta.core.pack.interaction_graph.FASTERNode) -> int get_total_energy_in_curr_state_assignment_for_all_states(...) from builtins.PyCapsule get_total_energy_in_curr_state_assignment_for_all_states(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType partial_assign_relaxed_state(...) from builtins.PyCapsule partial_assign_relaxed_state(self : rosetta.core.pack.interaction_graph.FASTERNode, probability : float) -> NoneType partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.FASTERNode, state : int) -> NoneType partial_assign_state_with_lowest_one_body_energy(...) from builtins.PyCapsule partial_assign_state_with_lowest_one_body_energy(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType prep_for_neighbors_perturbation(...) from builtins.PyCapsule prep_for_neighbors_perturbation(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType prepare_for_FASTER(...) from builtins.PyCapsule prepare_for_FASTER(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType prepare_for_perturbation(...) from builtins.PyCapsule prepare_for_perturbation(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.FASTERNode, alternate_state : int, prev_node_energy : float) -> float relax(...) from builtins.PyCapsule relax(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType relax_after_neighbors_perturbation(...) from builtins.PyCapsule relax_after_neighbors_perturbation(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType relax_neighbors(...) from builtins.PyCapsule relax_neighbors(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType reset_relaxed(...) from builtins.PyCapsule reset_relaxed(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType reset_relaxed_for_neighbors(...) from builtins.PyCapsule reset_relaxed_for_neighbors(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType set_no_longer_perturbed(...) from builtins.PyCapsule set_no_longer_perturbed(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType set_perturbed_state(...) from builtins.PyCapsule set_perturbed_state(self : rosetta.core.pack.interaction_graph.FASTERNode, perturbed_state : int) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.FASTERNode) -> bool tell_neighbors_to_prep_for_relaxation(...) from builtins.PyCapsule tell_neighbors_to_prep_for_relaxation(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.FASTERNode, energies : ObjexxFCL::FArray1<float>) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.FASTERNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.FASTERNode) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class FixedBBEdge(EdgeBase)       Method resolution order: FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.FixedBBEdge, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.FixedBBEdge) -> NoneType get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.FixedBBEdge,  : int,  : int) -> float set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType Methods inherited from EdgeBase: count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.EdgeBase, weight : float) -> NoneType set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class FixedBBInteractionGraph(InteractionGraphBase)       Method resolution order: FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> int get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, state : int) -> float get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int) -> float set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class FixedBBNode(NodeBase)       Method resolution order: FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.FixedBBNode, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.NodeBase, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.NodeBase) -> bool update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType   class HPatchEnergy(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy)     Defines a (pseudo) context-dependent one-body surface energy.  Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A.     Method resolution order: HPatchEnergy rosetta.core.scoring.methods.ContextDependentOneBodyEnergy rosetta.core.scoring.methods.OneBodyEnergy rosetta.core.scoring.methods.EnergyMethod builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.HPatchEnergy,  : rosetta.core.pack.interaction_graph.HPatchEnergy) -> rosetta.core.pack.interaction_graph.HPatchEnergy clone(...) from builtins.PyCapsule clone(rosetta.core.pack.interaction_graph.HPatchEnergy) -> rosetta.core.scoring.methods.EnergyMethod finalize_total_energy(...) from builtins.PyCapsule finalize_total_energy(self : rosetta.core.pack.interaction_graph.HPatchEnergy, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction, totals : rosetta.core.scoring.EMapVector) -> NoneType indicate_required_context_graphs(...) from builtins.PyCapsule indicate_required_context_graphs(self : rosetta.core.pack.interaction_graph.HPatchEnergy,  : rosetta.utility.vector1_bool) -> NoneType residue_energy(...) from builtins.PyCapsule residue_energy(self : rosetta.core.pack.interaction_graph.HPatchEnergy, rsd : rosetta.core.conformation.Residue,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.EMapVector) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.pack.interaction_graph.HPatchEnergy, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction) -> NoneType version(...) from builtins.PyCapsule version(rosetta.core.pack.interaction_graph.HPatchEnergy) -> int Methods inherited from rosetta.core.scoring.methods.ContextDependentOneBodyEnergy: method_type(...) from builtins.PyCapsule method_type(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType   Returns the cd_1b element of the EnergyMethodType enumeration; this method  should NOT be overridden by derived classes. Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy: defines_dof_derivatives(...) from builtins.PyCapsule defines_dof_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, p : rosetta.core.pose.Pose) -> bool   Use the dof_derivative interface for this energy method when  calculating derivatives?  It is possible to define both dof_derivatives and  atom-derivatives; they are not mutually exclusive. defines_score_for_residue(...) from builtins.PyCapsule defines_score_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy,  : rosetta.core.conformation.Residue) -> bool   During minimization, energy methods are allowed to decide that they say nothing  about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for  a derivative or an energy.  The default behavior is to return "true" for all residues. eval_residue_derivatives(...) from builtins.PyCapsule eval_residue_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType   Evaluate the derivatives for all atoms on this residue and increment them  into the input atom_derivs vector1.  The calling function must guarantee that  setup for derivatives is called before this function is, and that the atom_derivs  vector contains at least as many entries as there are atoms in the input Residue.  This base class provides a default noop implementation of this function. eval_residue_dof_derivative(...) from builtins.PyCapsule eval_residue_dof_derivative(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, dof_id : rosetta.core.id.DOF_ID, torsion_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector) -> float   Evaluate the DOF derivative for a particular residue.  The Pose merely serves as context,  and the input residue is not required to be a member of the Pose. requires_a_setup_for_derivatives_for_residue_opportunity(...) from builtins.PyCapsule requires_a_setup_for_derivatives_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : rosetta.core.pose.Pose) -> bool   Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins?  Not  all energy methods would.  The ScoreFunction will not ask energy methods to examine residues that are uninterested  in doing so. requires_a_setup_for_scoring_for_residue_opportunity(...) from builtins.PyCapsule requires_a_setup_for_scoring_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : rosetta.core.pose.Pose) -> bool   Does this EnergyMethod require the opportunity to examine the residue before scoring begins?  Not  all energy methods would.  The ScoreFunction will not ask energy methods to examine residues that are uninterested  in doing so. residue_energy_ext(...) from builtins.PyCapsule residue_energy_ext(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Evaluate the one-body energies for a particular residue, in the context of a  given Pose, and with the help of a piece of cached data for minimization, increment those  one body energies into the input EnergyMap.  The calling function must guarantee that this  EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object  for the given residue in a call to setup_for_minimizing_for_residue before this function is  invoked. This function should not be called unless the use_extended_residue_energy_interface()  method returns "true".  Default implementation provided by this base class calls  utility::exit(). The Pose merely serves as context, and the input residue is not required  to be a member of the Pose. setup_for_derivatives_for_residue(...) from builtins.PyCapsule setup_for_derivatives_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType   Do any setup work necessary before evaluating the derivatives for this residue setup_for_minimizing_for_residue(...) from builtins.PyCapsule setup_for_minimizing_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction,  : rosetta.core.kinematics.MinimizerMapBase,  : core::scoring::ResSingleMinimizationData) -> NoneType   Called at the beginning of minimization, allowing this energy method to cache data  pertinent for a single residue in the the ResSingleMinimizationData that is used for a  particular residue in the context of a particular Pose.  This base class provides a noop  implementation for this function if there is nothing that the derived class needs to perform  in this setup phase.   The Pose merely serves as context, and the input residue is not  required to be a member of the Pose. setup_for_scoring_for_residue(...) from builtins.PyCapsule setup_for_scoring_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType   Do any setup work should the coordinates of this residue, who is still guaranteed to be  of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically  as to possibly require some amount of setup work before scoring should proceed use_extended_residue_energy_interface(...) from builtins.PyCapsule use_extended_residue_energy_interface(rosetta.core.scoring.methods.OneBodyEnergy) -> bool   Rely on the extended version of the residue_energy function during score-function  evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData.  Return 'true' for the extended version.  The default method implemented in this class returns 'false' Methods inherited from rosetta.core.scoring.methods.EnergyMethod: defines_high_order_terms(...) from builtins.PyCapsule defines_high_order_terms(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose) -> bool   Should this EnergyMethod have score and derivative evaluation  evaluated both in the context of the whole Pose and in the context  of residue or residue-pairs?  This covers scoring terms like env-smooth  wherein the CBeta's get derivatives for increasing the neighbor counts  for surrounding residues, and terms like constraints, which are definable  on arbitrary number of residues (e.g. more than 2); both of these terms  could be used in RTMin, and both should use the residue and residue-pair  evaluation scheme with the MinimizationGraph for the majority of the  work they do.  (Now, high-order constraints (3-body or above) will not  be properly evaluated within RTMin.).  The default implementation  returns "false". eval_atom_derivative(...) from builtins.PyCapsule eval_atom_derivative(self : rosetta.core.scoring.methods.EnergyMethod, id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType   Evaluate the XYZ derivative for an atom in the pose.  Called during the atomtree derivative calculation, atom_tree_minimize.cc,  through the ScoreFunction::eval_atom_derivative intermediary.  F1 and F2 should not zeroed, rather, this class should accumulate its contribution  from this atom's XYZ derivative      The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984)  "Rapid Calculation of First and Second Derivatives of Conformational Energy with  Respect to Dihedral Angles for Proteins. General Recurrent Equations"  Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga,  respectively, of equations 7a & 7b in that paper. finalize_after_derivatives(...) from builtins.PyCapsule finalize_after_derivatives(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction) -> NoneType   called at the end of derivatives evaluation minimize_in_whole_structure_context(...) from builtins.PyCapsule minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose) -> bool   Should this EnergyMethod have score and derivative evaluation  evaluated only in the context of the whole Pose, or can it be included  in a decomposed manner for a residue or a set of residue-pairs that are  not part of the Pose that's serving as their context?  The default  method implemented in the base class returns true in order to grandfather  in EnergyMethods that have not had their derivatives changed to take  advantage of the new derivative-evaluation machinery.  Methods that return  "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext)  methods invoked by the ScoreFunction during its traversal of the  MinimizationGraph, and instead will be asked to perform all their work  during finalize_total_energies().  Similarly, they will be expected to  perform all their work during eval_atom_deriv() instead of during the  ScoreFunction's traversal of the MinimizationGraph for derivative evaluation.  IMPORTANT: Methods that return "true" cannot be included in RTMin. prepare_rotamers_for_packing(...) from builtins.PyCapsule prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType   If an energy method needs to cache data in a packing::RotamerSet object before  rotamer energies are calculated, it does so during this function. The packer  must ensure this function is called. The default behavior is to do nothing. score_types(...) from builtins.PyCapsule score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType   Returns the score types that this energy method computes. setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Called immediately before atom- and DOF-derivatives are calculated  allowing the derived class a chance to prepare for future calls. setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction,  : rosetta.core.kinematics.MinimizerMapBase) -> NoneType   Called at the beginning of atom tree minimization, this method  allows the derived class the opportunity to initialize pertinent data  that will be used during minimization.  During minimzation, the chemical  structure of the pose is constant, so assumptions on the number of atoms  per residue and their identities are safe so long as the pose's Energies  object's "use_nblist()" method returns true. setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool,  : rosetta.utility.vector1_bool) -> NoneType   if an energy method needs to cache data in the Energies object,  before packing begins, then it does so during this function. The packer  must ensure this function is called. The default behavior is to do nothing. update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose, resid : int) -> NoneType   If the pose changes in the middle of a packing (as happens in rotamer trials) and if  an energy method needs to cache data in the pose that corresponds to its current state,  then the method must update that data when this function is called.  The packer must  ensure this function gets called.  The default behavior is to do nothing.   class HPatchEnergyCreator(rosetta.core.scoring.methods.EnergyMethodCreator)       Method resolution order: HPatchEnergyCreator rosetta.core.scoring.methods.EnergyMethodCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.HPatchEnergyCreator,  : rosetta.core.pack.interaction_graph.HPatchEnergyCreator) -> rosetta.core.pack.interaction_graph.HPatchEnergyCreator create_energy_method(...) from builtins.PyCapsule create_energy_method(self : rosetta.core.pack.interaction_graph.HPatchEnergyCreator,  : core::scoring::methods::EnergyMethodOptions) -> rosetta.core.scoring.methods.EnergyMethod   Instantiate a new HPatchEnergy score_types_for_method(...) from builtins.PyCapsule score_types_for_method(rosetta.core.pack.interaction_graph.HPatchEnergyCreator) -> rosetta.utility.vector1_core_scoring_ScoreType   Return the set of score types claimed by the EnergyMethod  this EnergyMethodCreator creates in its create_energy_method() function   class InteractionGraphBase(AnnealableGraphBase)       Method resolution order: InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, state : int) -> float get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int) -> float set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class InteractionGraphFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.pack.interaction_graph.InteractionGraphFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_and_initialize_annealing_graph(...) from builtins.PyCapsule create_and_initialize_annealing_graph(packer_task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   Create and initialize annealable graph for the given  pose, rotamer sets, packer task and score function. Initalizes  two-body interaction graph, as well as other annealable graphs  sepecified by the given score function and task.    Call only valid after:  Pose has been scored by scorefxn.  Pose residue neighbors updated.  ScoreFunction setup for packing.  Rotamer sets built. create_and_initialize_two_body_interaction_graph(...) from builtins.PyCapsule create_and_initialize_two_body_interaction_graph(packer_task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction, packer_neighbor_graph : rosetta.core.graph.Graph) -> rosetta.core.pack.interaction_graph.InteractionGraphBase   Create and initialize two-body interaction graph for the given  pose, rotamer sets, packer task and score function.    Call only valid after:  Pose has been scored by scorefxn.  Pose residue neighbors updated.  ScoreFunction setup for packing.  Rotamer sets built. create_interaction_graph(...) from builtins.PyCapsule create_interaction_graph(packer_task : rosetta.core.pack.task.PackerTask, rotsets : rosetta.core.pack.rotamer_set.RotamerSets, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> rosetta.core.pack.interaction_graph.InteractionGraphBase   Create appropiate InteractionGraph instance for given  packer task, rotamer set, and pose.   class InvRotamerDots(builtins.object)     Used to determine whether the overlap between two atoms is buried or exposed.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.InvRotamerDots) -> NoneType   2. __init__(self : rosetta.core.pack.interaction_graph.InvRotamerDots, src : rosetta.core.pack.interaction_graph.InvRotamerDots) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.InvRotamerDots, rhs : rosetta.core.pack.interaction_graph.InvRotamerDots) -> rosetta.core.pack.interaction_graph.InvRotamerDots atom_overlap_is_exposed(...) from builtins.PyCapsule atom_overlap_is_exposed(*args, **kwargs) Overloaded function.   1. atom_overlap_is_exposed(self : rosetta.core.pack.interaction_graph.InvRotamerDots, at1 : int, at2 : int) -> bool   Is the intersection between two atoms on this inv-rotamer-dots object exposed?   2. atom_overlap_is_exposed(self : rosetta.core.pack.interaction_graph.InvRotamerDots, at_this : int, other : rosetta.core.pack.interaction_graph.InvRotamerDots, at_other : int) -> bool   Is the intersection between one atom on this inv-rotamer-dots object,  and one atom on another inv-rotamer-dots object exposed? dot_exposed(...) from builtins.PyCapsule dot_exposed(self : rosetta.core.pack.interaction_graph.InvRotamerDots, atomid : int, dot_index : int) -> bool rotamer(...) from builtins.PyCapsule rotamer(rosetta.core.pack.interaction_graph.InvRotamerDots) -> rosetta.core.conformation.Residue setup_from_rotamer_dots(...) from builtins.PyCapsule setup_from_rotamer_dots(*args, **kwargs) Overloaded function.   1. setup_from_rotamer_dots(self : rosetta.core.pack.interaction_graph.InvRotamerDots, rdots : rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType   2. setup_from_rotamer_dots(self : rosetta.core.pack.interaction_graph.InvRotamerDots, rdots : rosetta.core.pack.interaction_graph.RotamerDots, ats_to_update : rosetta.utility.vector1_unsigned_long) -> NoneType   class LazyEdge(OnTheFlyEdge)       Method resolution order: LazyEdge OnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_change(...) from builtins.PyCapsule acknowledge_partial_state_change(self : rosetta.core.pack.interaction_graph.LazyEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.LazyEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.LazyEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.LazyEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int, nodes_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType build_sc_only_rotamer(...) from builtins.PyCapsule build_sc_only_rotamer(rosetta.core.pack.interaction_graph.LazyEdge) -> bool count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LazyEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LazyEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.LazyEdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.LazyEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.LazyEdge) -> NoneType get_aa_submatrix_energies(...) from builtins.PyCapsule get_aa_submatrix_energies(self : rosetta.core.pack.interaction_graph.LazyEdge, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_alternate_state_energy_first_node(...) from builtins.PyCapsule get_alternate_state_energy_first_node(first_node_alt_state : int, second_node_orig_state : int, second_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1 : int, second_node_curr_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>) -> float get_alternate_state_energy_second_node(...) from builtins.PyCapsule get_alternate_state_energy_second_node(first_node_orig_state : int, second_node_alt_state : int, first_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>) -> float get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.LazyEdge) -> float get_edge_table_ptr(...) from builtins.PyCapsule get_edge_table_ptr(rosetta.core.pack.interaction_graph.LazyEdge) -> float get_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.LazyEdge) -> float get_offsets_for_aatypes(...) from builtins.PyCapsule get_offsets_for_aatypes(rosetta.core.pack.interaction_graph.LazyEdge) -> ObjexxFCL::FArray2D<int> get_second_node_num_states_per_aa(...) from builtins.PyCapsule get_second_node_num_states_per_aa(rosetta.core.pack.interaction_graph.LazyEdge) -> rosetta.utility.vector1_int get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.LazyEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.LazyEdge, node1state : int, node2state : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.LazyEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.LazyEdge) -> NoneType print_current_energy(...) from builtins.PyCapsule print_current_energy(rosetta.core.pack.interaction_graph.LazyEdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.LazyEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.LazyEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType store_interaction_energy_first_node(...) from builtins.PyCapsule store_interaction_energy_first_node(second_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1 : int, second_node_curr_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>, interaction_energy : float) -> NoneType store_interaction_energy_second_node(...) from builtins.PyCapsule store_interaction_energy_second_node(first_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>, interaction_energy : float) -> NoneType Methods inherited from OnTheFlyEdge: eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind : int, state : int) -> float long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType set_ProCorrection_values(...) from builtins.PyCapsule set_ProCorrection_values(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class LazyInteractionGraph(OnTheFlyInteractionGraph)       Method resolution order: LazyInteractionGraph OnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, numNodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> bool   Override the FixedBBInteractionGraph class's implementation of this function  to return 'true'. aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, node_ind : int, node_state : int) -> int blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> int get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> int get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, group_id : int) -> float print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.LazyInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.LazyInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from OnTheFlyInteractionGraph: add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_ProCorrection_values_for_edge(...) from builtins.PyCapsule set_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class LazyNode(OnTheFlyNode)       Method resolution order: LazyNode OnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aatype_for_state(...) from builtins.PyCapsule aatype_for_state(self : rosetta.core.pack.interaction_graph.LazyNode, state : int) -> int acknowledge_neighbors_partial_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_substitution(self : rosetta.core.pack.interaction_graph.LazyNode, edge_to_altered_neighbor : int, other_node_new_ : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.LazyNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.LazyNode, new_state : int) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType complete_state_assignment(...) from builtins.PyCapsule complete_state_assignment(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType compute_pair_energy_for_current_state(...) from builtins.PyCapsule compute_pair_energy_for_current_state(self : rosetta.core.pack.interaction_graph.LazyNode, edge_making_energy_request : int) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LazyNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LazyNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.LazyNode) -> int get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.LazyNode) -> float get_sparse_mat_info_for_curr_state(...) from builtins.PyCapsule get_sparse_mat_info_for_curr_state(rosetta.core.pack.interaction_graph.LazyNode) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_totalE(...) from builtins.PyCapsule get_totalE(rosetta.core.pack.interaction_graph.LazyNode) -> float partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.LazyNode, new_state : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.LazyNode, alternate_state : int, prev_node_energy : float) -> float state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.LazyNode) -> bool update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.LazyNode) -> NoneType Methods inherited from OnTheFlyNode: add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, setting : bool) -> NoneType get_num_aa_types(...) from builtins.PyCapsule get_num_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int get_num_states_for_aa_type(...) from builtins.PyCapsule get_num_states_for_aa_type(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aa_type : int) -> int get_num_states_for_aa_types(...) from builtins.PyCapsule get_num_states_for_aa_types(*args, **kwargs) Overloaded function.   1. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> float get_sparse_mat_info_for_state(...) from builtins.PyCapsule get_sparse_mat_info_for_state(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_state_offset_for_aatype(...) from builtins.PyCapsule get_state_offset_for_aatype(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aatype : int) -> int set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, rotamers : core::pack::rotamer_set::RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class LinearMemEdge(OnTheFlyEdge)       Method resolution order: LinearMemEdge OnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_change(...) from builtins.PyCapsule acknowledge_partial_state_change(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, bumped_recent_history_index : int, new_state_recent_history_index : int) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, bumped_recent_history_index : int, new_state_recent_history_index : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.LinearMemEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int, nodes_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, bumped_recent_history_index : int, new_state_recent_history_index : int, neighbors_curr_state : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LinearMemEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LinearMemEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.LinearMemEdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.LinearMemEdge) -> NoneType get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.LinearMemEdge) -> float get_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.LinearMemEdge) -> float get_energy_for_alt_state(...) from builtins.PyCapsule get_energy_for_alt_state(self : rosetta.core.pack.interaction_graph.LinearMemEdge, store_rpes : bool, changing_node_index : int, alternate_state : int, alternate_state_recent_history_index : int, other_node_curr_state : int, other_node_state_recent_history_index : int) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node1aa : int, node2aa : int) -> bool get_sparse_aa_neighbor_info(...) from builtins.PyCapsule get_sparse_aa_neighbor_info(rosetta.core.pack.interaction_graph.LinearMemEdge) -> ObjexxFCL::FArray2D<unsigned char> get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node1state : int, node2state : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.LinearMemEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.LinearMemEdge) -> NoneType print_current_energy(...) from builtins.PyCapsule print_current_energy(rosetta.core.pack.interaction_graph.LinearMemEdge) -> NoneType reset_state_energies(...) from builtins.PyCapsule reset_state_energies(self : rosetta.core.pack.interaction_graph.LinearMemEdge, node_index : int, state : int, recent_history_id : int) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.LinearMemEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.LinearMemEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType Methods inherited from OnTheFlyEdge: eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind : int, state : int) -> float long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType set_ProCorrection_values(...) from builtins.PyCapsule set_ProCorrection_values(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class LinearMemNode(OnTheFlyNode)       Method resolution order: LinearMemNode OnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_last_substititon_not_committed(...) from builtins.PyCapsule acknowledge_last_substititon_not_committed(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   update bookkeeping info to acknolwedge that the last alternative state considered was not  in fact chosen for the currently assigned state. acknowledge_neighbors_partial_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_substitution(self : rosetta.core.pack.interaction_graph.LinearMemNode, edge_to_altered_neighbor : int, other_node_new_state : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, other_state_recent_history_index : int) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.LinearMemNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, other_node_recent_history_index : int) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.LinearMemNode, new_state : int) -> NoneType   set to a particular state -- updates the energies internally assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   set to state 0 commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   proceed to change the currently assigned state to the alternative state considered in  the last call to project_deltaE_for_substitution complete_state_assignment(...) from builtins.PyCapsule complete_state_assignment(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   second half of the entire-graph state assignment. compute_pair_energy_for_alternate_state(...) from builtins.PyCapsule compute_pair_energy_for_alternate_state(self : rosetta.core.pack.interaction_graph.LinearMemNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the alternate state being considered on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two compute_pair_energy_for_current_state(...) from builtins.PyCapsule compute_pair_energy_for_current_state(self : rosetta.core.pack.interaction_graph.LinearMemNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the currently assigned state on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LinearMemNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LinearMemNode) -> int get_curr_state_recent_state_id(...) from builtins.PyCapsule get_curr_state_recent_state_id(rosetta.core.pack.interaction_graph.LinearMemNode) -> int   return the "recent state id" for the currently assigned state get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.LinearMemNode) -> int   return the index of the currently assigned state get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.LinearMemNode) -> float   return the one-body energy for the currently assigned state get_recent_history_size(...) from builtins.PyCapsule get_recent_history_size(rosetta.core.pack.interaction_graph.LinearMemNode) -> int get_sparse_mat_info_for_curr_state(...) from builtins.PyCapsule get_sparse_mat_info_for_curr_state(rosetta.core.pack.interaction_graph.LinearMemNode) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_totalE(...) from builtins.PyCapsule get_totalE(rosetta.core.pack.interaction_graph.LinearMemNode) -> float   return the total energy for this node; includes full energies to neighboring residues partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.LinearMemNode, new_state : int) -> NoneType   first half of an entire-graph state assignment that avoids unnecessary energy updates  as produced in assign_state.  Adjust all node's states first, then update all energies. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   linmem ig does not have to do anything before sim annealing begins print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType   write internal energy and bookkeeping data to standard out print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.LinearMemNode, alternate_state : int, prev_node_energy : float) -> float   compute the change in energy induced by substituting the currently assigned state with  some alternative state set_recent_history_size(...) from builtins.PyCapsule set_recent_history_size(self : rosetta.core.pack.interaction_graph.LinearMemNode, num_states_to_maintain_in_recent_history : int) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.LinearMemNode) -> bool   state 0 represents the unasigned state update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.LinearMemNode) -> NoneType Methods inherited from OnTheFlyNode: add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, setting : bool) -> NoneType get_num_aa_types(...) from builtins.PyCapsule get_num_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int get_num_states_for_aa_type(...) from builtins.PyCapsule get_num_states_for_aa_type(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aa_type : int) -> int get_num_states_for_aa_types(...) from builtins.PyCapsule get_num_states_for_aa_types(*args, **kwargs) Overloaded function.   1. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> float get_sparse_mat_info_for_state(...) from builtins.PyCapsule get_sparse_mat_info_for_state(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_state_offset_for_aatype(...) from builtins.PyCapsule get_state_offset_for_aatype(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aatype : int) -> int set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, rotamers : core::pack::rotamer_set::RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class LinearMemoryInteractionGraph(OnTheFlyInteractionGraph)       Method resolution order: LinearMemoryInteractionGraph OnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, numNodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> int get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> int get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, group_id : int) -> float get_recent_history_size(...) from builtins.PyCapsule get_recent_history_size(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_recent_history_size(...) from builtins.PyCapsule set_recent_history_size(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, recent_history_size : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from OnTheFlyInteractionGraph: add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_ProCorrection_values_for_edge(...) from builtins.PyCapsule set_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class MultiplexedAnnealableGraph(AnnealableGraphBase)       Method resolution order: MultiplexedAnnealableGraph AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> NoneType   3. __init__(self : handle, target_subgraphs : rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_std_allocator_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> bool   Are any states unassigned? assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph,  : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> NoneType   State initialization.  Set all nodes to state zero. commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> float   Accept the considered substitution. consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType   Consider a change in state at a particular node.      The node index.      The index of the state to which we're considering setting the node.      The computed change in energy that would result from the substitution.      The energy prior to the substituion, returned by this function. get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> float   Get the total energy from the current states of the nodes in the network. get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> int   Get the number of nodes in the graph. get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, node : int) -> int   Get the number of states for a given node.      The index of the node. get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> int   Get the total number of states for all nodes in the graph. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph) -> NoneType   Utility signal. set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, deltaE : float) -> NoneType   Set error thresshold.      Error thresshold value to set. set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, node_states : ObjexxFCL::FArray1<int>) -> float   Set the states for the entire network.      A Fortran-style 1-array of state indices for all nodes in the network. set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, node_ind : int, new_state : int) -> float   Explicit state modification: set node "node_ind" to state "new_state".      The index of the node.      The index of the state to which we're setting the node. Data descriptors defined here: subgraphs   class NodeBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.NodeBase,  : core::pack::interaction_graph::InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.NodeBase, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.NodeBase) -> bool update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType   class OnTheFlyEdge(FixedBBEdge)       Method resolution order: OnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> int eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind : int, state : int) -> float long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> NoneType set_ProCorrection_values(...) from builtins.PyCapsule set_ProCorrection_values(self : rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.OnTheFlyEdge) -> bool Methods inherited from FixedBBEdge: force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.FixedBBEdge) -> NoneType get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.FixedBBEdge,  : int,  : int) -> float set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType Methods inherited from EdgeBase: declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.EdgeBase, weight : float) -> NoneType set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class OnTheFlyInteractionGraph(FixedBBInteractionGraph)       Method resolution order: OnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_ProCorrection_values_for_edge(...) from builtins.PyCapsule set_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int) -> float set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class OnTheFlyNode(FixedBBNode)       Method resolution order: OnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, setting : bool) -> NoneType get_num_aa_types(...) from builtins.PyCapsule get_num_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> int get_num_states_for_aa_type(...) from builtins.PyCapsule get_num_states_for_aa_type(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aa_type : int) -> int get_num_states_for_aa_types(...) from builtins.PyCapsule get_num_states_for_aa_types(*args, **kwargs) Overloaded function.   1. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> rosetta.utility.vector1_int get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> float get_sparse_mat_info_for_state(...) from builtins.PyCapsule get_sparse_mat_info_for_state(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_state_offset_for_aatype(...) from builtins.PyCapsule get_state_offset_for_aatype(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, aatype : int) -> int set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, rotamers : core::pack::rotamer_set::RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.OnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.OnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.NodeBase) -> bool   class PDEdge(PrecomputedPairEnergiesEdge)       Method resolution order: PDEdge PrecomputedPairEnergiesEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.PDEdge, node_ind : int, new_state : int, new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.PDEdge, node_ind : int) -> NoneType   updates bookkeeping information when one of the two nodes enters its  "unassigned" state. acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.PDEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int, nodes_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType add_to_two_body_energies(...) from builtins.PyCapsule add_to_two_body_energies(self : rosetta.core.pack.interaction_graph.PDEdge, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType add_to_two_body_energy(...) from builtins.PyCapsule add_to_two_body_energy(self : rosetta.core.pack.interaction_graph.PDEdge,  : int,  : int,  : float) -> NoneType clear_two_body_energy(...) from builtins.PyCapsule clear_two_body_energy(self : rosetta.core.pack.interaction_graph.PDEdge,  : int,  : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.PDEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.PDEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.PDEdge) -> NoneType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.PDEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.PDEdge) -> NoneType get_aa_submatrix_energies(...) from builtins.PyCapsule get_aa_submatrix_energies(self : rosetta.core.pack.interaction_graph.PDEdge, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_alternate_state_energy_first_node(...) from builtins.PyCapsule get_alternate_state_energy_first_node(first_node_alt_state : int, second_node_orig_state : int, second_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1 : int, second_node_curr_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>) -> float get_alternate_state_energy_second_node(...) from builtins.PyCapsule get_alternate_state_energy_second_node(first_node_orig_state : int, second_node_alt_state : int, first_node_orig_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype : int, aa_neighbor_offset : int, edge_energy_table : ObjexxFCL::FArray1<float>) -> float get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.PDEdge) -> float get_edge_table_ptr(...) from builtins.PyCapsule get_edge_table_ptr(rosetta.core.pack.interaction_graph.PDEdge) -> float get_offsets_for_aatypes(...) from builtins.PyCapsule get_offsets_for_aatypes(rosetta.core.pack.interaction_graph.PDEdge) -> ObjexxFCL::FArray2D<int>   Returns the array of offsets into the sparse two-body energy table  for amino-acid neighbors.  Used in transferring information from edges  onto nodes for cache efficiency. get_second_node_num_states_per_aa(...) from builtins.PyCapsule get_second_node_num_states_per_aa(rosetta.core.pack.interaction_graph.PDEdge) -> rosetta.utility.vector1_int   returns an FArray of the number of states for each amino acid type for the  higher-indexed node get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.PDEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.PDEdge,  : int,  : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.PDEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.PDEdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.PDEdge, weight : float) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.PDEdge, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType set_two_body_energy(...) from builtins.PyCapsule set_two_body_energy(self : rosetta.core.pack.interaction_graph.PDEdge,  : int,  : int,  : float) -> NoneType Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class PDInteractionGraph(PrecomputedPairEnergiesInteractionGraph)       Method resolution order: PDInteractionGraph PrecomputedPairEnergiesInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> bool   Override the InteractionGraphBase class's implementation of this function  to return 'true'. aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind : int, node_state : int) -> int add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node1 : int, node2 : int) -> NoneType blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(*args, **kwargs) Overloaded function.   1. commit_considered_substitution(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> float   2. commit_considered_substitution(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, weights : ObjexxFCL::FArray2D<float>) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(*args, **kwargs) Overloaded function.   1. consider_substitution(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType   2. consider_substitution(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind : int, new_state : int, deltaE_unweighted : float, prevE_unweighted : float, deltaE_weighted : float, prevE_weighted : float, weights : ObjexxFCL::FArray2D<float>) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> int get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> int   older scheme for memory accounting -- replace this asap      returns the number of floats used in all edge two-body energy tables get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> float   @ brief O(1) total energy report.  Protected read access for derived classes. get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, group_id : int) -> float   a user may define subsets of the vertex set for which they would like to  know the internal energy sum. get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node : int, state : int) -> float get_weighted_energy(...) from builtins.PyCapsule get_weighted_energy(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, weights : ObjexxFCL::FArray2D<float>) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.PDInteractionGraph) -> NoneType   outputs the current state for each node, useful for debugging set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.PDInteractionGraph,  : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(*args, **kwargs) Overloaded function.   1. set_network_state(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float   2. set_network_state(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_states : ObjexxFCL::FArray1<int>, weights : ObjexxFCL::FArray2D<float>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from PrecomputedPairEnergiesInteractionGraph: add_to_two_body_energies_for_edge(...) from builtins.PyCapsule add_to_two_body_energies_for_edge(*args, **kwargs) Overloaded function.   1. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType   interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies   2. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies clear_two_body_energy_for_edge(...) from builtins.PyCapsule clear_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> NoneType   interface to PDEdge::clear_two_body_energy declare_edge_energies_final(...) from builtins.PyCapsule declare_edge_energies_final(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int) -> NoneType set_two_body_energy_for_edge(...) from builtins.PyCapsule set_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PDEdge::set_two_body_energy Methods inherited from FixedBBInteractionGraph: force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class PDNode(PrecomputedPairEnergiesNode)       Method resolution order: PDNode PrecomputedPairEnergiesNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aatype_for_state(...) from builtins.PyCapsule aatype_for_state(self : rosetta.core.pack.interaction_graph.PDNode, state : int) -> int   return the amino acid type for a particular state -- this indexing is of course completely  arbitrary acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.PDNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int, other_node_new_state_sparse_info : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.PDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType   adds all the energies in energies to the one-body energies for this node add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.PDNode, state : int, energy : float) -> NoneType   adds energy to the one-body energy for state state assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.PDNode, new_state : int) -> NoneType   assigns node a new_state assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.PDNode) -> NoneType   assigns node's state to it's zero, or "unassigned" state. commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.PDNode) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.PDNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.PDNode) -> int get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.PDNode) -> int   returns the state the node is currently assigned get_num_states_for_aa_type(...) from builtins.PyCapsule get_num_states_for_aa_type(self : rosetta.core.pack.interaction_graph.PDNode, aa_type : int) -> int get_num_states_for_aa_types(...) from builtins.PyCapsule get_num_states_for_aa_types(rosetta.core.pack.interaction_graph.PDNode) -> rosetta.utility.vector1_int   returns an FArray & with the number of states for each amino acid type get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.PDNode, state : int) -> float   returns the one body energy for a state get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.PDNode) -> float   returns the one body energy for the state the node is currently assigned get_sparse_mat_info_for_curr_state(...) from builtins.PyCapsule get_sparse_mat_info_for_curr_state(rosetta.core.pack.interaction_graph.PDNode) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_sparse_mat_info_for_state(...) from builtins.PyCapsule get_sparse_mat_info_for_state(self : rosetta.core.pack.interaction_graph.PDNode, state : int) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_weighted_energy_with_higher_indexed_nodes(...) from builtins.PyCapsule get_weighted_energy_with_higher_indexed_nodes(self : rosetta.core.pack.interaction_graph.PDNode, weights : ObjexxFCL::FArray2D<float>) -> float prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.PDNode) -> NoneType   prepares node for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.PDNode) -> NoneType   prints a description of the node and all of it's one-body energies print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.PDNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(*args, **kwargs) Overloaded function.   1. project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.PDNode, alternate_state : int, prev_node_energy : float) -> float   returns the change in energy that would be induced by switching this node  from its current state into another state   2. project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.PDNode, alternate_state : int, deltaE_unweighted : float, prevE_unweighted : float, deltaE_weighted : float, prevE_weighted : float, weights : ObjexxFCL::FArray2D<float>) -> NoneType   returns the change in weighted energy that would be induced  by switching this node from its current state into another state set_amino_acid_types(...) from builtins.PyCapsule set_amino_acid_types(self : rosetta.core.pack.interaction_graph.PDNode,  : rosetta.std.vector_int) -> NoneType   sets the amino acid type for each state state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.PDNode) -> bool update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.PDNode) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.PDNode, energies : ObjexxFCL::FArray1<float>) -> NoneType   set all the one-body energies for this node update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.PDNode, state : int, energy : float) -> NoneType   update energy to the one-body energy for state zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.PDNode) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class PrecomputedPairEnergiesEdge(FixedBBEdge)       Method resolution order: PrecomputedPairEnergiesEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_two_body_energies(...) from builtins.PyCapsule add_to_two_body_energies(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType add_to_two_body_energy(...) from builtins.PyCapsule add_to_two_body_energy(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge,  : int,  : int,  : float) -> NoneType clear_two_body_energy(...) from builtins.PyCapsule clear_two_body_energy(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge,  : int,  : int) -> NoneType set_two_body_energy(...) from builtins.PyCapsule set_two_body_energy(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge,  : int,  : int,  : float) -> NoneType Methods inherited from FixedBBEdge: force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> NoneType force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.FixedBBEdge) -> NoneType get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa : int, node2aa : int) -> bool get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.FixedBBEdge,  : int,  : int) -> float set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.FixedBBEdge, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType Methods inherited from EdgeBase: count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.EdgeBase) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.EdgeBase, weight : float) -> NoneType set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class PrecomputedPairEnergiesInteractionGraph(FixedBBInteractionGraph)       Method resolution order: PrecomputedPairEnergiesInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_two_body_energies_for_edge(...) from builtins.PyCapsule add_to_two_body_energies_for_edge(*args, **kwargs) Overloaded function.   1. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, res_res_energy_array : rosetta.ObjexxFCL.FArray2_float_t) -> NoneType   interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies   2. add_to_two_body_energies_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies clear_two_body_energy_for_edge(...) from builtins.PyCapsule clear_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> NoneType   interface to PDEdge::clear_two_body_energy declare_edge_energies_final(...) from builtins.PyCapsule declare_edge_energies_final(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int) -> NoneType set_two_body_energy_for_edge(...) from builtins.PyCapsule set_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int, two_body_energy : float) -> NoneType   interface to PDEdge::set_two_body_energy Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> int get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, state : int) -> float get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int) -> float set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class PrecomputedPairEnergiesNode(FixedBBNode)       Method resolution order: PrecomputedPairEnergiesNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.NodeBase, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.NodeBase) -> int depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.NodeBase) -> bool update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.NodeBase, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType   class ResidueArrayAnnealingEvaluator(AnnealableGraphBase)       Method resolution order: ResidueArrayAnnealingEvaluator AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> bool   Are there any nodes unassigned? assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator,  : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> NoneType   State initialization: set all nodes to state zero. commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> float   Set the node that we were considering to the state that we were considering (i.e. commit the change). consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType   Consider setting a particular node to a particular state.      Index of the node to be potentially modified.      Index of the state that we might set this node to.      The change in energy that would result from the substitution, returned by this function.      The previous energy for this node, prior to the substitution, returned by this function. get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> float   Get the energy fo the current state. get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> int   Get the number of nodes.      This lies a little bit.  It only returns the number of independent nodes. get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, node : int) -> int   Get the number of states for a specific node.      Index of the node. get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> int   Get the total number of states for all nodes.      This lies a little bit.  It only returns the total number of states for the independent nodes. has_methods(...) from builtins.PyCapsule has_methods(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> bool   Do any energy methods have a nonzero weight? initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, score_function : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, rotamer_sets : rosetta.core.pack.rotamer_set.RotamerSets,  : rosetta.core.graph.Graph) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) -> NoneType   Utility signal. set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, deltaE : float) -> NoneType   Set error threshold.      Error threshold value to set. set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, node_states : ObjexxFCL::FArray1<int>) -> float   Set states for all nodes across the network.      Fortran-style 1-array of state indices for all nodes in the network. set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, node_ind : int, new_state : int) -> float   Explicit state modification: set a particular node to a particular state.      Index of the node to modify.      Index of the state that we're setting this node TO.   class ResiduePairEvalType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.pack.interaction_graph.ResiduePairEvalType, rosetta.core.pack.interaction_graph.ResiduePairEvalType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.pack.interaction_graph.ResiduePairEvalType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.ResiduePairEvalType, int) -> NoneType   2. __init__(rosetta.core.pack.interaction_graph.ResiduePairEvalType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.pack.interaction_graph.ResiduePairEvalType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.pack.interaction_graph.ResiduePairEvalType, rosetta.core.pack.interaction_graph.ResiduePairEvalType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.pack.interaction_graph.ResiduePairEvalType) -> str Data and other attributes defined here: sc_sc = ResiduePairEvalType.sc_sc sc_whole = ResiduePairEvalType.sc_whole whole_sc = ResiduePairEvalType.whole_sc whole_whole = ResiduePairEvalType.whole_whole   class RotamerDots(builtins.object)     Handles sphere-sphere overlap calculations for the HPatchInteractionGraph.       One big change from the r++ version of this class is that this class now includes all of the information that was previously stored in the RotamerCoords class. Since I'm not storing atoms in trie ordering (perhaps I'll add this later), there is no need to have a separate class for the rotamer coordinates.   RotamerDots hold DotSphere objects for the atoms of a given Residue (or really, of the current state on some interaction graph Node). Default use of the class will result in RotamerDots objects keeping DotSpheres for every atom of a residue. For the hpatch interaction graph, though, we only care about the SASA of the heavy atoms.  No need to include the hydrogens when looking for hydrophobic patches. By not keeping track of the hydrogens, we save a huge amount of time on computing updates to the SASA score because hydrogen atoms generally make up half of a protein. So I'm adding a boolean flag to the non-default constructor which toggles whether we're tracking SASA of all atoms, or just the heavy atoms.   Two other big changes being made to this class are that 1) the class will now keep track of two kinds of SASA and 2) it will no longer keep score or score_is_current variables.  The two kinds of SASA the class will keep track of are the standard SASA, and a SASA with polar atom radii extended. The expanded polar SASA will only be kept if a boolean flag is set at construct time.  If not, it will just calculate standard SASA and that's it.  The second change is that this class is now only keeping track of SASA. RotamerDots objects will not be responsible for calculating a score.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType   2. __init__(rosetta.core.pack.interaction_graph.RotamerDots, rosetta.core.conformation.Residue) -> NoneType   doc   3. __init__(rosetta.core.pack.interaction_graph.RotamerDots, rosetta.core.conformation.Residue, bool) -> NoneType   doc   4. __init__(self : rosetta.core.pack.interaction_graph.RotamerDots, rotamer : rosetta.core.conformation.Residue, exclude_hydrogen_atoms : bool, use_expanded_polar_atom_radii : bool) -> NoneType   5. __init__(self : rosetta.core.pack.interaction_graph.RotamerDots, rhs : rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.pack.interaction_graph.RotamerDots, rhs : rosetta.core.pack.interaction_graph.RotamerDots) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.pack.interaction_graph.RotamerDots) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.RotamerDots, rhs : rosetta.core.pack.interaction_graph.RotamerDots) -> rosetta.core.pack.interaction_graph.RotamerDots copy(...) from builtins.PyCapsule copy(self : rosetta.core.pack.interaction_graph.RotamerDots, rhs : rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType decrement_from_cached(...) from builtins.PyCapsule decrement_from_cached(self : rosetta.core.pack.interaction_graph.RotamerDots, cached_dot_overlap : core::pack::interaction_graph::RotamerDotsCache) -> NoneType dot_coord(...) from builtins.PyCapsule dot_coord(index : int) -> rosetta.numeric.xyzVector_double_t get_atom_coords_xyz(...) from builtins.PyCapsule get_atom_coords_xyz(self : rosetta.core.pack.interaction_graph.RotamerDots, atom_index : int) -> rosetta.numeric.xyzVector_double_t get_atom_counts(...) from builtins.PyCapsule get_atom_counts(rosetta.core.pack.interaction_graph.RotamerDots) -> rosetta.utility.vector1_core_pack_interaction_graph_DotSphere get_atom_radius(...) from builtins.PyCapsule get_atom_radius(self : rosetta.core.pack.interaction_graph.RotamerDots, atom_index : int) -> float get_atom_sasa(...) from builtins.PyCapsule get_atom_sasa(self : rosetta.core.pack.interaction_graph.RotamerDots, atom_index : int) -> float get_num_atoms(...) from builtins.PyCapsule get_num_atoms(rosetta.core.pack.interaction_graph.RotamerDots) -> int get_num_covered_total(...) from builtins.PyCapsule get_num_covered_total(rosetta.core.pack.interaction_graph.RotamerDots) -> int get_num_uncovered(...) from builtins.PyCapsule get_num_uncovered(self : rosetta.core.pack.interaction_graph.RotamerDots, atom : int) -> int get_radii(...) from builtins.PyCapsule get_radii(rosetta.core.pack.interaction_graph.RotamerDots) -> rosetta.utility.vector1_double get_sasa(...) from builtins.PyCapsule get_sasa(rosetta.core.pack.interaction_graph.RotamerDots) -> float increment_both(...) from builtins.PyCapsule increment_both(self : rosetta.core.pack.interaction_graph.RotamerDots, other : rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType increment_both_and_cache(...) from builtins.PyCapsule increment_both_and_cache(self : rosetta.core.pack.interaction_graph.RotamerDots, other_rotamer : rosetta.core.pack.interaction_graph.RotamerDots, others_dots_covered_by_this : core::pack::interaction_graph::RotamerDotsCache, this_dots_covered_by_other : core::pack::interaction_graph::RotamerDotsCache, atom_atom_overlaps_cache : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> NoneType increment_from_cached(...) from builtins.PyCapsule increment_from_cached(self : rosetta.core.pack.interaction_graph.RotamerDots, cached_dot_overlap : core::pack::interaction_graph::RotamerDotsCache) -> NoneType increment_self_overlap(...) from builtins.PyCapsule increment_self_overlap(rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType increment_this_and_cache(...) from builtins.PyCapsule increment_this_and_cache(self : rosetta.core.pack.interaction_graph.RotamerDots, other : rosetta.core.pack.interaction_graph.RotamerDots, this_overlap_on_other : core::pack::interaction_graph::RotamerDotsCache, atom_atom_overlaps_cache : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> NoneType max_atom_radius(...) from builtins.PyCapsule max_atom_radius(rosetta.core.pack.interaction_graph.RotamerDots) -> float name3(...) from builtins.PyCapsule name3(rosetta.core.pack.interaction_graph.RotamerDots) -> str overlaps(...) from builtins.PyCapsule overlaps(self : rosetta.core.pack.interaction_graph.RotamerDots, other : rosetta.core.pack.interaction_graph.RotamerDots) -> bool radius_for_attype(...) from builtins.PyCapsule radius_for_attype(self : rosetta.core.pack.interaction_graph.RotamerDots, attype_index : int) -> float rotamer(...) from builtins.PyCapsule rotamer(rosetta.core.pack.interaction_graph.RotamerDots) -> rosetta.core.conformation.Residue seqpos(...) from builtins.PyCapsule seqpos(rosetta.core.pack.interaction_graph.RotamerDots) -> int state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.RotamerDots) -> bool zero(...) from builtins.PyCapsule zero(rosetta.core.pack.interaction_graph.RotamerDots) -> NoneType   class RotamerDotsCache(builtins.object)     A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes.       During packing, when a first class node has to respond to another Node changing state, it's faster to decrement the coverage the previous state produced and increment the coverage the new state produces than to completely recalculate how the new state overlaps the node. But instead of holding that coverage information in a RotamerDots object (which does alot of other things), hold it in this cache class instead.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.RotamerDotsCache) -> NoneType   2. __init__(self : rosetta.core.pack.interaction_graph.RotamerDotsCache, num_atoms : int) -> NoneType   3. __init__(self : rosetta.core.pack.interaction_graph.RotamerDotsCache, rhs : rosetta.core.pack.interaction_graph.RotamerDotsCache) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.RotamerDotsCache, rhs : rosetta.core.pack.interaction_graph.RotamerDotsCache) -> rosetta.core.pack.interaction_graph.RotamerDotsCache get_atom_counts(...) from builtins.PyCapsule get_atom_counts(rosetta.core.pack.interaction_graph.RotamerDotsCache) -> rosetta.utility.vector1_core_pack_interaction_graph_DotSphere resize(...) from builtins.PyCapsule resize(self : rosetta.core.pack.interaction_graph.RotamerDotsCache, num_atoms : int) -> NoneType zero(...) from builtins.PyCapsule zero(rosetta.core.pack.interaction_graph.RotamerDotsCache) -> NoneType   class RotamerDotsRadiusData(rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t)     A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class.       The RotamerDots class keeps track of the SASA of some rotamer using DotSphere objects and lots of get overlap calls on atoms. The SASA of a given atom (or residue) depends on what radii are used for the atoms. Different program use different sets of radii, and for the hpatch score, the polar atom radii are expanded. Previously RotamerDots objects would have a static vector member variable that represented the particular set of radii being used.  It would also have a second static vector member variable that represented the expanded polar version of the radii.  So, no matter how many instances of RotamerDots objects we created, we only maintained two vectors for the radii. Now, we want to make the RotamerDots class only use one set of radii for the hpatch score: the expanded polar radii. The super easy solution would be to remove all the logic that keeps track of SASA when using the standard radii and make the RotamerDots class only calculate that kind of SASA.  But, there will probably be more uses in the future for a RotamerDots class that can calculate SASA with a standard set of radii than with the expanded polar ones. So, that's where this class comes in. It will read in database files, depending on which set of radii are requested and provide access to that data in some way.   Let's say we have to create RotamerDots objects for two different sets of SASA radii. When those objects are constructed a pointer to the right set of radii will have to be set. Definitely don't want to copy/store the radii to each instance. If I make it a pointer to this class, then it would only work for one set of radii.  So at RotamerDots construct time we have to ask this class to give us a pointer to the set of radii that are requested. Then only one instance of this class exists, and all RotamerDots objects have pointers set to the radii they care about. What would this change in the RotamerDots API? The get_radius() function would dereference the pointer and index into the vector to get the right radius. This structure is similar to how the ChemicalManager works. But, in that class, the functions return AtomTypeSet objects.     Method resolution order: RotamerDotsRadiusData rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_NACCESS_SASA_radii(...) from builtins.PyCapsule get_NACCESS_SASA_radii(rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) -> rosetta.utility.vector1_double   return a pointer to the SASA radii used by NACCESS get_NACCESS_SASA_radii_with_expanded_polars(...) from builtins.PyCapsule get_NACCESS_SASA_radii_with_expanded_polars(rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) -> rosetta.utility.vector1_double   return a pointer to the SASA radii used by NACCESS, with polar atom radii expanded get_ROSETTA_SASA_radii(...) from builtins.PyCapsule get_ROSETTA_SASA_radii(rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) -> rosetta.utility.vector1_double   return a pointer to the standard Rosetta SASA radii Methods inherited from rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::pack::interaction_graph::RotamerDotsRadiusData   class SimpleEdge(rosetta.core.graph.Edge)       Method resolution order: SimpleEdge rosetta.core.graph.Edge builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, res1 : int, res2 : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. commit_change(...) from builtins.PyCapsule commit_change(rosetta.core.pack.interaction_graph.SimpleEdge) -> NoneType compute_energy(...) from builtins.PyCapsule compute_energy(self : rosetta.core.pack.interaction_graph.SimpleEdge, use_current_node1 : bool, use_current_node2 : bool) -> NoneType copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.pack.interaction_graph.SimpleEdge,  : rosetta.core.graph.Edge) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SimpleEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SimpleEdge) -> int get_current_energy(...) from builtins.PyCapsule get_current_energy(rosetta.core.pack.interaction_graph.SimpleEdge) -> float get_proposed_energy(...) from builtins.PyCapsule get_proposed_energy(rosetta.core.pack.interaction_graph.SimpleEdge) -> float update_current_energy(...) from builtins.PyCapsule update_current_energy(rosetta.core.pack.interaction_graph.SimpleEdge) -> NoneType update_proposed_energy(...) from builtins.PyCapsule update_proposed_energy(rosetta.core.pack.interaction_graph.SimpleEdge) -> NoneType Methods inherited from rosetta.core.graph.Edge: get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class SimpleInteractionGraph(rosetta.core.graph.Graph)     A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone.  This class is responsible for calculating energy changes, but is passive about how the sidechains are changing.  There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.     Method resolution order: SimpleInteractionGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph,  : rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> rosetta.core.pack.interaction_graph.SimpleInteractionGraph commit_change(...) from builtins.PyCapsule commit_change(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id : int) -> NoneType consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id : int, new_state : rosetta.core.conformation.Residue) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> int delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph,  : rosetta.core.graph.Edge) -> NoneType get_simple_node(...) from builtins.PyCapsule get_simple_node(*args, **kwargs) Overloaded function.   1. get_simple_node(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, ind : int) -> rosetta.core.pack.interaction_graph.SimpleNode   2. get_simple_node(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, ind : int) -> rosetta.core.pack.interaction_graph.SimpleNode initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, pose : rosetta.core.pose.Pose) -> NoneType   Initialization where the graph adds its own edges pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> rosetta.core.pose.Pose reject_change(...) from builtins.PyCapsule reject_change(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id : int) -> NoneType scorefunction(...) from builtins.PyCapsule scorefunction(rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_pose_no_initialize(...) from builtins.PyCapsule set_pose_no_initialize(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, pose : rosetta.core.pose.Pose) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.core.pack.interaction_graph.SimpleInteractionGraph, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType total_energy(...) from builtins.PyCapsule total_energy(rosetta.core.pack.interaction_graph.SimpleInteractionGraph) -> float Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class SimpleNode(rosetta.core.graph.Node)       Method resolution order: SimpleNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, resnum : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. alt_sc_centroid(...) from builtins.PyCapsule alt_sc_centroid(rosetta.core.pack.interaction_graph.SimpleNode) -> rosetta.numeric.xyzVector_double_t alt_sc_radius(...) from builtins.PyCapsule alt_sc_radius(rosetta.core.pack.interaction_graph.SimpleNode) -> float bb_centroid(...) from builtins.PyCapsule bb_centroid(rosetta.core.pack.interaction_graph.SimpleNode) -> rosetta.numeric.xyzVector_double_t bb_radius(...) from builtins.PyCapsule bb_radius(rosetta.core.pack.interaction_graph.SimpleNode) -> float commit_change(...) from builtins.PyCapsule commit_change(rosetta.core.pack.interaction_graph.SimpleNode) -> NoneType   Copy the alternate_residue_ pointer to the current_residue_ pointer;  copy the alternate energies to the current energies for this node and its  incident edges. commit_change_no_res_pointer_update(...) from builtins.PyCapsule commit_change_no_res_pointer_update(rosetta.core.pack.interaction_graph.SimpleNode) -> NoneType   Copy the alternate energies to the current energies for this node  and its incident edges. copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.pack.interaction_graph.SimpleNode,  : rosetta.core.graph.Node) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SimpleNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SimpleNode) -> int curr_sc_centroid(...) from builtins.PyCapsule curr_sc_centroid(rosetta.core.pack.interaction_graph.SimpleNode) -> rosetta.numeric.xyzVector_double_t curr_sc_radius(...) from builtins.PyCapsule curr_sc_radius(rosetta.core.pack.interaction_graph.SimpleNode) -> float current_one_body_energy(...) from builtins.PyCapsule current_one_body_energy(rosetta.core.pack.interaction_graph.SimpleNode) -> float get_alternate(...) from builtins.PyCapsule get_alternate(rosetta.core.pack.interaction_graph.SimpleNode) -> rosetta.core.conformation.Residue   return the pointer to the alternate state (might be 0) get_current(...) from builtins.PyCapsule get_current(rosetta.core.pack.interaction_graph.SimpleNode) -> rosetta.core.conformation.Residue   return the pointer to the current state (might be 0) moved(...) from builtins.PyCapsule moved(rosetta.core.pack.interaction_graph.SimpleNode) -> bool   Is this node considering a state substitution? one_body_energy(...) from builtins.PyCapsule one_body_energy(rosetta.core.pack.interaction_graph.SimpleNode) -> float print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.SimpleNode) -> NoneType proposed_one_body_energy(...) from builtins.PyCapsule proposed_one_body_energy(rosetta.core.pack.interaction_graph.SimpleNode) -> float reject_change(...) from builtins.PyCapsule reject_change(rosetta.core.pack.interaction_graph.SimpleNode) -> NoneType   Reset state on this node so that its incident edges will no longer  think it is considering an alternate conformation. set_alternate(...) from builtins.PyCapsule set_alternate(self : rosetta.core.pack.interaction_graph.SimpleNode, res : rosetta.core.conformation.Residue) -> NoneType   Set the alternate residue COP and follow by computing the energy  for this residue with its neighbors and storing those computed energies  on this node's edges as their "proposed" energies set_alternate_no_E_update(...) from builtins.PyCapsule set_alternate_no_E_update(self : rosetta.core.pack.interaction_graph.SimpleNode, res : rosetta.core.conformation.Residue) -> NoneType   Passive mode behavior: set the current residue pointer without updating  the alternate one body or proposed two body energies. set_current(...) from builtins.PyCapsule set_current(self : rosetta.core.pack.interaction_graph.SimpleNode, res : rosetta.core.conformation.Residue) -> NoneType   Set the current residue COP, and follow by computing the energy  for this residue with its neighbors and storing those computed energies  on this node's edges as their "current" energies. set_current_no_E_update(...) from builtins.PyCapsule set_current_no_E_update(self : rosetta.core.pack.interaction_graph.SimpleNode, res : rosetta.core.conformation.Residue) -> NoneType   Passive mode behavior: set the current residue pointer without updating  the current one body or two body energies. update_energies_after_passive_change(...) from builtins.PyCapsule update_energies_after_passive_change(rosetta.core.pack.interaction_graph.SimpleNode) -> NoneType Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class SparseMatrixIndex(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType   2. __init__(self : rosetta.core.pack.interaction_graph.SparseMatrixIndex,  : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.SparseMatrixIndex,  : rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> rosetta.core.pack.interaction_graph.SparseMatrixIndex get_aa_type(...) from builtins.PyCapsule get_aa_type(rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> int get_state_ind_for_this_aa_type(...) from builtins.PyCapsule get_state_ind_for_this_aa_type(rosetta.core.pack.interaction_graph.SparseMatrixIndex) -> int set_aa_type(...) from builtins.PyCapsule set_aa_type(self : rosetta.core.pack.interaction_graph.SparseMatrixIndex, aa : int) -> NoneType set_state_ind_for_this_aa_type(...) from builtins.PyCapsule set_state_ind_for_this_aa_type(self : rosetta.core.pack.interaction_graph.SparseMatrixIndex, state_ind : int) -> NoneType   class SurfaceEnergy(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy)     Defines a (pseudo) context-dependent one-body surface energy.  Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms.     Method resolution order: SurfaceEnergy rosetta.core.scoring.methods.ContextDependentOneBodyEnergy rosetta.core.scoring.methods.OneBodyEnergy rosetta.core.scoring.methods.EnergyMethod builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.SurfaceEnergy,  : rosetta.core.pack.interaction_graph.SurfaceEnergy) -> rosetta.core.pack.interaction_graph.SurfaceEnergy clone(...) from builtins.PyCapsule clone(rosetta.core.pack.interaction_graph.SurfaceEnergy) -> rosetta.core.scoring.methods.EnergyMethod finalize_total_energy(...) from builtins.PyCapsule finalize_total_energy(self : rosetta.core.pack.interaction_graph.SurfaceEnergy, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction, totals : rosetta.core.scoring.EMapVector) -> NoneType indicate_required_context_graphs(...) from builtins.PyCapsule indicate_required_context_graphs(self : rosetta.core.pack.interaction_graph.SurfaceEnergy,  : rosetta.utility.vector1_bool) -> NoneType residue_energy(...) from builtins.PyCapsule residue_energy(self : rosetta.core.pack.interaction_graph.SurfaceEnergy, rsd : rosetta.core.conformation.Residue,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.EMapVector) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.pack.interaction_graph.SurfaceEnergy, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.core.scoring.methods.ContextDependentOneBodyEnergy: method_type(...) from builtins.PyCapsule method_type(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType   Returns the cd_1b element of the EnergyMethodType enumeration; this method  should NOT be overridden by derived classes. Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy: defines_dof_derivatives(...) from builtins.PyCapsule defines_dof_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, p : rosetta.core.pose.Pose) -> bool   Use the dof_derivative interface for this energy method when  calculating derivatives?  It is possible to define both dof_derivatives and  atom-derivatives; they are not mutually exclusive. defines_score_for_residue(...) from builtins.PyCapsule defines_score_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy,  : rosetta.core.conformation.Residue) -> bool   During minimization, energy methods are allowed to decide that they say nothing  about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for  a derivative or an energy.  The default behavior is to return "true" for all residues. eval_residue_derivatives(...) from builtins.PyCapsule eval_residue_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType   Evaluate the derivatives for all atoms on this residue and increment them  into the input atom_derivs vector1.  The calling function must guarantee that  setup for derivatives is called before this function is, and that the atom_derivs  vector contains at least as many entries as there are atoms in the input Residue.  This base class provides a default noop implementation of this function. eval_residue_dof_derivative(...) from builtins.PyCapsule eval_residue_dof_derivative(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, dof_id : rosetta.core.id.DOF_ID, torsion_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector) -> float   Evaluate the DOF derivative for a particular residue.  The Pose merely serves as context,  and the input residue is not required to be a member of the Pose. requires_a_setup_for_derivatives_for_residue_opportunity(...) from builtins.PyCapsule requires_a_setup_for_derivatives_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : rosetta.core.pose.Pose) -> bool   Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins?  Not  all energy methods would.  The ScoreFunction will not ask energy methods to examine residues that are uninterested  in doing so. requires_a_setup_for_scoring_for_residue_opportunity(...) from builtins.PyCapsule requires_a_setup_for_scoring_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : rosetta.core.pose.Pose) -> bool   Does this EnergyMethod require the opportunity to examine the residue before scoring begins?  Not  all energy methods would.  The ScoreFunction will not ask energy methods to examine residues that are uninterested  in doing so. residue_energy_ext(...) from builtins.PyCapsule residue_energy_ext(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Evaluate the one-body energies for a particular residue, in the context of a  given Pose, and with the help of a piece of cached data for minimization, increment those  one body energies into the input EnergyMap.  The calling function must guarantee that this  EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object  for the given residue in a call to setup_for_minimizing_for_residue before this function is  invoked. This function should not be called unless the use_extended_residue_energy_interface()  method returns "true".  Default implementation provided by this base class calls  utility::exit(). The Pose merely serves as context, and the input residue is not required  to be a member of the Pose. setup_for_derivatives_for_residue(...) from builtins.PyCapsule setup_for_derivatives_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType   Do any setup work necessary before evaluating the derivatives for this residue setup_for_minimizing_for_residue(...) from builtins.PyCapsule setup_for_minimizing_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction,  : rosetta.core.kinematics.MinimizerMapBase,  : core::scoring::ResSingleMinimizationData) -> NoneType   Called at the beginning of minimization, allowing this energy method to cache data  pertinent for a single residue in the the ResSingleMinimizationData that is used for a  particular residue in the context of a particular Pose.  This base class provides a noop  implementation for this function if there is nothing that the derived class needs to perform  in this setup phase.   The Pose merely serves as context, and the input residue is not  required to be a member of the Pose. setup_for_scoring_for_residue(...) from builtins.PyCapsule setup_for_scoring_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType   Do any setup work should the coordinates of this residue, who is still guaranteed to be  of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically  as to possibly require some amount of setup work before scoring should proceed use_extended_residue_energy_interface(...) from builtins.PyCapsule use_extended_residue_energy_interface(rosetta.core.scoring.methods.OneBodyEnergy) -> bool   Rely on the extended version of the residue_energy function during score-function  evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData.  Return 'true' for the extended version.  The default method implemented in this class returns 'false' Methods inherited from rosetta.core.scoring.methods.EnergyMethod: defines_high_order_terms(...) from builtins.PyCapsule defines_high_order_terms(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose) -> bool   Should this EnergyMethod have score and derivative evaluation  evaluated both in the context of the whole Pose and in the context  of residue or residue-pairs?  This covers scoring terms like env-smooth  wherein the CBeta's get derivatives for increasing the neighbor counts  for surrounding residues, and terms like constraints, which are definable  on arbitrary number of residues (e.g. more than 2); both of these terms  could be used in RTMin, and both should use the residue and residue-pair  evaluation scheme with the MinimizationGraph for the majority of the  work they do.  (Now, high-order constraints (3-body or above) will not  be properly evaluated within RTMin.).  The default implementation  returns "false". eval_atom_derivative(...) from builtins.PyCapsule eval_atom_derivative(self : rosetta.core.scoring.methods.EnergyMethod, id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType   Evaluate the XYZ derivative for an atom in the pose.  Called during the atomtree derivative calculation, atom_tree_minimize.cc,  through the ScoreFunction::eval_atom_derivative intermediary.  F1 and F2 should not zeroed, rather, this class should accumulate its contribution  from this atom's XYZ derivative      The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984)  "Rapid Calculation of First and Second Derivatives of Conformational Energy with  Respect to Dihedral Angles for Proteins. General Recurrent Equations"  Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga,  respectively, of equations 7a & 7b in that paper. finalize_after_derivatives(...) from builtins.PyCapsule finalize_after_derivatives(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction) -> NoneType   called at the end of derivatives evaluation minimize_in_whole_structure_context(...) from builtins.PyCapsule minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose) -> bool   Should this EnergyMethod have score and derivative evaluation  evaluated only in the context of the whole Pose, or can it be included  in a decomposed manner for a residue or a set of residue-pairs that are  not part of the Pose that's serving as their context?  The default  method implemented in the base class returns true in order to grandfather  in EnergyMethods that have not had their derivatives changed to take  advantage of the new derivative-evaluation machinery.  Methods that return  "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext)  methods invoked by the ScoreFunction during its traversal of the  MinimizationGraph, and instead will be asked to perform all their work  during finalize_total_energies().  Similarly, they will be expected to  perform all their work during eval_atom_deriv() instead of during the  ScoreFunction's traversal of the MinimizationGraph for derivative evaluation.  IMPORTANT: Methods that return "true" cannot be included in RTMin. prepare_rotamers_for_packing(...) from builtins.PyCapsule prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType   If an energy method needs to cache data in a packing::RotamerSet object before  rotamer energies are calculated, it does so during this function. The packer  must ensure this function is called. The default behavior is to do nothing. score_types(...) from builtins.PyCapsule score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType   Returns the score types that this energy method computes. setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Called immediately before atom- and DOF-derivatives are calculated  allowing the derived class a chance to prepare for future calls. setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction,  : rosetta.core.kinematics.MinimizerMapBase) -> NoneType   Called at the beginning of atom tree minimization, this method  allows the derived class the opportunity to initialize pertinent data  that will be used during minimization.  During minimzation, the chemical  structure of the pose is constant, so assumptions on the number of atoms  per residue and their identities are safe so long as the pose's Energies  object's "use_nblist()" method returns true. setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool,  : rosetta.utility.vector1_bool) -> NoneType   if an energy method needs to cache data in the Energies object,  before packing begins, then it does so during this function. The packer  must ensure this function is called. The default behavior is to do nothing. update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose, resid : int) -> NoneType   If the pose changes in the middle of a packing (as happens in rotamer trials) and if  an energy method needs to cache data in the pose that corresponds to its current state,  then the method must update that data when this function is called.  The packer must  ensure this function gets called.  The default behavior is to do nothing. version(...) from builtins.PyCapsule version(rosetta.core.scoring.methods.EnergyMethod) -> int   Return the version of the energy method   class SurfaceEnergyCreator(rosetta.core.scoring.methods.EnergyMethodCreator)       Method resolution order: SurfaceEnergyCreator rosetta.core.scoring.methods.EnergyMethodCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.SurfaceEnergyCreator,  : rosetta.core.pack.interaction_graph.SurfaceEnergyCreator) -> rosetta.core.pack.interaction_graph.SurfaceEnergyCreator create_energy_method(...) from builtins.PyCapsule create_energy_method(self : rosetta.core.pack.interaction_graph.SurfaceEnergyCreator,  : core::scoring::methods::EnergyMethodOptions) -> rosetta.core.scoring.methods.EnergyMethod   Instantiate a new SurfaceEnergy score_types_for_method(...) from builtins.PyCapsule score_types_for_method(rosetta.core.pack.interaction_graph.SurfaceEnergyCreator) -> rosetta.utility.vector1_core_scoring_ScoreType   Return the set of score types claimed by the EnergyMethod  this EnergyMethodCreator creates in its create_energy_method() function   class SurfacePotential(rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t)     With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class.  These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered.  No point in reading database files for a term if that term is not being used in some score function.  However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function.  The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods.  However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class.  It uses the Singleton design pattern so the database will only get read in once during a run.     Method resolution order: SurfacePotential rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. average_residue_hASA(...) from builtins.PyCapsule average_residue_hASA(self : rosetta.core.pack.interaction_graph.SurfacePotential, aa_type : rosetta.core.chemical.AA, num_nbs : int) -> float compute_pose_hpatch_score(...) from builtins.PyCapsule compute_pose_hpatch_score(*args, **kwargs) Overloaded function.   1. compute_pose_hpatch_score(self : rosetta.core.pack.interaction_graph.SurfacePotential, pose : rosetta.core.pose.Pose) -> float   return the hpatch score for an entire pose   2. compute_pose_hpatch_score(self : rosetta.core.pack.interaction_graph.SurfacePotential, pose : rosetta.core.pose.Pose, total_hpatch_energy_ : float, patch_scores_ : rosetta.std.map_unsigned_long_std_pair_double_double_t, atoms_in_patches_ : rosetta.std.map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t) -> NoneType compute_pose_surface_energy(...) from builtins.PyCapsule compute_pose_surface_energy(*args, **kwargs) Overloaded function.   1. compute_pose_surface_energy(self : rosetta.core.pack.interaction_graph.SurfacePotential, pose : rosetta.core.pose.Pose, surface_energy_ : float) -> NoneType   2. compute_pose_surface_energy(self : rosetta.core.pack.interaction_graph.SurfacePotential, pose : rosetta.core.pose.Pose, total_surface_energy_ : float, residue_surface_energy_ : rosetta.utility.vector1_double) -> NoneType compute_residue_surface_energy(...) from builtins.PyCapsule compute_residue_surface_energy(self : rosetta.core.pack.interaction_graph.SurfacePotential, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector, resid : int, num_neighbors_ : rosetta.utility.vector1_unsigned_long) -> NoneType hASA_patch_energy(...) from builtins.PyCapsule hASA_patch_energy(self : rosetta.core.pack.interaction_graph.SurfacePotential, patch_area : float, num_nbs : int) -> float hpatch_score(...) from builtins.PyCapsule hpatch_score(self : rosetta.core.pack.interaction_graph.SurfacePotential, patch_area : float) -> float Methods inherited from rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::pack::interaction_graph::SurfacePotential   class SymmLinearMemEdge(SymmOnTheFlyEdge)       Method resolution order: SymmLinearMemEdge SymmOnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_change(...) from builtins.PyCapsule acknowledge_partial_state_change(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_ind : int, new_state : int, bumped_recent_history_index : int, new_state_recent_history_index : int) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_ind : int, new_state : int, bumped_recent_history_index : int, new_state_recent_history_index : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int, bumped_recent_history_index : int, new_state_recent_history_index : int, neighbors_curr_state : int) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> int declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> NoneType get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> float get_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> float get_energy_for_alt_state(...) from builtins.PyCapsule get_energy_for_alt_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, store_rpes : bool, changing_node_index : int, alternate_state : int, alternate_state_recent_history_index : int, other_node_curr_state : int, other_node_state_recent_history_index : int) -> float get_symmlinmem_ig_owner(...) from builtins.PyCapsule get_symmlinmem_ig_owner(*args, **kwargs) Overloaded function.   1. get_symmlinmem_ig_owner(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> core::pack::interaction_graph::SymmLinearMemoryInteractionGraph   2. get_symmlinmem_ig_owner(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> core::pack::interaction_graph::SymmLinearMemoryInteractionGraph get_symmlinmem_node(...) from builtins.PyCapsule get_symmlinmem_node(*args, **kwargs) Overloaded function.   1. get_symmlinmem_node(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, index : int) -> rosetta.core.pack.interaction_graph.SymmLinearMemNode   2. get_symmlinmem_node(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, index : int) -> rosetta.core.pack.interaction_graph.SymmLinearMemNode get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node1state : int, node2state : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> NoneType print_current_energy(...) from builtins.PyCapsule print_current_energy(rosetta.core.pack.interaction_graph.SymmLinearMemEdge) -> NoneType reset_state_energies(...) from builtins.PyCapsule reset_state_energies(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_index : int, state : int, recent_history_id : int) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.SymmLinearMemEdge, weight : float) -> NoneType Methods inherited from SymmOnTheFlyEdge: add_ProCorrection_values(...) from builtins.PyCapsule add_ProCorrection_values(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind : int, state : int) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> bool   fullfilling base class virtual member request -- however, this function does not quite  make sense for a symmetric otf ig, so this is just stubbed out to return true. long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int, whichnode_restypegroup : int, othernode_restypegroup : int) -> int set_residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class SymmLinearMemNode(SymmOnTheFlyNode)       Method resolution order: SymmLinearMemNode SymmOnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_last_substititon_not_committed(...) from builtins.PyCapsule acknowledge_last_substititon_not_committed(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   update bookkeeping info to acknolwedge that the last alternative state considered was not  in fact chosen for the currently assigned state. acknowledge_neighbors_partial_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_substitution(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_to_altered_neighbor : int, other_node_new_state : int, other_state_recent_history_index : int) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int, other_node_recent_history_index : int) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, new_state : int) -> NoneType   set to a particular state -- updates the energies internally assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   set to state 0 commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   proceed to change the currently assigned state to the alternative state considered in  the last call to project_deltaE_for_substitution complete_state_assignment(...) from builtins.PyCapsule complete_state_assignment(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   second half of the entire-graph state assignment. compute_pair_energy_for_alternate_state(...) from builtins.PyCapsule compute_pair_energy_for_alternate_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the alternate state being considered on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two compute_pair_energy_for_current_state(...) from builtins.PyCapsule compute_pair_energy_for_current_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the currently assigned state on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> int get_adjacent_symmlinmem_node(...) from builtins.PyCapsule get_adjacent_symmlinmem_node(*args, **kwargs) Overloaded function.   1. get_adjacent_symmlinmem_node(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, index : int) -> rosetta.core.pack.interaction_graph.SymmLinearMemNode   2. get_adjacent_symmlinmem_node(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, index : int) -> rosetta.core.pack.interaction_graph.SymmLinearMemNode get_curr_state_recent_state_id(...) from builtins.PyCapsule get_curr_state_recent_state_id(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> int   return the "recent state id" for the currently assigned state get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> int   return the index of the currently assigned state get_incident_symmlinmem_edge(...) from builtins.PyCapsule get_incident_symmlinmem_edge(*args, **kwargs) Overloaded function.   1. get_incident_symmlinmem_edge(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, index : int) -> core::pack::interaction_graph::SymmLinearMemEdge   2. get_incident_symmlinmem_edge(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, index : int) -> core::pack::interaction_graph::SymmLinearMemEdge get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> float   return the one-body energy for the currently assigned state get_recent_history_size(...) from builtins.PyCapsule get_recent_history_size(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> int get_symmlinmem_ig_owner(...) from builtins.PyCapsule get_symmlinmem_ig_owner(*args, **kwargs) Overloaded function.   1. get_symmlinmem_ig_owner(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> core::pack::interaction_graph::SymmLinearMemoryInteractionGraph   2. get_symmlinmem_ig_owner(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> core::pack::interaction_graph::SymmLinearMemoryInteractionGraph get_totalE(...) from builtins.PyCapsule get_totalE(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> float   return the total energy for this node; includes full energies to neighboring residues partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, new_state : int) -> NoneType   first half of an entire-graph state assignment that avoids unnecessary energy updates  as produced in assign_state.  Adjust all node's states first, then update all energies. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   symmlinmem ig does not have to do anything before sim annealing begins print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType   write internal energy and bookkeeping data to standard out print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, alternate_state : int, prev_node_energy : float) -> float   compute the change in energy induced by substituting the currently assigned state with  some alternative state set_recent_history_size(...) from builtins.PyCapsule set_recent_history_size(self : rosetta.core.pack.interaction_graph.SymmLinearMemNode, num_states_to_maintain_in_recent_history : int) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> bool   state 0 represents the unasigned state update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.SymmLinearMemNode) -> NoneType Methods inherited from SymmOnTheFlyNode: add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType bb_bounding_sphere(...) from builtins.PyCapsule bb_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the backbone on a particular subunit. compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting : bool) -> NoneType get_adjacent_otf_node(...) from builtins.PyCapsule get_adjacent_otf_node(*args, **kwargs) Overloaded function.   1. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_asu_rotamer(...) from builtins.PyCapsule get_asu_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the asymmetric unit. get_incident_otf_edge(...) from builtins.PyCapsule get_incident_otf_edge(*args, **kwargs) Overloaded function.   1. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge   2. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge get_num_res_types(...) from builtins.PyCapsule get_num_res_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of distinct ResidueType objects pointed to by all of the  rotamrs for this node. get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of ResidueType groups, as defined by the RotamerSet's logic  for grouping different ResidueType objects which have the same "name3" and  the same neighbor radius. get_num_states_for_restype_group(...) from builtins.PyCapsule get_num_states_for_restype_group(*args, **kwargs) Overloaded function.   1. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   3. get_num_states_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int get_on_the_fly_owner(...) from builtins.PyCapsule get_on_the_fly_owner(*args, **kwargs) Overloaded function.   1. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph   2. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> float get_rotamer(...) from builtins.PyCapsule get_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the requested subunit.  This reference  is valid only until the next call to get_rotamer, and which point, the coordinates inside  the requested rotamer may change. get_state_offset_for_restype_group(...) from builtins.PyCapsule get_state_offset_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int sc_bounding_sphere(...) from builtins.PyCapsule sc_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the sidechain of a given state on a particular subunit. set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class SymmLinearMemoryInteractionGraph(SymmOnTheFlyInteractionGraph)       Method resolution order: SymmLinearMemoryInteractionGraph SymmOnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, numNodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> int get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> int get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, group_id : int) -> float get_recent_history_size(...) from builtins.PyCapsule get_recent_history_size(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_recent_history_size(...) from builtins.PyCapsule set_recent_history_size(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, recent_history_size : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from SymmOnTheFlyInteractionGraph: active_score_types(...) from builtins.PyCapsule active_score_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.utility.vector1_core_scoring_ScoreType add_ProCorrection_values_for_edge(...) from builtins.PyCapsule add_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType asymmetric_unit(...) from builtins.PyCapsule asymmetric_unit(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_on_the_fly_node(...) from builtins.PyCapsule get_on_the_fly_node(*args, **kwargs) Overloaded function.   1. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_residues_adjacent_for_subunit_pair_for_edge(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, asu_node_index : int, other_node_subunit : int) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType symm_info(...) from builtins.PyCapsule symm_info(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.conformation.symmetry.SymmetryInfo symmetric_transform(...) from builtins.PyCapsule symmetric_transform(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit : int) -> rosetta.numeric.HomogeneousTransform_double_t   Return the homogeneous transform to translate and rotate coordinates  originally in the asymmetric unit into a given destination subunit. zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class SymmMinimalistEdge(SymmOnTheFlyEdge)       Method resolution order: SymmMinimalistEdge SymmOnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_partial_state_change(...) from builtins.PyCapsule acknowledge_partial_state_change(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, node_ind : int, new_state : int) -> NoneType acknowledge_state_change(...) from builtins.PyCapsule acknowledge_state_change(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, node_ind : int, new_state : int, new_energy : float) -> NoneType acknowledge_state_zeroed(...) from builtins.PyCapsule acknowledge_state_zeroed(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, node_ind : int) -> NoneType acknowledge_substitution(...) from builtins.PyCapsule acknowledge_substitution(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, substituted_node_index : int, curr_state_energy : float, nodes_new_state : int) -> NoneType alt_state_energy(...) from builtins.PyCapsule alt_state_energy(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> int curr_state_energy(...) from builtins.PyCapsule curr_state_energy(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> float declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> NoneType get_current_two_body_energy(...) from builtins.PyCapsule get_current_two_body_energy(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> float get_energy_following_partial_state_assignment(...) from builtins.PyCapsule get_energy_following_partial_state_assignment(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> float get_energy_for_alt_state(...) from builtins.PyCapsule get_energy_for_alt_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, changing_node_index : int) -> float get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, node1state : int, node2state : int) -> float get_two_body_table_size(...) from builtins.PyCapsule get_two_body_table_size(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> NoneType print_current_energy(...) from builtins.PyCapsule print_current_energy(rosetta.core.pack.interaction_graph.SymmMinimalistEdge) -> NoneType set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.SymmMinimalistEdge, weight : float) -> NoneType Methods inherited from SymmOnTheFlyEdge: add_ProCorrection_values(...) from builtins.PyCapsule add_ProCorrection_values(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind : int, state : int) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> bool   fullfilling base class virtual member request -- however, this function does not quite  make sense for a symmetric otf ig, so this is just stubbed out to return true. long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int, whichnode_restypegroup : int, othernode_restypegroup : int) -> int set_residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool Methods inherited from EdgeBase: edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class SymmMinimalistInteractionGraph(SymmOnTheFlyInteractionGraph)       Method resolution order: SymmMinimalistInteractionGraph SymmOnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, numNodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> int get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> int get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph, group_id : int) -> float prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph, node_states : ObjexxFCL::FArray1<int>) -> float set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph, node_ind : int, new_state : int) -> float Methods inherited from SymmOnTheFlyInteractionGraph: active_score_types(...) from builtins.PyCapsule active_score_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.utility.vector1_core_scoring_ScoreType add_ProCorrection_values_for_edge(...) from builtins.PyCapsule add_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType asymmetric_unit(...) from builtins.PyCapsule asymmetric_unit(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_on_the_fly_node(...) from builtins.PyCapsule get_on_the_fly_node(*args, **kwargs) Overloaded function.   1. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_residues_adjacent_for_subunit_pair_for_edge(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, asu_node_index : int, other_node_subunit : int) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType symm_info(...) from builtins.PyCapsule symm_info(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.conformation.symmetry.SymmetryInfo symmetric_transform(...) from builtins.PyCapsule symmetric_transform(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit : int) -> rosetta.numeric.HomogeneousTransform_double_t   Return the homogeneous transform to translate and rotate coordinates  originally in the asymmetric unit into a given destination subunit. zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class SymmMinimalistNode(SymmOnTheFlyNode)       Method resolution order: SymmMinimalistNode SymmOnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. acknowledge_last_substititon_not_committed(...) from builtins.PyCapsule acknowledge_last_substititon_not_committed(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   update bookkeeping info to acknolwedge that the last alternative state considered was not  in fact chosen for the currently assigned state. acknowledge_neighbors_partial_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_partial_state_substitution(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_to_altered_neighbor : int, other_node_new_state : int) -> NoneType acknowledge_neighbors_state_substitution(...) from builtins.PyCapsule acknowledge_neighbors_state_substitution(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_to_altered_neighbor : int, new_edge_energy : float, other_node_new_state : int) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, new_state : int) -> NoneType   set to a particular state -- updates the energies internally assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   set to state 0 commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   proceed to change the currently assigned state to the alternative state considered in  the last call to project_deltaE_for_substitution complete_state_assignment(...) from builtins.PyCapsule complete_state_assignment(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   second half of the entire-graph state assignment. compute_pair_energy_for_alternate_state(...) from builtins.PyCapsule compute_pair_energy_for_alternate_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the alternate state being considered on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two compute_pair_energy_for_current_state(...) from builtins.PyCapsule compute_pair_energy_for_current_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_making_energy_request : int) -> float   comupute the interaction energy between the currently assigned state on this residue and  the currently assigned state on a neighboring residue, identified by the index of the edge connecting  the two count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> int get_adjacent_symmin_node(...) from builtins.PyCapsule get_adjacent_symmin_node(*args, **kwargs) Overloaded function.   1. get_adjacent_symmin_node(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, index : int) -> rosetta.core.pack.interaction_graph.SymmMinimalistNode   2. get_adjacent_symmin_node(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, index : int) -> rosetta.core.pack.interaction_graph.SymmMinimalistNode get_current_state(...) from builtins.PyCapsule get_current_state(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> int   return the index of the currently assigned state get_incident_symmin_edge(...) from builtins.PyCapsule get_incident_symmin_edge(*args, **kwargs) Overloaded function.   1. get_incident_symmin_edge(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, index : int) -> core::pack::interaction_graph::SymmMinimalistEdge   2. get_incident_symmin_edge(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, index : int) -> core::pack::interaction_graph::SymmMinimalistEdge get_one_body_energy_current_state(...) from builtins.PyCapsule get_one_body_energy_current_state(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> float   return the one-body energy for the currently assigned state get_symmin_ig_owner(...) from builtins.PyCapsule get_symmin_ig_owner(*args, **kwargs) Overloaded function.   1. get_symmin_ig_owner(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> core::pack::interaction_graph::SymmMinimalistInteractionGraph   2. get_symmin_ig_owner(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> core::pack::interaction_graph::SymmMinimalistInteractionGraph get_totalE(...) from builtins.PyCapsule get_totalE(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> float   return the total energy for this node; includes full energies to neighboring residues partial_assign_state(...) from builtins.PyCapsule partial_assign_state(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, new_state : int) -> NoneType   first half of an entire-graph state assignment that avoids unnecessary energy updates  as produced in assign_state.  Adjust all node's states first, then update all energies. prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   symmin ig does not have to do anything before sim annealing begins print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType   write internal energy and bookkeeping data to standard out print_internal_energies(...) from builtins.PyCapsule print_internal_energies(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType project_deltaE_for_substitution(...) from builtins.PyCapsule project_deltaE_for_substitution(self : rosetta.core.pack.interaction_graph.SymmMinimalistNode, alternate_state : int, prev_node_energy : float) -> float   compute the change in energy induced by substituting the currently assigned state with  some alternative state state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> bool   state 0 represents the unasigned state update_internal_energy_sums(...) from builtins.PyCapsule update_internal_energy_sums(rosetta.core.pack.interaction_graph.SymmMinimalistNode) -> NoneType Methods inherited from SymmOnTheFlyNode: add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType bb_bounding_sphere(...) from builtins.PyCapsule bb_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the backbone on a particular subunit. compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting : bool) -> NoneType get_adjacent_otf_node(...) from builtins.PyCapsule get_adjacent_otf_node(*args, **kwargs) Overloaded function.   1. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_asu_rotamer(...) from builtins.PyCapsule get_asu_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the asymmetric unit. get_incident_otf_edge(...) from builtins.PyCapsule get_incident_otf_edge(*args, **kwargs) Overloaded function.   1. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge   2. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge get_num_res_types(...) from builtins.PyCapsule get_num_res_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of distinct ResidueType objects pointed to by all of the  rotamrs for this node. get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of ResidueType groups, as defined by the RotamerSet's logic  for grouping different ResidueType objects which have the same "name3" and  the same neighbor radius. get_num_states_for_restype_group(...) from builtins.PyCapsule get_num_states_for_restype_group(*args, **kwargs) Overloaded function.   1. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   3. get_num_states_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int get_on_the_fly_owner(...) from builtins.PyCapsule get_on_the_fly_owner(*args, **kwargs) Overloaded function.   1. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph   2. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> float get_rotamer(...) from builtins.PyCapsule get_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the requested subunit.  This reference  is valid only until the next call to get_rotamer, and which point, the coordinates inside  the requested rotamer may change. get_state_offset_for_restype_group(...) from builtins.PyCapsule get_state_offset_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int sc_bounding_sphere(...) from builtins.PyCapsule sc_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the sidechain of a given state on a particular subunit. set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int   class SymmOnTheFlyEdge(FixedBBEdge)       Method resolution order: SymmOnTheFlyEdge FixedBBEdge EdgeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_ProCorrection_values(...) from builtins.PyCapsule add_ProCorrection_values(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> int eval_type(...) from builtins.PyCapsule eval_type(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_index : int) -> rosetta.core.pack.interaction_graph.ResiduePairEvalType force_aa_neighbors(...) from builtins.PyCapsule force_aa_neighbors(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. force_all_aa_neighbors(...) from builtins.PyCapsule force_all_aa_neighbors(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. get_proline_correction_for_node(...) from builtins.PyCapsule get_proline_correction_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind : int, state : int) -> float get_sparse_aa_info(...) from builtins.PyCapsule get_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> bool   fullfilling base class virtual member request -- however, this function does not quite  make sense for a symmetric otf ig, so this is just stubbed out to return true. get_two_body_energy(...) from builtins.PyCapsule get_two_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : int,  : int) -> float long_range_interactions_exist(...) from builtins.PyCapsule long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool note_long_range_interactions_exist(...) from builtins.PyCapsule note_long_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType note_short_range_interactions_exist(...) from builtins.PyCapsule note_short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> NoneType residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int, whichnode_restypegroup : int, othernode_restypegroup : int) -> int set_residues_adjacent_for_subunit_pair(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node : int, other_node_subunit : int) -> NoneType set_sparse_aa_info(...) from builtins.PyCapsule set_sparse_aa_info(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge,  : ObjexxFCL::FArray2<bool>) -> NoneType   fullfilling base class virtual member request -- however, this funciton does not quite  make sense for a symmetric oft ig so this is just stubbed out as a noop. short_range_interactions_exist(...) from builtins.PyCapsule short_range_interactions_exist(rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge) -> bool Methods inherited from EdgeBase: declare_energies_final(...) from builtins.PyCapsule declare_energies_final(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType edge_weight(...) from builtins.PyCapsule edge_weight(rosetta.core.pack.interaction_graph.EdgeBase) -> float get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> int get_other_node(...) from builtins.PyCapsule get_other_node(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_owner(...) from builtins.PyCapsule get_owner(*args, **kwargs) Overloaded function.   1. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase   2. get_owner(rosetta.core.pack.interaction_graph.EdgeBase) -> core::pack::interaction_graph::InteractionGraphBase get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.pack.interaction_graph.EdgeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.EdgeBase) -> NoneType same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.pack.interaction_graph.EdgeBase, node1 : int, node2 : int) -> bool set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.EdgeBase, weight : float) -> NoneType set_pos_in_node_edgevector(...) from builtins.PyCapsule set_pos_in_node_edgevector(self : rosetta.core.pack.interaction_graph.EdgeBase, callers_index : int, position : int) -> NoneType set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.pack.interaction_graph.EdgeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType   class SymmOnTheFlyInteractionGraph(FixedBBInteractionGraph)       Method resolution order: SymmOnTheFlyInteractionGraph FixedBBInteractionGraph InteractionGraphBase AnnealableGraphBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, num_nodes : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. active_score_types(...) from builtins.PyCapsule active_score_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.utility.vector1_core_scoring_ScoreType add_ProCorrection_values_for_edge(...) from builtins.PyCapsule add_ProCorrection_values_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, node_not_neccessarily_proline : int, state : int, bb_nonprobb_E : float, bb_probb_E : float, sc_nonprobb_E : float, sc_probb_E : float) -> NoneType add_to_one_body_energy_for_node_state(...) from builtins.PyCapsule add_to_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType asymmetric_unit(...) from builtins.PyCapsule asymmetric_unit(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int distinguish_backbone_and_sidechain_for_node(...) from builtins.PyCapsule distinguish_backbone_and_sidechain_for_node(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int) -> bool   2. distinguish_backbone_and_sidechain_for_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, setting : bool) -> NoneType get_num_aatypes(...) from builtins.PyCapsule get_num_aatypes(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_num_rpe_calculations_count(...) from builtins.PyCapsule get_num_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> int get_on_the_fly_node(...) from builtins.PyCapsule get_on_the_fly_node(*args, **kwargs) Overloaded function.   1. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_on_the_fly_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_one_body_energy_for_node_state(...) from builtins.PyCapsule get_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node : int, state : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, rot_sets : rosetta.core.pack.rotamer_set.RotamerSetsBase) -> NoneType non_const_pose(...) from builtins.PyCapsule non_const_pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose   debugging only -- modify the pose during simulated annealing, if you're so inclined note_long_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_long_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType note_rpe_calculated(...) from builtins.PyCapsule note_rpe_calculated(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType   to be called by owned OTF node only note_short_range_interactions_exist_for_edge(...) from builtins.PyCapsule note_short_range_interactions_exist_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int) -> NoneType pose(...) from builtins.PyCapsule pose(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.pose.Pose reset_rpe_calculations_count(...) from builtins.PyCapsule reset_rpe_calculations_count(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> NoneType score_function(...) from builtins.PyCapsule score_function(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.scoring.ScoreFunction set_one_body_energy_for_node_state(...) from builtins.PyCapsule set_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int, one_body_energy : float) -> NoneType set_pose(...) from builtins.PyCapsule set_pose(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.pose.Pose) -> NoneType set_residues_adjacent_for_subunit_pair_for_edge(...) from builtins.PyCapsule set_residues_adjacent_for_subunit_pair_for_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1 : int, node2 : int, asu_node_index : int, other_node_subunit : int) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph,  : rosetta.core.scoring.ScoreFunction) -> NoneType symm_info(...) from builtins.PyCapsule symm_info(rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) -> rosetta.core.conformation.symmetry.SymmetryInfo symmetric_transform(...) from builtins.PyCapsule symmetric_transform(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit : int) -> rosetta.numeric.HomogeneousTransform_double_t   Return the homogeneous transform to translate and rotate coordinates  originally in the asymmetric unit into a given destination subunit. zero_one_body_energy_for_node_state(...) from builtins.PyCapsule zero_one_body_energy_for_node_state(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_ind : int, state : int) -> NoneType Methods inherited from FixedBBInteractionGraph: aa_submatrix_energies_retrievable(...) from builtins.PyCapsule aa_submatrix_energies_retrievable(rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) -> bool aatype_for_node_state(...) from builtins.PyCapsule aatype_for_node_state(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind : int, node_state : int) -> int force_aa_neighbors_for_edge(...) from builtins.PyCapsule force_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> NoneType   interface to FixedBBEdge::force_aa_neighbors force_all_aa_neighbors_for_edge(...) from builtins.PyCapsule force_all_aa_neighbors_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int) -> NoneType   interface to PDEdge::force_aa_neighbors get_aa_submatrix_energies_for_edge(...) from builtins.PyCapsule get_aa_submatrix_energies_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> ObjexxFCL::FArray2D<float> get_sparse_aa_info_for_edge(...) from builtins.PyCapsule get_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, node1aa : int, node2aa : int) -> bool   returns true if node1aa and node2aa are amino acid neighbors get_two_body_energy_for_edge(...) from builtins.PyCapsule get_two_body_energy_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, state_node1 : int, state_node2 : int) -> float   interface to FixedBBEdge::get_two_body_energy   - returns the state pair energy set_sparse_aa_info_for_edge(...) from builtins.PyCapsule set_sparse_aa_info_for_edge(self : rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1 : int, node2 : int, sparse_conn_info : ObjexxFCL::FArray2<bool>) -> NoneType   interface to PDEdge::set_sparse_aa_info Methods inherited from InteractionGraphBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> NoneType add_to_nodes_one_body_energy(...) from builtins.PyCapsule add_to_nodes_one_body_energy(*args, **kwargs) Overloaded function.   1. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : rosetta.utility.vector1_float) -> NoneType   2. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType   3. add_to_nodes_one_body_energy(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, state_id : int, one_body_energy : float) -> NoneType   interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies : ObjexxFCL::FArray1<float>) -> NoneType any_vertex_state_unassigned(...) from builtins.PyCapsule any_vertex_state_unassigned(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool blanket_assign_state_0(...) from builtins.PyCapsule blanket_assign_state_0(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType commit_considered_substitution(...) from builtins.PyCapsule commit_considered_substitution(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float consider_substitution(...) from builtins.PyCapsule consider_substitution(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int, delta_energy : float, prev_energy_for_node : float) -> NoneType count_connected_components_and_initialize_vertex_groups(...) from builtins.PyCapsule count_connected_components_and_initialize_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index1 : int, index2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, num_states : int) -> rosetta.core.pack.interaction_graph.NodeBase drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType edge_list_iterator_at_end(...) from builtins.PyCapsule edge_list_iterator_at_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> bool   test: have we arrived at the edge list end? find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase   The following functions provide access to the nodes and edges in the graph  though, their use is strongly discouraged except for in writing unit tests  to ensure that the graphs are properly implemented.   2. find_edge(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> rosetta.core.pack.interaction_graph.EdgeBase getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge(...) from builtins.PyCapsule get_edge(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> rosetta.core.pack.interaction_graph.EdgeBase   return a const reference to an edge pointed at by the list iterator get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> bool get_edge_list_begin(...) from builtins.PyCapsule get_edge_list_begin(*args, **kwargs) Overloaded function.   1. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*>   2. get_edge_list_begin(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_list_end(...) from builtins.PyCapsule get_edge_list_end(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> get_edge_memory_usage(...) from builtins.PyCapsule get_edge_memory_usage(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_edge_weight(...) from builtins.PyCapsule get_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int) -> float get_energy_current_state_assignment(...) from builtins.PyCapsule get_energy_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> float get_energy_sum_for_vertex_group(...) from builtins.PyCapsule get_energy_sum_for_vertex_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id : int) -> float get_node(...) from builtins.PyCapsule get_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_num_edges(...) from builtins.PyCapsule get_num_edges(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_nodes(...) from builtins.PyCapsule get_num_nodes(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_num_states_for_node(...) from builtins.PyCapsule get_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> int get_num_total_states(...) from builtins.PyCapsule get_num_total_states(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> int get_vertex_member_of_energy_sum_group(...) from builtins.PyCapsule get_vertex_member_of_energy_sum_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int, group_id : int) -> bool increment_edge_list_iterator(...) from builtins.PyCapsule increment_edge_list_iterator(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   increment the (single) edge list iterator to the next element note_vertex_reached(...) from builtins.PyCapsule note_vertex_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType   iterate across edges and nodes and allow them to prepare  for simulated annealing print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_current_state_assignment(...) from builtins.PyCapsule print_current_state_assignment(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertex_groups(...) from builtins.PyCapsule print_vertex_groups(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.pack.interaction_graph.InteractionGraphBase) -> NoneType reset_edge_list_iterator_for_node(...) from builtins.PyCapsule reset_edge_list_iterator_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> NoneType   set the Graph's (single) edge list iterator to the beginning of the edge list  for a particular node set_edge_weight(...) from builtins.PyCapsule set_edge_weight(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node1 : int, node2 : int, edge_weight : float) -> NoneType set_errorfull_deltaE_threshold(...) from builtins.PyCapsule set_errorfull_deltaE_threshold(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, deltaE : float) -> NoneType set_network_state(...) from builtins.PyCapsule set_network_state(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_states : ObjexxFCL::FArray1<int>) -> float set_num_states_for_node(...) from builtins.PyCapsule set_num_states_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int, num_states : int) -> NoneType set_number_of_energy_sum_vertex_groups(...) from builtins.PyCapsule set_number_of_energy_sum_vertex_groups(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups : int) -> NoneType set_state_for_node(...) from builtins.PyCapsule set_state_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind : int, new_state : int) -> float set_vertex_member_of_group(...) from builtins.PyCapsule set_vertex_member_of_group(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex : int, group : int) -> NoneType update_one_body_energies(...) from builtins.PyCapsule update_one_body_energies(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b : ObjexxFCL::FArray1<float>, new_energy1b : ObjexxFCL::FArray1<float>) -> NoneType vertex_already_reached(...) from builtins.PyCapsule vertex_already_reached(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index : int) -> bool zero_one_body_energies_for_node(...) from builtins.PyCapsule zero_one_body_energies_for_node(self : rosetta.core.pack.interaction_graph.InteractionGraphBase, node : int) -> NoneType Methods inherited from AnnealableGraphBase: assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.interaction_graph.AnnealableGraphBase,  : rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase   class SymmOnTheFlyNode(FixedBBNode)       Method resolution order: SymmOnTheFlyNode FixedBBNode NodeBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, owner : rosetta.core.pack.interaction_graph.InteractionGraphBase, node_id : int, num_states : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_one_body_energies(...) from builtins.PyCapsule add_to_one_body_energies(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b : ObjexxFCL::FArray1<float>) -> NoneType add_to_one_body_energy(...) from builtins.PyCapsule add_to_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType bb_bounding_sphere(...) from builtins.PyCapsule bb_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the backbone on a particular subunit. compute_rotamer_pair_energy(...) from builtins.PyCapsule compute_rotamer_pair_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request : int, state_this : int, state_other : int) -> float count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int distinguish_backbone_and_sidechain(...) from builtins.PyCapsule distinguish_backbone_and_sidechain(*args, **kwargs) Overloaded function.   1. distinguish_backbone_and_sidechain(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> bool   2. distinguish_backbone_and_sidechain(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting : bool) -> NoneType get_adjacent_otf_node(...) from builtins.PyCapsule get_adjacent_otf_node(*args, **kwargs) Overloaded function.   1. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode   2. get_adjacent_otf_node(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index : int) -> rosetta.core.pack.interaction_graph.SymmOnTheFlyNode get_asu_rotamer(...) from builtins.PyCapsule get_asu_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the asymmetric unit. get_incident_otf_edge(...) from builtins.PyCapsule get_incident_otf_edge(*args, **kwargs) Overloaded function.   1. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge   2. get_incident_otf_edge(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge : int) -> core::pack::interaction_graph::SymmOnTheFlyEdge get_num_res_types(...) from builtins.PyCapsule get_num_res_types(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of distinct ResidueType objects pointed to by all of the  rotamrs for this node. get_num_restype_groups(...) from builtins.PyCapsule get_num_restype_groups(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> int   the number of ResidueType groups, as defined by the RotamerSet's logic  for grouping different ResidueType objects which have the same "name3" and  the same neighbor radius. get_num_states_for_restype_group(...) from builtins.PyCapsule get_num_states_for_restype_group(*args, **kwargs) Overloaded function.   1. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   2. get_num_states_for_restype_group(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> rosetta.utility.vector1_int   3. get_num_states_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int get_on_the_fly_owner(...) from builtins.PyCapsule get_on_the_fly_owner(*args, **kwargs) Overloaded function.   1. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph   2. get_on_the_fly_owner(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> core::pack::interaction_graph::SymmOnTheFlyInteractionGraph get_one_body_energy(...) from builtins.PyCapsule get_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> float get_rotamer(...) from builtins.PyCapsule get_rotamer(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> rosetta.core.conformation.Residue   Returns a reference to the rotamer object in the requested subunit.  This reference  is valid only until the next call to get_rotamer, and which point, the coordinates inside  the requested rotamer may change. get_state_offset_for_restype_group(...) from builtins.PyCapsule get_state_offset_for_restype_group(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group : int) -> int sc_bounding_sphere(...) from builtins.PyCapsule sc_bounding_sphere(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, subunit : int) -> (rosetta.numeric.xyzVector_double_t, float)   Returns a bounding sphere for the sidechain of a given state on a particular subunit. set_one_body_energy(...) from builtins.PyCapsule set_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType set_rotamers(...) from builtins.PyCapsule set_rotamers(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType update_one_body_energy(...) from builtins.PyCapsule update_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int, energy : float) -> NoneType zero_one_body_energies(...) from builtins.PyCapsule zero_one_body_energies(rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> NoneType zero_one_body_energy(...) from builtins.PyCapsule zero_one_body_energy(self : rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state : int) -> NoneType Methods inherited from NodeBase: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_ptr : core::pack::interaction_graph::EdgeBase) -> std::_List_iterator<core::pack::interaction_graph::EdgeBase*> assign_zero_state(...) from builtins.PyCapsule assign_zero_state(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType depth_first_connected_component_counting(...) from builtins.PyCapsule depth_first_connected_component_counting(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.pack.interaction_graph.NodeBase, edge_iterator : std::_List_iterator<core::pack::interaction_graph::EdgeBase*>) -> NoneType edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.pack.interaction_graph.NodeBase) -> std::_List_const_iterator<core::pack::interaction_graph::EdgeBase*> find_edge(...) from builtins.PyCapsule find_edge(self : rosetta.core.pack.interaction_graph.NodeBase, other_node_index : int) -> core::pack::interaction_graph::EdgeBase get_adjacent_node(...) from builtins.PyCapsule get_adjacent_node(*args, **kwargs) Overloaded function.   1. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase   2. get_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> rosetta.core.pack.interaction_graph.NodeBase get_incident_edge(...) from builtins.PyCapsule get_incident_edge(*args, **kwargs) Overloaded function.   1. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase   These functions are public for the sake of writing good unit tests   2. get_incident_edge(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> core::pack::interaction_graph::EdgeBase get_index_of_adjacent_node(...) from builtins.PyCapsule get_index_of_adjacent_node(self : rosetta.core.pack.interaction_graph.NodeBase, index : int) -> int get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_incident_edges(...) from builtins.PyCapsule get_num_incident_edges(rosetta.core.pack.interaction_graph.NodeBase) -> int get_num_states(...) from builtins.PyCapsule get_num_states(rosetta.core.pack.interaction_graph.NodeBase) -> int prepare_for_simulated_annealing(...) from builtins.PyCapsule prepare_for_simulated_annealing(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.pack.interaction_graph.NodeBase) -> NoneType state_unassigned(...) from builtins.PyCapsule state_unassigned(rosetta.core.pack.interaction_graph.NodeBase) -> bool   class exposed_hydrophobic_data(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.pack.interaction_graph.exposed_hydrophobic_data, fc_bg : int, node_ind : int, exhphobe_ind : int) -> NoneType   2. __init__(self : rosetta.core.pack.interaction_graph.exposed_hydrophobic_data,  : rosetta.core.pack.interaction_graph.exposed_hydrophobic_data) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: exhphobe_index_ fc_bg_ node_index_   class history_queue_struct(builtins.object)     for storing three peices of associated data describing the recent history structure on a LinearMemNode.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.pack.interaction_graph.history_queue_struct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: more_ancient_ptr more_recent_ptr state_in_rh