interaction_graph

Bindings for core::pack::interaction_graph namespace

class pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

Bases: pybind11_builtins.pybind11_object

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) bool

Is any state of any vertex unassigned?

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) None

State initialization

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

commit_considered_substitution(self: pyrosetta.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.

C++: core::pack::interaction_graph::AnnealableGraphBase::commit_considered_substitution() –> float

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

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.

C++: core::pack::interaction_graph::AnnealableGraphBase::consider_substitution(int, int, float &, float &) –> void

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) float

Get the energy resulting from the current set of state assignments.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::get_energy_current_state_assignment() –> float

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) int

Get the number of nodes in the graph.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::get_num_nodes() const –> int

get_num_states_for_node(self: pyrosetta.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.

C++: core::pack::interaction_graph::AnnealableGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) int

Get the total number of states.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::get_num_total_states() const –> int

prepare_graph_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) None

Utility signal.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::prepare_graph_for_simulated_annealing() –> void

set_errorfull_deltaE_threshold(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, deltaE: float) None

Set an error threshold.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::set_errorfull_deltaE_threshold(float) –> void

set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) float

Explicit state modification for the network.

Must be implemented by derived classes.

C++: core::pack::interaction_graph::AnnealableGraphBase::set_network_state(class ObjexxFCL::FArray1<int> &) –> float

set_state_for_node(self: pyrosetta.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.

C++: core::pack::interaction_graph::AnnealableGraphBase::set_state_for_node(int, int) –> float

class pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, node_ind: int, new_state: int, new_energy: float) None

C++: core::pack::interaction_graph::DensePDEdge::acknowledge_state_change(int, int, float &) –> void

acknowledge_state_zeroed(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, node_ind: int) None

C++: core::pack::interaction_graph::DensePDEdge::acknowledge_state_zeroed(int) –> void

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int) None

C++: core::pack::interaction_graph::DensePDEdge::acknowledge_substitution(int, const float, int) –> void

add_to_two_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) None

C++: core::pack::interaction_graph::DensePDEdge::add_to_two_body_energies(const class ObjexxFCL::FArray2<float> &) –> void

add_to_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int, : float) None

C++: core::pack::interaction_graph::DensePDEdge::add_to_two_body_energy(const int, const int, const float) –> void

clear_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int) None

C++: core::pack::interaction_graph::DensePDEdge::clear_two_body_energy(const int, const int) –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) int

C++: core::pack::interaction_graph::DensePDEdge::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) int

C++: core::pack::interaction_graph::DensePDEdge::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) None

C++: core::pack::interaction_graph::DensePDEdge::declare_energies_final() –> void

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

force_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int) None

C++: core::pack::interaction_graph::DensePDEdge::force_aa_neighbors(int, int) –> void

force_all_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) None

C++: core::pack::interaction_graph::DensePDEdge::force_all_aa_neighbors() –> void

get_aa_submatrix_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

return all energies on this edge…

C++: core::pack::interaction_graph::DensePDEdge::get_aa_submatrix_energies() const –> class ObjexxFCL::FArray2D<float>

static get_alternate_state_energy(first_node_state: int, second_node_state: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) float

C++: core::pack::interaction_graph::DensePDEdge::get_alternate_state_energy(int, int, class ObjexxFCL::FArray2<float> &) –> float

get_current_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) float

C++: core::pack::interaction_graph::DensePDEdge::get_current_two_body_energy() –> float

get_edge_table_ptr(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t

C++: core::pack::interaction_graph::DensePDEdge::get_edge_table_ptr() –> class ObjexxFCL::FArray2A<float>

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

get_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int) bool

C++: core::pack::interaction_graph::DensePDEdge::get_sparse_aa_info(int, int) const –> bool

get_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int) float

C++: core::pack::interaction_graph::DensePDEdge::get_two_body_energy(const int, const int) const –> float

get_two_body_table_size(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) int

C++: core::pack::interaction_graph::DensePDEdge::get_two_body_table_size() const –> int

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge) None

C++: core::pack::interaction_graph::DensePDEdge::prepare_for_simulated_annealing() –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, weight: float) None

C++: core::pack::interaction_graph::DensePDEdge::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::DensePDEdge::set_sparse_aa_info(const class ObjexxFCL::FArray2<bool> &) –> void

set_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, : int, : int, : float) None

C++: core::pack::interaction_graph::DensePDEdge::set_two_body_energy(const int, const int, const float) –> void

swap_edge_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge, new_edge_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::pack::interaction_graph::DensePDEdge::swap_edge_energies(class ObjexxFCL::FArray2D<float> &) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph

aa_submatrix_energies_retrievable(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) bool
Override the InteractionGraphBase class’s implementation of this function

to return ‘true’.

C++: core::pack::interaction_graph::DensePDInteractionGraph::aa_submatrix_energies_retrievable() const –> bool

aatype_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind: int, node_state: int) int

C++: core::pack::interaction_graph::DensePDInteractionGraph::aatype_for_node_state(int, int) const –> int

add_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_edge(int, int) –> void

add_longrange_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, lr_energy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes and a long-range energy, compute the long-range energy of all

interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::methods::LongRangeTwoBodyEnergy>, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.utility.vector1_float) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class utility::vector1<float, class std::allocator<float> > &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class ObjexxFCL::FArray1<float> &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, state_id: int, one_body_energy: float) -> None

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, int, const float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_two_body_energies_for_edge(*args, **kwargs)

Overloaded function.

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) -> None

  2. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t, use_threadsafe_method: bool) -> None

interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies

If use_threadsafe_method is true, we don’t cache the edge index for faster future lookups.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, const class ObjexxFCL::FArray2<float> &, const bool) –> void

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) -> None

interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, int, int, const float) –> void

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

C++: core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) None

C++: core::pack::interaction_graph::DensePDInteractionGraph::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

clear_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int) None

interface to PDEdge::clear_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::clear_two_body_energy_for_edge(int, int, int, int) –> void

commit_considered_substitution(self: pyrosetta.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

C++: core::pack::interaction_graph::DensePDInteractionGraph::commit_considered_substitution() –> float

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

C++: core::pack::interaction_graph::DensePDInteractionGraph::consider_substitution(int, int, float &, float &) –> void

count_connected_components_and_initialize_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups() –> int

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) int

C++: core::pack::interaction_graph::DensePDInteractionGraph::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) int

C++: core::pack::interaction_graph::DensePDInteractionGraph::count_static_memory() const –> unsigned int

create_new_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index1: int, index2: int) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_edge(int, int) –> class core::pack::interaction_graph::EdgeBase *

create_new_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, num_states: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_node(int, int) –> class core::pack::interaction_graph::NodeBase *

declare_all_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
Iterates over all edges and calls declare_energies_final() on

all of them. Takes O(N) time, where N is the number of edges.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final() –> void

declare_edge_energies_final(*args, **kwargs)

Overloaded function.

  1. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None

  2. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, use_threadsafe_lookup: bool) -> None

call this if you’re done storing energies in an edge - it will reduce

the memory usage for that edge if possible

  • [in] - the index of the smaller-indexed node

  • [in] - the index of the larger-indexed node

  • [in] - If true, we don’t cache the last edge

found for faster future lookups. False by default.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::declare_edge_energies_final(int, int, const bool) –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node(int) –> void

edge_list_iterator_at_end(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

test: have we arrived at the edge list end?

C++: core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end() const –> bool

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

  2. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, use_threadsafe_lookup: bool) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

C++: core::pack::interaction_graph::InteractionGraphBase::find_edge(int, int, const bool) –> class core::pack::interaction_graph::EdgeBase *

force_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) None

interface to FixedBBEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_aa_neighbors_for_edge(int, int, int, int) –> void

force_all_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int) None

interface to PDEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_all_aa_neighbors_for_edge(int, int) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned int

get_aa_submatrix_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_aa_submatrix_energies_for_edge(int, int, int, int) const –> class ObjexxFCL::FArray2D<float>

get_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

return a const reference to an edge pointed at by the list iterator

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge() const –> const class core::pack::interaction_graph::EdgeBase &

get_edge_exists(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(int, int) const –> bool

get_edge_memory_usage(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) int

returns the number of floats used in all edge two-body energy tables

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_edge_memory_usage() const –> int

get_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(int, int) const –> double

get_energy_PD_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) float

Hook for classes derived from AdditionalBackgroundNodesInteractionGraph

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_energy_PD_current_state_assignment() –> float

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) float
removes all accumulated numerical drift and returns the

energy for the current state assignment.

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_energy_current_state_assignment() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.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.

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_energy_sum_for_vertex_group(int) –> float

get_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::get_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_num_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) int

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_num_aatypes() const –> int

get_num_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_edges() const –> int

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_nodes() const –> int

get_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_total_states() const –> int

get_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node: int, state: int) float

C++: core::pack::interaction_graph::DensePDInteractionGraph::get_one_body_energy_for_node_state(int, int) –> float

get_sparse_aa_info_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_sparse_aa_info_for_edge(int, int, int, int) –> bool

get_two_body_energy_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_two_body_energy_for_edge(int, int, int, int) const –> float

get_vertex_member_of_energy_sum_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, group_id: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group(int, int) –> bool

increment_edge_list_iterator(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

increment the (single) edge list iterator to the next element

C++: core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator() const –> void

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) None

C++: core::pack::interaction_graph::DensePDInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

note_vertex_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(int) –> void

output_connectivity(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_dimacs(std::ostream &) const –> void

prepare_graph_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
iterate across edges and nodes and allow them to prepare

for simulated annealing

C++: core::pack::interaction_graph::InteractionGraphBase::prepare_graph_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print() const –> void

print_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph) None

outputs the current state for each node, useful for debugging

C++: core::pack::interaction_graph::DensePDInteractionGraph::print_current_state_assignment() const –> void

print_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups() –> void

print_vertices(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertices() const –> void

reset_edge_list_iterator_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None
set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

C++: core::pack::interaction_graph::InteractionGraphBase::reset_edge_list_iterator_for_node(int) const –> void

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, edge_weight: float) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_edge_weight(int, int, double) –> void

set_errorfull_deltaE_threshold(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, : float) None

C++: core::pack::interaction_graph::DensePDInteractionGraph::set_errorfull_deltaE_threshold(float) –> void

set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) float

C++: core::pack::interaction_graph::DensePDInteractionGraph::set_network_state(class ObjexxFCL::FArray1<int> &) –> float

set_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int, num_states: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(int, int) –> void

set_number_of_energy_sum_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_number_of_energy_sum_vertex_groups(int) –> void

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) None
Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded(const unsigned long, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class basic::thread_manager::RosettaThreadAssignmentInfo &) –> void

set_sparse_aa_info_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

interface to PDEdge::set_sparse_aa_info

C++: core::pack::interaction_graph::FixedBBInteractionGraph::set_sparse_aa_info_for_edge(int, int, const class ObjexxFCL::FArray2<bool> &) –> void

set_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node_ind: int, new_state: int) float

C++: core::pack::interaction_graph::DensePDInteractionGraph::set_state_for_node(int, int) –> float

set_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) None

interface to PDEdge::set_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_two_body_energy_for_edge(int, int, int, int, const float) –> void

set_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes, compute the energy of all interacting rotamers and add those

energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

set_vertex_member_of_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex: int, group: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_vertex_member_of_group(int, int) –> void

swap_edge_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph, node1: int, node2: int, new_edge_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

Swap the contents of the edge pair-energy table with the contents in the new_edge_table

C++: core::pack::interaction_graph::DensePDInteractionGraph::swap_edge_energies(int, int, class ObjexxFCL::FArray2D<float> &) –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, new_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::update_one_body_energies(class ObjexxFCL::FArray1<float> &, class ObjexxFCL::FArray1<float> &) –> void

vertex_already_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached(int) –> bool

zero_one_body_energies_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::zero_one_body_energies_for_node(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode

acknowledge_neighbors_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, edge_to_altered_neighbor: int, new_edge_energy: float, other_node_new_state: int) None

C++: core::pack::interaction_graph::DensePDNode::acknowledge_neighbors_state_substitution(int, float, int) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::DensePDNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, state: int, energy: float) None

C++: core::pack::interaction_graph::DensePDNode::add_to_one_body_energy(int, float) –> void

assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, new_state: int) None

C++: core::pack::interaction_graph::DensePDNode::assign_state(int) –> void

assign_zero_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::assign_zero_state() –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::commit_considered_substitution() –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) int

C++: core::pack::interaction_graph::DensePDNode::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) int

C++: core::pack::interaction_graph::DensePDNode::count_static_memory() const –> unsigned int

depth_first_connected_component_counting(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting() –> void

drop_all_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::drop_all_edges() –> void

find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, other_node_index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::find_edge(int) const –> class core::pack::interaction_graph::EdgeBase *

get_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::NodeBase::get_adjacent_node(int) –> class core::pack::interaction_graph::NodeBase *

get_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) int

C++: core::pack::interaction_graph::DensePDNode::get_current_state() const –> int

get_incident_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::get_incident_edge(int) –> class core::pack::interaction_graph::EdgeBase *

get_index_of_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) int

C++: core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(int) const –> int

get_node_index(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_node_index() const –> int

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_larger_indexed_nodes() const –> int

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes() const –> int

get_num_incident_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_incident_edges() const –> int

get_num_states(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_states() const –> int

get_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, state: int) float

C++: core::pack::interaction_graph::DensePDNode::get_one_body_energy(int) const –> float

get_one_body_energy_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) float

C++: core::pack::interaction_graph::DensePDNode::get_one_body_energy_current_state() const –> float

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::print_internal_energies() const –> void

project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, alternate_state: int, prev_node_energy: float) float

C++: core::pack::interaction_graph::DensePDNode::project_deltaE_for_substitution(int, float &) –> float

state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) bool

C++: core::pack::interaction_graph::DensePDNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::update_internal_energy_sums() –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::DensePDNode::update_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

update_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode, state: int, energy: float) None

C++: core::pack::interaction_graph::DensePDNode::update_one_body_energy(int, float) –> void

zero_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode) None

C++: core::pack::interaction_graph::DensePDNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DotSphere

Bases: pybind11_builtins.pybind11_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.

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere, rhs: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) pyrosetta.rosetta.core.pack.interaction_graph.DotSphere

C++: core::pack::interaction_graph::DotSphere::operator=(const class core::pack::interaction_graph::DotSphere &) –> class core::pack::interaction_graph::DotSphere &

count_num_covered(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) None

C++: core::pack::interaction_graph::DotSphere::count_num_covered() const –> void

get_dot_covered(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere, dot_index: int) bool

C++: core::pack::interaction_graph::DotSphere::get_dot_covered(unsigned long) const –> bool

get_num_covered(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) int

C++: core::pack::interaction_graph::DotSphere::get_num_covered() const –> unsigned long

get_num_uncovered(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) int

C++: core::pack::interaction_graph::DotSphere::get_num_uncovered() const –> unsigned long

get_total_dots(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) int

C++: core::pack::interaction_graph::DotSphere::get_total_dots() const –> unsigned long

print(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::DotSphere::print(std::ostream &) const –> void

zero(self: pyrosetta.rosetta.core.pack.interaction_graph.DotSphere) None

C++: core::pack::interaction_graph::DotSphere::zero() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, node_ind: int, new_state: int, new_energy: float) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_change(int, int, float &) –> void

acknowledge_state_zeroed(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, node_ind: int) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_zeroed(int) –> void

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_substitution(int, const float, int) –> void

add_to_two_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::add_to_two_body_energies(const class ObjexxFCL::FArray2<float> &) –> void

add_to_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int, : float) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::add_to_two_body_energy(const int, const int, const float) –> void

clear_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::clear_two_body_energy(const int, const int) –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) int

C++: core::pack::interaction_graph::DoubleDensePDEdge::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) int

C++: core::pack::interaction_graph::DoubleDensePDEdge::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::declare_energies_final() –> void

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

force_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::force_aa_neighbors(int, int) –> void

force_all_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::force_all_aa_neighbors() –> void

static get_alternate_state_energy(first_node_state: int, second_node_state: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) float

C++: core::pack::interaction_graph::DoubleDensePDEdge::get_alternate_state_energy(int, int, class ObjexxFCL::FArray2<float> &) –> float

get_current_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) float

C++: core::pack::interaction_graph::DoubleDensePDEdge::get_current_two_body_energy() –> float

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

get_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int) bool

C++: core::pack::interaction_graph::DoubleDensePDEdge::get_sparse_aa_info(int, int) const –> bool

get_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int) float

C++: core::pack::interaction_graph::DoubleDensePDEdge::get_two_body_energy(const int, const int) const –> float

get_two_body_table_size(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) int

C++: core::pack::interaction_graph::DoubleDensePDEdge::get_two_body_table_size() const –> int

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::prepare_for_simulated_annealing() –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, weight: float) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::set_sparse_aa_info(const class ObjexxFCL::FArray2<bool> &) –> void

set_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge, : int, : int, : float) None

C++: core::pack::interaction_graph::DoubleDensePDEdge::set_two_body_energy(const int, const int, const float) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph

aa_submatrix_energies_retrievable(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) bool

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aa_submatrix_energies_retrievable() const –> bool

aatype_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind: int, node_state: int) int

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aatype_for_node_state(int, int) const –> int

add_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_edge(int, int) –> void

add_longrange_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, lr_energy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes and a long-range energy, compute the long-range energy of all

interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::methods::LongRangeTwoBodyEnergy>, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.utility.vector1_float) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class utility::vector1<float, class std::allocator<float> > &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class ObjexxFCL::FArray1<float> &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, state_id: int, one_body_energy: float) -> None

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, int, const float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_two_body_energies_for_edge(*args, **kwargs)

Overloaded function.

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) -> None

  2. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t, use_threadsafe_method: bool) -> None

interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies

If use_threadsafe_method is true, we don’t cache the edge index for faster future lookups.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, const class ObjexxFCL::FArray2<float> &, const bool) –> void

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) -> None

interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, int, int, const float) –> void

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

C++: core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) None

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

clear_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int) None

interface to PDEdge::clear_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::clear_two_body_energy_for_edge(int, int, int, int) –> void

commit_considered_substitution(self: pyrosetta.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

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::commit_considered_substitution() –> float

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::consider_substitution(int, int, float &, float &) –> void

count_connected_components_and_initialize_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups() –> int

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) int

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) int

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::count_static_memory() const –> unsigned int

create_new_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index1: int, index2: int) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_edge(int, int) –> class core::pack::interaction_graph::EdgeBase *

create_new_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, num_states: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_node(int, int) –> class core::pack::interaction_graph::NodeBase *

declare_all_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
Iterates over all edges and calls declare_energies_final() on

all of them. Takes O(N) time, where N is the number of edges.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final() –> void

declare_edge_energies_final(*args, **kwargs)

Overloaded function.

  1. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None

  2. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, use_threadsafe_lookup: bool) -> None

call this if you’re done storing energies in an edge - it will reduce

the memory usage for that edge if possible

  • [in] - the index of the smaller-indexed node

  • [in] - the index of the larger-indexed node

  • [in] - If true, we don’t cache the last edge

found for faster future lookups. False by default.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::declare_edge_energies_final(int, int, const bool) –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node(int) –> void

edge_list_iterator_at_end(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

test: have we arrived at the edge list end?

C++: core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end() const –> bool

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

  2. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, use_threadsafe_lookup: bool) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

C++: core::pack::interaction_graph::InteractionGraphBase::find_edge(int, int, const bool) –> class core::pack::interaction_graph::EdgeBase *

force_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) None

interface to FixedBBEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_aa_neighbors_for_edge(int, int, int, int) –> void

force_all_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int) None

interface to PDEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_all_aa_neighbors_for_edge(int, int) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned int

get_aa_submatrix_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_aa_submatrix_energies_for_edge(int, int, int, int) const –> class ObjexxFCL::FArray2D<float>

get_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

return a const reference to an edge pointed at by the list iterator

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge() const –> const class core::pack::interaction_graph::EdgeBase &

get_edge_exists(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(int, int) const –> bool

get_edge_memory_usage(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) int

returns the number of floats used in all edge two-body energy tables

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_edge_memory_usage() const –> int

get_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(int, int) const –> double

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) float
removes all accumulated numerical drift and returns the

energy for the current state assignment.

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_current_state_assignment() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.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.

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_sum_for_vertex_group(int) –> float

get_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::get_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_num_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) int

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_num_aatypes() const –> int

get_num_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_edges() const –> int

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_nodes() const –> int

get_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_total_states() const –> int

get_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node: int, state: int) float

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_one_body_energy_for_node_state(int, int) –> float

get_sparse_aa_info_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_sparse_aa_info_for_edge(int, int, int, int) –> bool

get_two_body_energy_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_two_body_energy_for_edge(int, int, int, int) const –> float

get_vertex_member_of_energy_sum_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, group_id: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group(int, int) –> bool

increment_edge_list_iterator(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

increment the (single) edge list iterator to the next element

C++: core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator() const –> void

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) None

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

note_vertex_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(int) –> void

output_connectivity(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_dimacs(std::ostream &) const –> void

prepare_graph_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
iterate across edges and nodes and allow them to prepare

for simulated annealing

C++: core::pack::interaction_graph::InteractionGraphBase::prepare_graph_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print() const –> void

print_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph) None

outputs the current state for each node, useful for debugging

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::print_current_state_assignment() const –> void

print_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups() –> void

print_vertices(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertices() const –> void

reset_edge_list_iterator_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None
set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

C++: core::pack::interaction_graph::InteractionGraphBase::reset_edge_list_iterator_for_node(int) const –> void

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, edge_weight: float) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_edge_weight(int, int, double) –> void

set_errorfull_deltaE_threshold(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, : float) None

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_errorfull_deltaE_threshold(float) –> void

set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) float

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_network_state(class ObjexxFCL::FArray1<int> &) –> float

set_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int, num_states: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(int, int) –> void

set_number_of_energy_sum_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_number_of_energy_sum_vertex_groups(int) –> void

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) None
Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded(const unsigned long, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class basic::thread_manager::RosettaThreadAssignmentInfo &) –> void

set_sparse_aa_info_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

interface to PDEdge::set_sparse_aa_info

C++: core::pack::interaction_graph::FixedBBInteractionGraph::set_sparse_aa_info_for_edge(int, int, const class ObjexxFCL::FArray2<bool> &) –> void

set_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph, node_ind: int, new_state: int) float

C++: core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_state_for_node(int, int) –> float

set_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) None

interface to PDEdge::set_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_two_body_energy_for_edge(int, int, int, int, const float) –> void

set_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes, compute the energy of all interacting rotamers and add those

energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

set_vertex_member_of_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex: int, group: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_vertex_member_of_group(int, int) –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, new_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::update_one_body_energies(class ObjexxFCL::FArray1<float> &, class ObjexxFCL::FArray1<float> &) –> void

vertex_already_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached(int) –> bool

zero_one_body_energies_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::zero_one_body_energies_for_node(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode

acknowledge_neighbors_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, edge_to_altered_neighbor: int, new_edge_energy: float, other_node_new_state: int) None

C++: core::pack::interaction_graph::DoubleDensePDNode::acknowledge_neighbors_state_substitution(int, float, int) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::DoubleDensePDNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, state: int, energy: float) None

C++: core::pack::interaction_graph::DoubleDensePDNode::add_to_one_body_energy(int, float) –> void

assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, new_state: int) None

C++: core::pack::interaction_graph::DoubleDensePDNode::assign_state(int) –> void

assign_zero_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state() –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution() –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) int

C++: core::pack::interaction_graph::DoubleDensePDNode::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) int

C++: core::pack::interaction_graph::DoubleDensePDNode::count_static_memory() const –> unsigned int

depth_first_connected_component_counting(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting() –> void

drop_all_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::drop_all_edges() –> void

find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, other_node_index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::find_edge(int) const –> class core::pack::interaction_graph::EdgeBase *

get_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::NodeBase::get_adjacent_node(int) –> class core::pack::interaction_graph::NodeBase *

get_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) int

C++: core::pack::interaction_graph::DoubleDensePDNode::get_current_state() const –> int

get_incident_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::get_incident_edge(int) –> class core::pack::interaction_graph::EdgeBase *

get_index_of_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) int

C++: core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(int) const –> int

get_node_index(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_node_index() const –> int

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_larger_indexed_nodes() const –> int

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes() const –> int

get_num_incident_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_incident_edges() const –> int

get_num_states(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_states() const –> int

get_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, state: int) float

C++: core::pack::interaction_graph::DoubleDensePDNode::get_one_body_energy(int) const –> float

get_one_body_energy_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) float

C++: core::pack::interaction_graph::DoubleDensePDNode::get_one_body_energy_current_state() –> float

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies() const –> void

project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, alternate_state: int, prev_node_energy: float) float

C++: core::pack::interaction_graph::DoubleDensePDNode::project_deltaE_for_substitution(int, float &) –> float

state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) bool

C++: core::pack::interaction_graph::DoubleDensePDNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::update_internal_energy_sums() –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::DoubleDensePDNode::update_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

update_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode, state: int, energy: float) None

C++: core::pack::interaction_graph::DoubleDensePDNode::update_one_body_energy(int, float) –> void

zero_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode) None

C++: core::pack::interaction_graph::DoubleDensePDNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge

Bases: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge

acknowledge_partial_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind: int, new_state: int, new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) None

C++: core::pack::interaction_graph::DoubleLazyEdge::acknowledge_partial_state_change(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind: int, new_state: int, new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, new_energy: float) None

C++: core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_change(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, float &) –> void

acknowledge_state_zeroed(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node_ind: int) None

C++: core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_zeroed(int) –> void

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int, nodes_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) None

C++: core::pack::interaction_graph::DoubleLazyEdge::acknowledge_substitution(int, const float, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

actual_twobody_memory_use(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) int

C++: core::pack::interaction_graph::DoubleLazyEdge::actual_twobody_memory_use() const –> unsigned int

build_sc_only_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) bool

C++: core::pack::interaction_graph::DoubleLazyEdge::build_sc_only_rotamer() –> bool

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) int

C++: core::pack::interaction_graph::DoubleLazyEdge::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) int

C++: core::pack::interaction_graph::DoubleLazyEdge::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) None

C++: core::pack::interaction_graph::DoubleLazyEdge::declare_energies_final() –> void

drop_aa_submatrix(self: pyrosetta.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

C++: core::pack::interaction_graph::DoubleLazyEdge::drop_aa_submatrix(int) const –> int

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

eval_type(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_index: int) pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType

C++: core::pack::interaction_graph::OnTheFlyEdge::eval_type(int) const –> enum core::pack::interaction_graph::ResiduePairEvalType

force_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa: int, node2aa: int) None

C++: core::pack::interaction_graph::DoubleLazyEdge::force_aa_neighbors(int, int) –> void

force_all_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) None

C++: core::pack::interaction_graph::DoubleLazyEdge::force_all_aa_neighbors() –> void

get_aa_submatrix_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(int, int) const –> class ObjexxFCL::FArray2D<float>

get_current_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) float

C++: core::pack::interaction_graph::DoubleLazyEdge::get_current_two_body_energy() const –> float

get_energy_following_partial_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) float

C++: core::pack::interaction_graph::DoubleLazyEdge::get_energy_following_partial_state_assignment() –> float

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_glycine_correction_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind: int, state: int) float

C++: core::pack::interaction_graph::OnTheFlyEdge::get_glycine_correction_for_node(int, int) const –> float

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_proline_correction_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_ind: int, state: int) float

C++: core::pack::interaction_graph::OnTheFlyEdge::get_proline_correction_for_node(int, int) const –> float

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

get_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1aa: int, node2aa: int) bool

C++: core::pack::interaction_graph::DoubleLazyEdge::get_sparse_aa_info(int, int) const –> bool

get_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1state: int, node2state: int) float

C++: core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy(const int, const int) const –> float

get_two_body_energy_smi(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, node1state: int, node2state: int, node1info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, node2info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) float

C++: core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy_smi(const int, const int, const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &) const –> float

get_two_body_table_size(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) int

C++: core::pack::interaction_graph::DoubleLazyEdge::get_two_body_table_size() const –> int

long_range_interactions_exist(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge) bool

C++: core::pack::interaction_graph::OnTheFlyEdge::long_range_interactions_exist() const –> bool

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

note_long_range_interactions_exist(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge) None

C++: core::pack::interaction_graph::OnTheFlyEdge::note_long_range_interactions_exist() –> void

note_short_range_interactions_exist(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge) None

C++: core::pack::interaction_graph::OnTheFlyEdge::note_short_range_interactions_exist() –> void

potential_twobody_memory_use(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) int

C++: core::pack::interaction_graph::DoubleLazyEdge::potential_twobody_memory_use() const –> unsigned int

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) None

C++: core::pack::interaction_graph::DoubleLazyEdge::prepare_for_simulated_annealing() –> void

print_current_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge) None

C++: core::pack::interaction_graph::DoubleLazyEdge::print_current_energy() const –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_GlyCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_glycine: int, state: int, bb_regbb_E: float, bb_glybb_E: float, sc_regbb_E: float, sc_glybb_E: float) None

C++: core::pack::interaction_graph::OnTheFlyEdge::set_GlyCorrection_values(int, int, float, float, float, float) –> void

set_ProCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge, node_not_necessarily_proline: int, state: int, bb_regbb_E: float, bb_probb_E: float, sc_regbb_E: float, sc_probb_E: float) None

C++: core::pack::interaction_graph::OnTheFlyEdge::set_ProCorrection_values(int, int, float, float, float, float) –> void

set_edge_index(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, index: int) None
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.

C++: core::pack::interaction_graph::DoubleLazyEdge::set_edge_index(int) –> void

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, weight: float) None

C++: core::pack::interaction_graph::DoubleLazyEdge::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::DoubleLazyEdge::set_sparse_aa_info(const class ObjexxFCL::FArray2<bool> &) –> void

short_range_interactions_exist(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge) bool

C++: core::pack::interaction_graph::OnTheFlyEdge::short_range_interactions_exist() const –> bool

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph

Bases: pyrosetta.rosetta.core.pack.interaction_graph.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.

aa_submatrix_energies_retrievable(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) bool
Override the FixedBBInteractionGraph class’s implementation of this function

to return ‘true’.

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::aa_submatrix_energies_retrievable() const –> bool

aatype_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind: int, node_state: int) int

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::aatype_for_node_state(int, int) const –> int

add_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_edge(int, int) –> void

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.utility.vector1_float) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class utility::vector1<float, class std::allocator<float> > &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class ObjexxFCL::FArray1<float> &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, state_id: int, one_body_energy: float) -> None

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, int, const float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::add_to_one_body_energy_for_node_state(int, int, float) –> void

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

C++: core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) float

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::commit_considered_substitution() –> float

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::consider_substitution(int, int, float &, float &) –> void

count_connected_components_and_initialize_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups() –> int

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) int

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) int

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::count_static_memory() const –> unsigned int

create_new_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index1: int, index2: int) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_edge(int, int) –> class core::pack::interaction_graph::EdgeBase *

create_new_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, num_states: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_node(int, int) –> class core::pack::interaction_graph::NodeBase *

declare_all_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
Iterates over all edges and calls declare_energies_final() on

all of them. Takes O(N) time, where N is the number of edges.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final() –> void

distinguish_backbone_and_sidechain_for_node(*args, **kwargs)

Overloaded function.

  1. distinguish_backbone_and_sidechain_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node: int) -> bool

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::distinguish_backbone_and_sidechain_for_node(int) const –> bool

  1. distinguish_backbone_and_sidechain_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node: int, setting: bool) -> None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::distinguish_backbone_and_sidechain_for_node(int, bool) –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node(int) –> void

edge_list_iterator_at_end(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

test: have we arrived at the edge list end?

C++: core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end() const –> bool

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

  2. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, use_threadsafe_lookup: bool) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

C++: core::pack::interaction_graph::InteractionGraphBase::find_edge(int, int, const bool) –> class core::pack::interaction_graph::EdgeBase *

force_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) None

interface to FixedBBEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_aa_neighbors_for_edge(int, int, int, int) –> void

force_all_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int) None

interface to PDEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_all_aa_neighbors_for_edge(int, int) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned int

get_aa_submatrix_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::get_aa_submatrix_energies_for_edge(int, int, int, int) const –> class ObjexxFCL::FArray2D<float>

get_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

return a const reference to an edge pointed at by the list iterator

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge() const –> const class core::pack::interaction_graph::EdgeBase &

get_edge_exists(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(int, int) const –> bool

get_edge_memory_usage(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) int

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::get_edge_memory_usage() const –> int

get_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(int, int) const –> double

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) float

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_current_state_assignment() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, group_id: int) float

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_sum_for_vertex_group(int) –> float

get_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::get_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_num_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) int

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::get_num_aatypes() const –> int

get_num_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_edges() const –> int

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_nodes() const –> int

get_num_rpe_calculations_count(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) int

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::get_num_rpe_calculations_count() const –> unsigned long

get_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_total_states() const –> int

get_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node: int, state: int) float

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::get_one_body_energy_for_node_state(int, int) –> float

get_sparse_aa_info_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_sparse_aa_info_for_edge(int, int, int, int) –> bool

get_two_body_energy_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_two_body_energy_for_edge(int, int, int, int) const –> float

get_vertex_member_of_energy_sum_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, group_id: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group(int, int) –> bool

increment_edge_list_iterator(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

increment the (single) edge list iterator to the next element

C++: core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator() const –> void

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

non_const_pose(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) pyrosetta.rosetta.core.pose.Pose

debugging only – modify the pose during simulated annealing, if you’re so inclined

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::non_const_pose() –> class core::pose::Pose &

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1: int, node2: int) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

note_rpe_calculated(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) None

to be called by owned OTF node only

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::note_rpe_calculated() const –> void

note_short_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1: int, node2: int) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(int, int) –> void

note_submatrix_accessed(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, edge_index: int, submatrix_index: int) None
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.

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_accessed(int, int) const –> void

note_submatrix_added(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, edge_index: int, submatrix_index: int, submatrix_size: int) None
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.

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_added(int, int, int) const –> void

note_vertex_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(int) –> void

output_connectivity(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_dimacs(std::ostream &) const –> void

pose(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::pose() const –> const class core::pose::Pose &

prepare_graph_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_graph_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print() const –> void

print_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::print_current_state_assignment() const –> void

print_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups() –> void

print_vertices(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertices() const –> void

reset_edge_list_iterator_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None
set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

C++: core::pack::interaction_graph::InteractionGraphBase::reset_edge_list_iterator_for_node(int) const –> void

reset_rpe_calculations_count(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::reset_rpe_calculations_count() –> void

score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::score_function() const –> const class core::scoring::ScoreFunction &

set_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1: int, node2: int, node_not_neccessarily_glycine: int, state: int, bb_regbb_E: float, bb_glybb_E: float, sc_regbb_E: float, sc_glybb_E: float) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_GlyCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

set_ProCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1: int, node2: int, node_not_neccessarily_proline: int, state: int, bb_regbb_E: float, bb_probb_E: float, sc_regbb_E: float, sc_probb_E: float) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_ProCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, edge_weight: float) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_edge_weight(int, int, double) –> void

set_errorfull_deltaE_threshold(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, deltaE: float) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::set_errorfull_deltaE_threshold(float) –> void

set_memory_max_for_rpes(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, setting: int) None

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::set_memory_max_for_rpes(int) –> void

set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) float

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::set_network_state(class ObjexxFCL::FArray1<int> &) –> float

set_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int, num_states: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(int, int) –> void

set_number_of_energy_sum_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_number_of_energy_sum_vertex_groups(int) –> void

set_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_one_body_energy_for_node_state(int, int, float) –> void

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) None
Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded(const unsigned long, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class basic::thread_manager::RosettaThreadAssignmentInfo &) –> void

set_pose(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, : pyrosetta.rosetta.core.pose.Pose) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_score_function(const class core::scoring::ScoreFunction &) –> void

set_sparse_aa_info_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node1: int, node2: int, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::set_sparse_aa_info_for_edge(int, int, const class ObjexxFCL::FArray2<bool> &) –> void

set_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph, node_ind: int, new_state: int) float

C++: core::pack::interaction_graph::DoubleLazyInteractionGraph::set_state_for_node(int, int) –> float

set_vertex_member_of_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex: int, group: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_vertex_member_of_group(int, int) –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, new_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::update_one_body_energies(class ObjexxFCL::FArray1<float> &, class ObjexxFCL::FArray1<float> &) –> void

vertex_already_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached(int) –> bool

zero_one_body_energies_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::zero_one_body_energies_for_node(int) –> void

zero_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph, node_ind: int, state: int) None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::zero_one_body_energy_for_node_state(int, int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode

Bases: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode

aatype_for_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, state: int) int

C++: core::pack::interaction_graph::DoubleLazyNode::aatype_for_state(int) const –> int

acknowledge_neighbors_partial_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, edge_to_altered_neighbor: int, other_node_new_: int, other_node_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) None

C++: core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_partial_state_substitution(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

acknowledge_neighbors_state_substitution(self: pyrosetta.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: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) None

C++: core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_state_substitution(int, float, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::OnTheFlyNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int, energy: float) None

C++: core::pack::interaction_graph::OnTheFlyNode::add_to_one_body_energy(int, float) –> void

assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, new_state: int) None

C++: core::pack::interaction_graph::DoubleLazyNode::assign_state(int) –> void

assign_zero_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::assign_zero_state() –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution() –> void

complete_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::complete_state_assignment() –> void

compute_pair_energy_for_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, edge_making_energy_request: int) float

C++: core::pack::interaction_graph::DoubleLazyNode::compute_pair_energy_for_current_state(int) –> float

compute_rotamer_pair_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, edge_making_energy_request: int, state_this: int, state_other: int) float

C++: core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(int, int, int) const –> float

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) int

C++: core::pack::interaction_graph::DoubleLazyNode::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) int

C++: core::pack::interaction_graph::DoubleLazyNode::count_static_memory() const –> unsigned int

depth_first_connected_component_counting(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting() –> void

distinguish_backbone_and_sidechain(*args, **kwargs)

Overloaded function.

  1. distinguish_backbone_and_sidechain(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode) -> bool

C++: core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain() const –> bool

  1. distinguish_backbone_and_sidechain(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, setting: bool) -> None

C++: core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain(bool) –> void

drop_all_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::drop_all_edges() –> void

find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, other_node_index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::find_edge(int) const –> class core::pack::interaction_graph::EdgeBase *

get_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::NodeBase::get_adjacent_node(int) –> class core::pack::interaction_graph::NodeBase *

get_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) int

C++: core::pack::interaction_graph::DoubleLazyNode::get_current_state() const –> int

get_incident_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::get_incident_edge(int) –> class core::pack::interaction_graph::EdgeBase *

get_index_of_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) int

C++: core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(int) const –> int

get_node_index(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_node_index() const –> int

get_num_aa_types(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode) int

C++: core::pack::interaction_graph::OnTheFlyNode::get_num_aa_types() const –> int

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_larger_indexed_nodes() const –> int

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes() const –> int

get_num_incident_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_incident_edges() const –> int

get_num_states(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_states() const –> int

get_num_states_for_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, aa_type: int) int

C++: core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_type(int) –> int

get_num_states_for_aa_types(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode) pyrosetta.rosetta.utility.vector1_int

C++: core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types() –> class utility::vector1<int, class std::allocator<int> > &

get_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int) float

C++: core::pack::interaction_graph::OnTheFlyNode::get_one_body_energy(int) const –> float

get_one_body_energy_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) float

C++: core::pack::interaction_graph::DoubleLazyNode::get_one_body_energy_current_state() const –> float

get_sparse_mat_info_for_curr_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::DoubleLazyNode::get_sparse_mat_info_for_curr_state() const –> const class core::pack::interaction_graph::SparseMatrixIndex &

get_sparse_mat_info_for_state(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int) pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state(int) const –> const class core::pack::interaction_graph::SparseMatrixIndex &

get_state_offset_for_aatype(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, aatype: int) int

C++: core::pack::interaction_graph::OnTheFlyNode::get_state_offset_for_aatype(int) const –> int

get_totalE(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) float

C++: core::pack::interaction_graph::DoubleLazyNode::get_totalE() const –> float

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, new_state: int) None

C++: core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(int) –> void

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::print_internal_energies() const –> void

project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode, alternate_state: int, prev_node_energy: float) float

C++: core::pack::interaction_graph::DoubleLazyNode::project_deltaE_for_substitution(int, float &) –> float

set_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int, energy: float) None

C++: core::pack::interaction_graph::OnTheFlyNode::set_one_body_energy(int, float) –> void

set_rotamers(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, rotamers: core::pack::rotamer_set::RotamerSet) None

C++: core::pack::interaction_graph::OnTheFlyNode::set_rotamers(class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>) –> void

state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) bool

C++: core::pack::interaction_graph::DoubleLazyNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode) None

C++: core::pack::interaction_graph::DoubleLazyNode::update_internal_energy_sums() –> void

update_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int, energy: float) None

C++: core::pack::interaction_graph::OnTheFlyNode::update_one_body_energy(int, float) –> void

zero_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode) None

C++: core::pack::interaction_graph::OnTheFlyNode::zero_one_body_energies() –> void

zero_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode, state: int) None

C++: core::pack::interaction_graph::OnTheFlyNode::zero_one_body_energy(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Bases: pybind11_builtins.pybind11_object

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) None

C++: core::pack::interaction_graph::EdgeBase::declare_energies_final() –> void

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) None

C++: core::pack::interaction_graph::EdgeBase::prepare_for_simulated_annealing() –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, weight: float) None

C++: core::pack::interaction_graph::EdgeBase::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge

acknowledge_partial_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node: int, new_state: int) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_partial_state_assignment(int, int) –> void

acknowledge_participation_in_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_participation_in_perturbation() –> void

acknowledge_perturbed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node: int, neighbors_context_state: int) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_perturbed_state(int, int) –> void

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node_ind: int, new_state: int, new_energy: float) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_state_change(int, int, float &) –> void

acknowledge_state_zeroed(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node_ind: int) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_state_zeroed(int) –> void

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int) None

C++: core::pack::interaction_graph::FASTEREdge::acknowledge_substitution(int, const float, int) –> void

add_to_two_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) None

C++: core::pack::interaction_graph::FASTEREdge::add_to_two_body_energies(const class ObjexxFCL::FArray2<float> &) –> void

add_to_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int, : float) None

C++: core::pack::interaction_graph::FASTEREdge::add_to_two_body_energy(const int, const int, const float) –> void

clear_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int) None

C++: core::pack::interaction_graph::FASTEREdge::clear_two_body_energy(const int, const int) –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) int

C++: core::pack::interaction_graph::FASTEREdge::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) int

C++: core::pack::interaction_graph::FASTEREdge::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) None

C++: core::pack::interaction_graph::FASTEREdge::declare_energies_final() –> void

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

force_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int) None

C++: core::pack::interaction_graph::FASTEREdge::force_aa_neighbors(int, int) –> void

force_all_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) None

C++: core::pack::interaction_graph::FASTEREdge::force_all_aa_neighbors() –> void

static get_alternate_state_energy(first_node_state: int, second_node_state: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) float

C++: core::pack::interaction_graph::FASTEREdge::get_alternate_state_energy(int, int, class ObjexxFCL::FArray2<float> &) –> float

get_curr_state_energy_following_partial_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) float

C++: core::pack::interaction_graph::FASTEREdge::get_curr_state_energy_following_partial_state_assignment() –> float

get_current_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) float

C++: core::pack::interaction_graph::FASTEREdge::get_current_two_body_energy() –> float

get_deltaE_for_neighbor_following_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node_index: int) float

C++: core::pack::interaction_graph::FASTEREdge::get_deltaE_for_neighbor_following_perturbation(int) –> float

get_deltaE_for_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) float

C++: core::pack::interaction_graph::FASTEREdge::get_deltaE_for_perturbation() –> float

get_edge_table_ptr(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t

C++: core::pack::interaction_graph::FASTEREdge::get_edge_table_ptr() –> class ObjexxFCL::FArray2A<float>

get_energy_for_perturbed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, node: int, nodes_perturbed_state: int) float

C++: core::pack::interaction_graph::FASTEREdge::get_energy_for_perturbed_state(int, int) –> float

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

get_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int) bool

C++: core::pack::interaction_graph::FASTEREdge::get_sparse_aa_info(int, int) const –> bool

get_two_body_energies_for_relaxed_states(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) float

C++: core::pack::interaction_graph::FASTEREdge::get_two_body_energies_for_relaxed_states() –> float

get_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int) float

C++: core::pack::interaction_graph::FASTEREdge::get_two_body_energy(const int, const int) const –> float

get_two_body_table_size(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) int

C++: core::pack::interaction_graph::FASTEREdge::get_two_body_table_size() const –> int

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

prepare_for_FASTER(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) None

C++: core::pack::interaction_graph::FASTEREdge::prepare_for_FASTER() –> void

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge) None

C++: core::pack::interaction_graph::FASTEREdge::prepare_for_simulated_annealing() –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, weight: float) None

C++: core::pack::interaction_graph::FASTEREdge::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::FASTEREdge::set_sparse_aa_info(const class ObjexxFCL::FArray2<bool> &) –> void

set_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, : int, : int, : float) None

C++: core::pack::interaction_graph::FASTEREdge::set_two_body_energy(const int, const int, const float) –> void

swap_edge_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge, new_edge_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::pack::interaction_graph::FASTEREdge::swap_edge_energies(class ObjexxFCL::FArray2D<float> &) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph

aa_submatrix_energies_retrievable(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) bool

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aa_submatrix_energies_retrievable() const –> bool

aatype_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind: int, node_state: int) int

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aatype_for_node_state(int, int) const –> int

add_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_edge(int, int) –> void

add_longrange_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, lr_energy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes and a long-range energy, compute the long-range energy of all

interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::methods::LongRangeTwoBodyEnergy>, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.utility.vector1_float) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class utility::vector1<float, class std::allocator<float> > &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class ObjexxFCL::FArray1<float> &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, state_id: int, one_body_energy: float) -> None

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, int, const float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_two_body_energies_for_edge(*args, **kwargs)

Overloaded function.

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t) -> None

  2. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, res_res_energy_array: pyrosetta.rosetta.ObjexxFCL.FArray2_float_t, use_threadsafe_method: bool) -> None

interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies

If use_threadsafe_method is true, we don’t cache the edge index for faster future lookups.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, const class ObjexxFCL::FArray2<float> &, const bool) –> void

  1. add_to_two_body_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) -> None

interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge(int, int, int, int, const float) –> void

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

C++: core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

assign_BMEC(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::assign_BMEC() –> void

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

clear_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int) None

interface to PDEdge::clear_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::clear_two_body_energy_for_edge(int, int, int, int) –> void

commit_considered_substitution(self: pyrosetta.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

C++: core::pack::interaction_graph::FASTERInteractionGraph::commit_considered_substitution() –> float

commit_relaxation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::commit_relaxation() –> void

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::consider_substitution(int, int, float &, float &) –> void

count_connected_components_and_initialize_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups() –> int

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) int

C++: core::pack::interaction_graph::FASTERInteractionGraph::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) int

C++: core::pack::interaction_graph::FASTERInteractionGraph::count_static_memory() const –> unsigned int

create_new_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index1: int, index2: int) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_edge(int, int) –> class core::pack::interaction_graph::EdgeBase *

create_new_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, num_states: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_node(int, int) –> class core::pack::interaction_graph::NodeBase *

declare_all_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
Iterates over all edges and calls declare_energies_final() on

all of them. Takes O(N) time, where N is the number of edges.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final() –> void

declare_edge_energies_final(*args, **kwargs)

Overloaded function.

  1. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None

  2. declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, use_threadsafe_lookup: bool) -> None

call this if you’re done storing energies in an edge - it will reduce

the memory usage for that edge if possible

  • [in] - the index of the smaller-indexed node

  • [in] - the index of the larger-indexed node

  • [in] - If true, we don’t cache the last edge

found for faster future lookups. False by default.

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::declare_edge_energies_final(int, int, const bool) –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node(int) –> void

edge_list_iterator_at_end(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

test: have we arrived at the edge list end?

C++: core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end() const –> bool

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

  2. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, use_threadsafe_lookup: bool) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

C++: core::pack::interaction_graph::InteractionGraphBase::find_edge(int, int, const bool) –> class core::pack::interaction_graph::EdgeBase *

force_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) None

interface to FixedBBEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_aa_neighbors_for_edge(int, int, int, int) –> void

force_all_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int) None

interface to PDEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_all_aa_neighbors_for_edge(int, int) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned int

get_aa_submatrix_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_aa_submatrix_energies_for_edge(int, int, int, int) const –> class ObjexxFCL::FArray2D<float>

get_current_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, netstate: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_current_network_state(class ObjexxFCL::FArray1<int> &) –> void

get_current_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind: int) int

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_current_state_for_node(int) const –> int

get_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

return a const reference to an edge pointed at by the list iterator

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge() const –> const class core::pack::interaction_graph::EdgeBase &

get_edge_exists(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(int, int) const –> bool

get_edge_memory_usage(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) int

returns the number of core::PackerEnergys used in all edge two-body energy tables

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_edge_memory_usage() const –> int

get_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(int, int) const –> double

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) float
removes all accumulated numerical drift and returns the

energy for the current state assignment.

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_energy_current_state_assignment() –> float

get_energy_following_relaxation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_energy_following_relaxation() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.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.

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_energy_sum_for_vertex_group(int) –> float

get_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::get_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_num_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) int

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_num_aatypes() const –> int

get_num_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_edges() const –> int

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_nodes() const –> int

get_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_total_states() const –> int

get_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node: int, state: int) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_one_body_energy_for_node_state(int, int) –> float

get_random_neighbor_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node: int) int

C++: core::pack::interaction_graph::FASTERInteractionGraph::get_random_neighbor_for_node(int) –> int

get_sparse_aa_info_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_sparse_aa_info_for_edge(int, int, int, int) –> bool

get_two_body_energy_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_two_body_energy_for_edge(int, int, int, int) const –> float

get_vertex_member_of_energy_sum_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, group_id: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group(int, int) –> bool

increment_edge_list_iterator(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

increment the (single) edge list iterator to the next element

C++: core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator() const –> void

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

note_vertex_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(int) –> void

output_connectivity(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, os: pyrosetta.rosetta.std.ostream) None

C++: core::pack::interaction_graph::InteractionGraphBase::output_dimacs(std::ostream &) const –> void

perturb_dBR_and_relax(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node1: int, perturbed_state1: int, node2: int, perturbed_state2: int) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(int, int, int, int) –> float

perturb_sBR_and_relax(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node: int, perturbed_state: int) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax(int, int) –> float

prepare_for_FASTER(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::prepare_for_FASTER() –> void

prepare_graph_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
iterate across edges and nodes and allow them to prepare

for simulated annealing

C++: core::pack::interaction_graph::InteractionGraphBase::prepare_graph_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print() const –> void

print_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

outputs the current state for each node, useful for debugging

C++: core::pack::interaction_graph::FASTERInteractionGraph::print_current_state_assignment() const –> void

print_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups() –> void

print_vertices(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::print_vertices() const –> void

probabilistically_commit_relaxation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, probability: float) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::probabilistically_commit_relaxation(double) –> void

reject_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::reject_perturbation() –> void

relax_in_current_context(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::relax_in_current_context() –> void

reset_edge_list_iterator_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) None
set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

C++: core::pack::interaction_graph::InteractionGraphBase::reset_edge_list_iterator_for_node(int) const –> void

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, edge_weight: float) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_edge_weight(int, int, double) –> void

set_errorfull_deltaE_threshold(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, : float) None

C++: core::pack::interaction_graph::FASTERInteractionGraph::set_errorfull_deltaE_threshold(float) –> void

set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::set_network_state(class ObjexxFCL::FArray1<int> &) –> float

set_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int, num_states: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(int, int) –> void

set_number_of_energy_sum_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, num_groups: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_number_of_energy_sum_vertex_groups(int) –> void

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) None
Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded(const unsigned long, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class basic::thread_manager::RosettaThreadAssignmentInfo &) –> void

set_sparse_aa_info_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

interface to PDEdge::set_sparse_aa_info

C++: core::pack::interaction_graph::FixedBBInteractionGraph::set_sparse_aa_info_for_edge(int, int, const class ObjexxFCL::FArray2<bool> &) –> void

set_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node_ind: int, new_state: int) float

C++: core::pack::interaction_graph::FASTERInteractionGraph::set_state_for_node(int, int) –> float

set_two_body_energy_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int, state_node1: int, state_node2: int, two_body_energy: float) None

interface to PDEdge::set_two_body_energy

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_two_body_energy_for_edge(int, int, int, int, const float) –> void

set_twobody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, nodes: Tuple[int, int], rotsets: Tuple[core::pack::rotamer_set::RotamerSet, core::pack::rotamer_set::RotamerSet], pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, thread_info: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo, finalize_edges: bool, symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, resids: Tuple[int, int], do_orient: bool, symmetric_swap: bool) None
Given two nodes, compute the energy of all interacting rotamers and add those

energies to the edge between the nodes. This is suitable for use in a multithreaded context.

The edge must already exist. The “do_orient” and “symmetric_swap” inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.

If this is a symmetric packing case, symminfo must be provided. The resid1 and resid2 values need only be provided in the symmetric case.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded(const struct std::pair<unsigned long, unsigned long> &, struct std::pair<class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>, class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet> >, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class basic::thread_manager::RosettaThreadAssignmentInfo &, const bool, class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>, const struct std::pair<unsigned long, unsigned long> &, const bool, const bool) –> void

set_vertex_member_of_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, vertex: int, group: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::set_vertex_member_of_group(int, int) –> void

swap_edge_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph, node1: int, node2: int, new_edge_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

Swap the contents of the edge pair-energy table with the contents in the new_edge_table

C++: core::pack::interaction_graph::FASTERInteractionGraph::swap_edge_energies(int, int, class ObjexxFCL::FArray2D<float> &) –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, old_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, new_energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::update_one_body_energies(class ObjexxFCL::FArray1<float> &, class ObjexxFCL::FArray1<float> &) –> void

vertex_already_reached(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached(int) –> bool

zero_one_body_energies_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::zero_one_body_energies_for_node(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode

Bases: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode

acknowledge_neighbors_partial_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, which_neighbor: int, neighbors_new_state: int) None

C++: core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_partial_state_assignment(int, int) –> void

acknowledge_neighbors_perturbed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, which_neighbor: int, neighbors_perturbed_state: int) None

C++: core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_perturbed_state(int, const int) –> void

acknowledge_neighbors_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, edge_to_altered_neighbor: int, new_edge_energy: float, other_node_new_state: int) None

C++: core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_state_substitution(int, float, int) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::FASTERNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, state: int, energy: float) None

C++: core::pack::interaction_graph::FASTERNode::add_to_one_body_energy(int, float) –> void

assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, new_state: int) None

C++: core::pack::interaction_graph::FASTERNode::assign_state(int) –> void

assign_zero_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::assign_zero_state() –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::commit_considered_substitution() –> void

complete_partial_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::complete_partial_state_assignment() –> void

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) int

C++: core::pack::interaction_graph::FASTERNode::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) int

C++: core::pack::interaction_graph::FASTERNode::count_static_memory() const –> unsigned int

depth_first_connected_component_counting(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting() –> void

drop_all_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) None

C++: core::pack::interaction_graph::NodeBase::drop_all_edges() –> void

find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, other_node_index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::find_edge(int) const –> class core::pack::interaction_graph::EdgeBase *

get_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::NodeBase::get_adjacent_node(int) –> class core::pack::interaction_graph::NodeBase *

get_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) int

C++: core::pack::interaction_graph::FASTERNode::get_current_state() const –> int

get_deltaE_for_relaxed_state_following_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) float

C++: core::pack::interaction_graph::FASTERNode::get_deltaE_for_relaxed_state_following_perturbation() –> float

get_incident_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) core::pack::interaction_graph::EdgeBase

C++: core::pack::interaction_graph::NodeBase::get_incident_edge(int) –> class core::pack::interaction_graph::EdgeBase *

get_index_of_adjacent_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, index: int) int

C++: core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(int) const –> int

get_node_index(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_node_index() const –> int

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_larger_indexed_nodes() const –> int

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes() const –> int

get_num_incident_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_incident_edges() const –> int

get_num_states(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase) int

C++: core::pack::interaction_graph::NodeBase::get_num_states() const –> int

get_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, state: int) float

C++: core::pack::interaction_graph::FASTERNode::get_one_body_energy(int) const –> float

get_one_body_energy_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) float

C++: core::pack::interaction_graph::FASTERNode::get_one_body_energy_current_state() const –> float

get_one_body_energy_for_relaxed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) float

C++: core::pack::interaction_graph::FASTERNode::get_one_body_energy_for_relaxed_state() const –> float

get_random_neighbor(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) int

C++: core::pack::interaction_graph::FASTERNode::get_random_neighbor() –> int

get_relaxed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) int

C++: core::pack::interaction_graph::FASTERNode::get_relaxed_state() const –> int

get_total_energy_in_curr_state_assignment_for_all_states(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::get_total_energy_in_curr_state_assignment_for_all_states() –> void

partial_assign_relaxed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, probability: float) None

C++: core::pack::interaction_graph::FASTERNode::partial_assign_relaxed_state(double) –> void

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, state: int) None

C++: core::pack::interaction_graph::FASTERNode::partial_assign_state(int) –> void

partial_assign_state_with_lowest_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::partial_assign_state_with_lowest_one_body_energy() –> void

prep_for_neighbors_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::prep_for_neighbors_perturbation() –> void

prepare_for_FASTER(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::prepare_for_FASTER() –> void

prepare_for_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::prepare_for_perturbation() –> void

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::print_internal_energies() const –> void

project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, alternate_state: int, prev_node_energy: float) float

C++: core::pack::interaction_graph::FASTERNode::project_deltaE_for_substitution(int, float &) –> float

relax(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::relax() –> void

relax_after_neighbors_perturbation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::relax_after_neighbors_perturbation() –> void

relax_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::relax_neighbors() –> void

reset_relaxed(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::reset_relaxed() –> void

reset_relaxed_for_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::reset_relaxed_for_neighbors() –> void

set_no_longer_perturbed(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::set_no_longer_perturbed() –> void

set_perturbed_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, perturbed_state: int) None

C++: core::pack::interaction_graph::FASTERNode::set_perturbed_state(int) –> void

state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) bool

C++: core::pack::interaction_graph::FASTERNode::state_unassigned() const –> bool

tell_neighbors_to_prep_for_relaxation(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::tell_neighbors_to_prep_for_relaxation() –> void

update_internal_energy_sums(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::update_internal_energy_sums() –> void

update_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::FASTERNode::update_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

update_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode, state: int, energy: float) None

C++: core::pack::interaction_graph::FASTERNode::update_one_body_energy(int, float) –> void

zero_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode) None

C++: core::pack::interaction_graph::FASTERNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge

Bases: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

count_dynamic_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::count_static_memory() const –> unsigned int

declare_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) None

C++: core::pack::interaction_graph::EdgeBase::declare_energies_final() –> void

edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) float

C++: core::pack::interaction_graph::EdgeBase::edge_weight() const –> double

force_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa: int, node2aa: int) None

C++: core::pack::interaction_graph::FixedBBEdge::force_aa_neighbors(int, int) –> void

force_all_aa_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge) None

C++: core::pack::interaction_graph::FixedBBEdge::force_all_aa_neighbors() –> void

get_first_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_first_node_ind() const –> int

get_other_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) int

C++: core::pack::interaction_graph::EdgeBase::get_other_ind(int) const –> int

get_other_node(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::EdgeBase::get_other_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) core::pack::interaction_graph::InteractionGraphBase

C++: core::pack::interaction_graph::EdgeBase::get_owner() –> class core::pack::interaction_graph::InteractionGraphBase *

get_second_node_ind(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) int

C++: core::pack::interaction_graph::EdgeBase::get_second_node_ind() const –> int

get_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge, node1aa: int, node2aa: int) bool

C++: core::pack::interaction_graph::FixedBBEdge::get_sparse_aa_info(int, int) const –> bool

get_two_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge, : int, : int) float

C++: core::pack::interaction_graph::FixedBBEdge::get_two_body_energy(const int, const int) const –> float

marked_for_deletion(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) bool

Has this edge indicated that it can be deleted?

C++: core::pack::interaction_graph::EdgeBase::marked_for_deletion() const –> bool

prepare_for_simulated_annealing(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase) None

C++: core::pack::interaction_graph::EdgeBase::prepare_for_simulated_annealing() –> void

same_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::EdgeBase::same_edge(int, int) const –> bool

set_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, weight: float) None

C++: core::pack::interaction_graph::EdgeBase::set_edge_weight(double) –> void

set_pos_in_node_edgevector(self: pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase, callers_index: int, position: int) None

C++: core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector(int, int) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) None

C++: core::pack::interaction_graph::FixedBBEdge::set_sparse_aa_info(const class ObjexxFCL::FArray2<bool> &) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph

Bases: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

aa_submatrix_energies_retrievable(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) bool

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aa_submatrix_energies_retrievable() const –> bool

aatype_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node_ind: int, node_state: int) int

C++: core::pack::interaction_graph::FixedBBInteractionGraph::aatype_for_node_state(int, int) const –> int

add_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_edge(int, int) –> void

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.utility.vector1_float) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class utility::vector1<float, class std::allocator<float> > &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, const class ObjexxFCL::FArray1<float> &) –> void

  1. add_to_nodes_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, state_id: int, one_body_energy: float) -> None

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(int, int, const float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, one_body_energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) None

C++: core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

any_vertex_state_unassigned(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

C++: core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, : pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: core::pack::interaction_graph::AnnealableGraphBase::operator=(const class core::pack::interaction_graph::AnnealableGraphBase &) –> class core::pack::interaction_graph::AnnealableGraphBase &

blanket_assign_state_0(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None

C++: core::pack::interaction_graph::InteractionGraphBase::blanket_assign_state_0() –> void

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, pose: pyrosetta.rosetta.core.pose.Pose) None

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

Base class function does nothing; may be overridden in derived classes.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::interaction_graph::AnnealableGraphBase::clean_up_after_packing(class core::pose::Pose &) –> void

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) float

C++: core::pack::interaction_graph::InteractionGraphBase::commit_considered_substitution() –> float

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) None

C++: core::pack::interaction_graph::InteractionGraphBase::consider_substitution(int, int, float &, float &) –> void

count_connected_components_and_initialize_vertex_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups() –> int

create_new_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index1: int, index2: int) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_edge(int, int) –> class core::pack::interaction_graph::EdgeBase *

create_new_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, num_states: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::create_new_node(int, int) –> class core::pack::interaction_graph::NodeBase *

declare_all_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) None
Iterates over all edges and calls declare_energies_final() on

all of them. Takes O(N) time, where N is the number of edges.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final() –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) None

C++: core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node(int) –> void

edge_list_iterator_at_end(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) bool

test: have we arrived at the edge list end?

C++: core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end() const –> bool

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

  2. find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int, use_threadsafe_lookup: bool) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

C++: core::pack::interaction_graph::InteractionGraphBase::find_edge(int, int, const bool) –> class core::pack::interaction_graph::EdgeBase *

force_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) None

interface to FixedBBEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_aa_neighbors_for_edge(int, int, int, int) –> void

force_all_aa_neighbors_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int) None

interface to PDEdge::force_aa_neighbors

C++: core::pack::interaction_graph::FixedBBInteractionGraph::force_all_aa_neighbors_for_edge(int, int) –> void

getTotalMemoryUsage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned int

get_aa_submatrix_energies_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_aa_submatrix_energies_for_edge(int, int, int, int) const –> class ObjexxFCL::FArray2D<float>

get_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase

return a const reference to an edge pointed at by the list iterator

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge() const –> const class core::pack::interaction_graph::EdgeBase &

get_edge_exists(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) bool

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(int, int) const –> bool

get_edge_memory_usage(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_memory_usage() const –> int

get_edge_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(int, int) const –> double

get_energy_current_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_energy_current_state_assignment() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, group_id: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_energy_sum_for_vertex_group(int) –> float

get_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, index: int) pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

C++: core::pack::interaction_graph::InteractionGraphBase::get_node(int) const –> class core::pack::interaction_graph::NodeBase *

get_num_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph) int

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_num_aatypes() const –> int

get_num_edges(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_edges() const –> int

get_num_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_nodes() const –> int

get_num_states_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node(int) const –> int

get_num_total_states(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase) int

C++: core::pack::interaction_graph::InteractionGraphBase::get_num_total_states() const –> int

get_one_body_energy_for_node_state(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node: int, state: int) float

C++: core::pack::interaction_graph::InteractionGraphBase::get_one_body_energy_for_node_state(int, int) –> float

get_sparse_aa_info_for_edge(self: pyrosetta.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

C++: core::pack::interaction_graph::FixedBBInteractionGraph::get_sparse_aa_info_for_edge(int, int, int, int) –> bool

get_two_body_energy_for_edge(