interaction_graph

Bindings for core::pack::interaction_graph namespace

class pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t

Bases: pybind11_object

add(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, val: float) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::add(const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, const float) –> void

blanket_set(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, val: float) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::blanket_set(float) –> void

drop_all_submatrices(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::drop_all_submatrices() –> void

drop_small_submatrices_where_possible(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, epsilon: float) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::drop_small_submatrices_where_possible(const float) –> void

drop_zero_submatrices_where_possible(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::drop_zero_submatrices_where_possible() –> void

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

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::force_aa_neighbors(int, int) –> void

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

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::force_all_aa_neighbors() –> void

get(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → float

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::get(const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &) const –> float

getAANeighborOffsets(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::getAANeighborOffsets() –> const class ObjexxFCL::FArray2D<int> &

getMatrixPointer(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → float

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::getMatrixPointer() –> float &

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

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

get_offset_table_size_in_bytes(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → int

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::get_offset_table_size_in_bytes() const –> unsigned int

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

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::get_sparse_aa_info(int, int) const –> bool

get_table_size(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → int

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::get_table_size() const –> int

scale(*args, **kwargs)

Overloaded function.

1. scale(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, scaler: float) -> None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::scale(const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, const float) –> void

2. scale(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, scaler: float) -> None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::scale(const float) –> void

set(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, val: float) → None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::set(const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, const float) –> void

set_sparse_aa_info(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) → None

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

size(self: pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t) → int

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::size() const –> int

static static_get(*args, **kwargs)

Overloaded function.

1. static_get(ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2num_states_per_aatype: int, aa_offset: int, sparse_matrix: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> float

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::static_get(const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, int, int, const class ObjexxFCL::FArray1<float> &) –> float

2. static_get(ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind1_node_state_offset_minus_1: int, ind2_num_states_per_aatype: int, aa_offset: int, sparse_matrix: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) -> float

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::static_get(class core::pack::interaction_graph::SparseMatrixIndex, int, int, int, const class ObjexxFCL::FArray1<float> &) –> float

static static_set(*args, **kwargs)

Overloaded function.

1. static_set(ind1: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind2num_states_per_aatype: int, aa_offset: int, sparse_matrix: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, val: float) -> None

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

2. static_set(ind2: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, ind1_node_state_offset_minus_1: int, ind2_num_states_per_aatype: int, aa_offset: int, sparse_matrix: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, val: float) -> None

C++: core::pack::interaction_graph::AminoAcidNeighborSparseMatrix<float>::static_set(class core::pack::interaction_graph::SparseMatrixIndex, int, int, int, class ObjexxFCL::FArray1<float> &, float) –> void

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

Bases: 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: 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: 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

2. 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

3. 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

3. 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: 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_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: 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: 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

2. 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

3. 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

3. 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: 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: 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: 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

2. 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

3. 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

2. 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: 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

2. 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_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: 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: 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

2. 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

3. 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

3. 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: 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: 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: 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

2. 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

3. 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(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.InteractionGraphBase, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::InteractionGraphBase::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

class pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode

Bases: NodeBase

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::NodeBase::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_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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy

Bases: ContextDependentOneBodyEnergy

Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A.

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

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

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

C++: core::pack::interaction_graph::HPatchEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, p: core::pose::Pose) → bool

Use the dof_derivative interface for this energy method when

calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.

C++: core::scoring::methods::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

defines_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

C++: core::scoring::methods::OneBodyEnergy::defines_score_for_residue(const class core::conformation::Residue &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) → float

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → None

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::interaction_graph::HPatchEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?

Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

indicate_required_context_graphs(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::pack::interaction_graph::HPatchEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the cd_1b element of the EnergyMethodType enumeration; this method

should NOT be overridden by derived classes.

C++: core::scoring::methods::ContextDependentOneBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

residue_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::interaction_graph::HPatchEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work necessary before evaluating the derivatives for this residue

C++: core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None

if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

1. setup_for_packing() is called for all energy methods

2. rotamers are built

3. setup_for_packing_with_rotsets() is called for all energy methods

4. prepare_rotamers_for_packing() is called for all energy methods

5. The energy methods are asked to score all rotamers and rotamer pairs

6. Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::HPatchEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) → None

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy) → int

C++: core::pack::interaction_graph::HPatchEnergy::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator

Bases: EnergyMethodCreator

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

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

create_energy_method(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new HPatchEnergy

C++: core::pack::interaction_graph::HPatchEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: core::pack::interaction_graph::HPatchEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

Bases: AnnealableGraphBase

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

2. 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

3. 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 *

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

C++: core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage() const –> unsigned 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.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_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_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.InteractionGraphBase, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::InteractionGraphBase::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_state_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::InteractionGraphBase::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

class pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphFactory

Bases: pybind11_object

static create_and_initialize_annealing_graph(*args, **kwargs)

Overloaded function.

1. create_and_initialize_annealing_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

2. create_and_initialize_annealing_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, nloop: int) -> pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

Create and initialize annealable graph for the given

pose, rotamer sets, packer task and score function. Initalizes two-body interaction graph, as well as other annealable graphs sepecified by the given score function and task.

Call only valid after: Pose has been scored by scorefxn. Pose residue neighbors updated. ScoreFunction setup for packing. Rotamer sets built.

Pose is nonconst as there may still be data to cache in the pose at this point. Also note that in multi-threaded builds, this function takes an extra parameter: a number of threads to request, for multi-threaded construction of the interaction graph.

C++: core::pack::interaction_graph::InteractionGraphFactory::create_and_initialize_annealing_graph(const class core::pack::task::PackerTask &, class core::pack::rotamer_set::RotamerSets &, class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>, unsigned long) –> class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase>

static create_and_initialize_two_body_interaction_graph(*args, **kwargs)

Overloaded function.

1. create_and_initialize_two_body_interaction_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

2. create_and_initialize_two_body_interaction_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, nloop: int) -> pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

Create and initialize two-body interaction graph for the given

pose, rotamer sets, packer task and score function.

Call only valid after: Pose has been scored by scorefxn. Pose residue neighbors updated. ScoreFunction setup for packing. Rotamer sets built.

In multi-threaded builds, this function takes an extra parameter: a number of threads to request, for multi-threaded construction of the interaction graph.

C++: core::pack::interaction_graph::InteractionGraphFactory::create_and_initialize_two_body_interaction_graph(const class core::pack::task::PackerTask &, class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>, unsigned long) –> class std::shared_ptr<class core::pack::interaction_graph::InteractionGraphBase>

static create_interaction_graph(*args, **kwargs)

Overloaded function.

1. create_interaction_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

2. create_interaction_graph(packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, nloop: int) -> pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase

Create appropiate InteractionGraph instance for given

packer task, rotamer set, and pose.

C++: core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(const class core::pack::task::PackerTask &, const class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class utility::graph::Graph &, unsigned long) –> class std::shared_ptr<class core::pack::interaction_graph::InteractionGraphBase>

class pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots

Bases: pybind11_object

Used to determine whether the overlap between two atoms is buried or exposed.

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

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

atom_overlap_is_exposed(*args, **kwargs)

Overloaded function.

1. atom_overlap_is_exposed(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, at1: int, at2: int) -> bool

Is the intersection between two atoms on this inv-rotamer-dots object exposed?

C++: core::pack::interaction_graph::InvRotamerDots::atom_overlap_is_exposed(unsigned long, unsigned long) const –> bool

2. atom_overlap_is_exposed(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, at_this: int, other: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, at_other: int) -> bool

Is the intersection between one atom on this inv-rotamer-dots object,

and one atom on another inv-rotamer-dots object exposed?

C++: core::pack::interaction_graph::InvRotamerDots::atom_overlap_is_exposed(unsigned long, const class core::pack::interaction_graph::InvRotamerDots &, unsigned long) const –> bool

dot_exposed(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, atomid: int, dot_index: int) → bool

C++: core::pack::interaction_graph::InvRotamerDots::dot_exposed(unsigned long, unsigned long) const –> bool

rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::InvRotamerDots::rotamer() const –> class std::shared_ptr<const class core::conformation::Residue>

setup_from_rotamer_dots(*args, **kwargs)

Overloaded function.

1. setup_from_rotamer_dots(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, rdots: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) -> None

C++: core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots(const class core::pack::interaction_graph::RotamerDots &) –> void

2. setup_from_rotamer_dots(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, rdots: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, ats_to_update: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots(const class core::pack::interaction_graph::RotamerDots &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

write_circle_intersection_mask_to_kinemage(*args, **kwargs)

Overloaded function.

1. write_circle_intersection_mask_to_kinemage(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, ostr: pyrosetta.rosetta.std.ostream, atom_this: int, invdots_other: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, atom_other: int) -> None

2. write_circle_intersection_mask_to_kinemage(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, ostr: pyrosetta.rosetta.std.ostream, atom_this: int, invdots_other: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, atom_other: int, group: bool) -> None

C++: core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage(std::ostream &, const unsigned long, const class core::pack::interaction_graph::InvRotamerDots &, const unsigned long, bool) const –> void

write_exposed_dots_to_kinemage(*args, **kwargs)

Overloaded function.

1. write_exposed_dots_to_kinemage(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, ostr: pyrosetta.rosetta.std.ostream) -> None

2. write_exposed_dots_to_kinemage(self: pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots, ostr: pyrosetta.rosetta.std.ostream, group: bool) -> None

C++: core::pack::interaction_graph::InvRotamerDots::write_exposed_dots_to_kinemage(std::ostream &, bool) const –> void

class pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge

Bases: OnTheFlyEdge

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

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

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge, 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::LazyEdge::acknowledge_state_change(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, float &) –> void

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

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

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge, 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::LazyEdge::acknowledge_substitution(int, const float, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::LazyEdge::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

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.LazyEdge, node1aa: int, node2aa: int) → None

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

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

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

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

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

static get_alternate_state_energy_first_node(first_node_alt_state: int, second_node_orig_state: int, second_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1: int, second_node_curr_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → float

C++: core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_first_node(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, int, int, int, class ObjexxFCL::FArray1<float> &) –> float

static get_alternate_state_energy_second_node(first_node_orig_state: int, second_node_alt_state: int, first_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → float

C++: core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_second_node(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, int, int, class ObjexxFCL::FArray1<float> &) –> float

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

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

get_edge_table_ptr(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge) → float

C++: core::pack::interaction_graph::LazyEdge::get_edge_table_ptr() –> float &

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

C++: core::pack::interaction_graph::LazyEdge::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_offsets_for_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: core::pack::interaction_graph::LazyEdge::get_offsets_for_aatypes() –> const class ObjexxFCL::FArray2D<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_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_second_node_num_states_per_aa(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge) → pyrosetta.rosetta.utility.vector1_int

C++: core::pack::interaction_graph::LazyEdge::get_second_node_num_states_per_aa() –> const class utility::vector1<int, class std::allocator<int> > &

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

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

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

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

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

C++: core::pack::interaction_graph::LazyEdge::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

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

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

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

C++: core::pack::interaction_graph::LazyEdge::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_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge, weight: float) → None

C++: core::pack::interaction_graph::LazyEdge::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.LazyEdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) → None

C++: core::pack::interaction_graph::LazyEdge::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

static store_interaction_energy_first_node(second_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1: int, second_node_curr_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, interaction_energy: float) → None

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

static store_interaction_energy_second_node(first_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t, interaction_energy: float) → None

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

class pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph

Bases: OnTheFlyInteractionGraph

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

Override the FixedBBInteractionGraph class’s implementation of this function

to return ‘true’.

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

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

C++: core::pack::interaction_graph::LazyInteractionGraph::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

2. 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

3. 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.LazyInteractionGraph) → None

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph) → int

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

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

C++: core::pack::interaction_graph::LazyInteractionGraph::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

2. 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.LazyInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) → pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph) → int

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::LazyInteractionGraph::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.OnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::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_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.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.LazyInteractionGraph) → None

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyInteractionGraph, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::LazyInteractionGraph::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.LazyNode

Bases: OnTheFlyNode

aatype_for_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode, state: int) → int

C++: core::pack::interaction_graph::LazyNode::aatype_for_state(int) const –> int

acknowledge_neighbors_partial_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode, 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::LazyNode::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.LazyNode, 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::LazyNode::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.LazyNode, new_state: int) → None

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

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

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

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

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

complete_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode) → None

C++: core::pack::interaction_graph::LazyNode::complete_state_assignment() –> void

compute_pair_energy_for_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode, edge_making_energy_request: int) → float

C++: core::pack::interaction_graph::LazyNode::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.LazyNode) → int

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

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

C++: core::pack::interaction_graph::LazyNode::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

2. 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.LazyNode) → int

C++: core::pack::interaction_graph::LazyNode::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.LazyNode) → float

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

get_sparse_mat_info_for_curr_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode) → pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::LazyNode::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.LazyNode) → float

C++: core::pack::interaction_graph::LazyNode::get_totalE() const –> float

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LazyNode, new_state: int) → None

C++: core::pack::interaction_graph::LazyNode::partial_assign_state(int) –> void

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::LazyNode::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.LazyNode) → bool

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

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

C++: core::pack::interaction_graph::LazyNode::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.LinearMemEdge

Bases: OnTheFlyEdge

acknowledge_partial_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge, node_ind: int, new_state: int, new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, bumped_recent_history_index: int, new_state_recent_history_index: int) → None

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

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

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

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

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

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int, nodes_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, bumped_recent_history_index: int, new_state_recent_history_index: int, neighbors_curr_state: int) → None

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

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

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

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

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

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

C++: core::pack::interaction_graph::LinearMemEdge::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

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.LinearMemEdge, node1aa: int, node2aa: int) → None

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

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

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

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

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

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

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

get_energy_for_alt_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge, store_rpes: bool, changing_node_index: int, alternate_state: int, alternate_state_recent_history_index: int, other_node_curr_state: int, other_node_state_recent_history_index: int) → float

C++: core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(bool, int, int, int, 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_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.LinearMemEdge, node1aa: int, node2aa: int) → bool

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

get_sparse_aa_neighbor_info(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge) → pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t

C++: core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_neighbor_info() –> const class ObjexxFCL::FArray2D<unsigned char> &

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

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

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

C++: core::pack::interaction_graph::LinearMemEdge::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

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

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

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

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

reset_state_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge, node_index: int, state: int, recent_history_id: int) → None

C++: core::pack::interaction_graph::LinearMemEdge::reset_state_energies(int, int, int) –> 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_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge, weight: float) → None

C++: core::pack::interaction_graph::LinearMemEdge::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.LinearMemEdge, : pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) → None

C++: core::pack::interaction_graph::LinearMemEdge::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.LinearMemNode

Bases: OnTheFlyNode

acknowledge_last_substititon_not_committed(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode) → None

update bookkeeping info to acknolwedge that the last alternative state considered was not

in fact chosen for the currently assigned state.

C++: core::pack::interaction_graph::LinearMemNode::acknowledge_last_substititon_not_committed() –> void

acknowledge_neighbors_partial_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, edge_to_altered_neighbor: int, other_node_new_state: int, other_node_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, other_state_recent_history_index: int) → None

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

acknowledge_neighbors_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, edge_to_altered_neighbor: int, new_edge_energy: float, other_node_new_state: int, other_node_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, other_node_recent_history_index: int) → None

C++: core::pack::interaction_graph::LinearMemNode::acknowledge_neighbors_state_substitution(int, float, int, const class core::pack::interaction_graph::SparseMatrixIndex &, int) –> 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.LinearMemNode, new_state: int) → None

set to a particular state – updates the energies internally

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

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

set to state 0

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

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

proceed to change the currently assigned state to the alternative state considered in

the last call to project_deltaE_for_substitution

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

complete_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode) → None

second half of the entire-graph state assignment.

C++: core::pack::interaction_graph::LinearMemNode::complete_state_assignment() –> void

compute_pair_energy_for_alternate_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, edge_making_energy_request: int) → float

comupute the interaction energy between the alternate state being considered on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::LinearMemNode::compute_pair_energy_for_alternate_state(int) –> float

compute_pair_energy_for_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, edge_making_energy_request: int) → float

comupute the interaction energy between the currently assigned state on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::LinearMemNode::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.LinearMemNode) → int

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

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

C++: core::pack::interaction_graph::LinearMemNode::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

2. 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_curr_state_recent_state_id(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode) → int

return the “recent state id” for the currently assigned state

C++: core::pack::interaction_graph::LinearMemNode::get_curr_state_recent_state_id() const –> int

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

return the index of the currently assigned state

C++: core::pack::interaction_graph::LinearMemNode::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.LinearMemNode) → float

return the one-body energy for the currently assigned state

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

get_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode) → int

C++: core::pack::interaction_graph::LinearMemNode::get_recent_history_size() const –> int

get_sparse_mat_info_for_curr_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode) → pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::LinearMemNode::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.LinearMemNode) → float

return the total energy for this node; includes full energies to neighboring residues

C++: core::pack::interaction_graph::LinearMemNode::get_totalE() const –> float

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, new_state: int) → None

first half of an entire-graph state assignment that avoids unnecessary energy updates

as produced in assign_state. Adjust all node’s states first, then update all energies.

C++: core::pack::interaction_graph::LinearMemNode::partial_assign_state(int) –> void

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

linmem ig does not have to do anything before sim annealing begins

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

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

write internal energy and bookkeeping data to standard out

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

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

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

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

compute the change in energy induced by substituting the currently assigned state with

some alternative state

C++: core::pack::interaction_graph::LinearMemNode::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_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode, num_states_to_maintain_in_recent_history: int) → None

C++: core::pack::interaction_graph::LinearMemNode::set_recent_history_size(int) –> 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.LinearMemNode) → bool

state 0 represents the unasigned state

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

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

C++: core::pack::interaction_graph::LinearMemNode::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.LinearMemoryInteractionGraph

Bases: OnTheFlyInteractionGraph

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

2. 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

3. 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.LinearMemoryInteractionGraph) → None

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.LinearMemoryInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.LinearMemoryInteractionGraph) → int

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

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

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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

2. 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.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.LinearMemoryInteractionGraph) → int

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.LinearMemoryInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph) → int

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::get_recent_history_size() const –> unsigned long

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.OnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::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_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.LinearMemoryInteractionGraph) → None

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.LinearMemoryInteractionGraph) → None

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.LinearMemoryInteractionGraph, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph, recent_history_size: int) → None

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::set_recent_history_size(unsigned long) –> 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.LinearMemoryInteractionGraph, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::LinearMemoryInteractionGraph::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.MultiplexedAnnealableGraph

Bases: AnnealableGraphBase

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

Are any states unassigned?

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

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

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

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

State initialization. Set all nodes to state zero.

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

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph, 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.

This version calls contained AnnealableGraph clean_up_after_packing() methods.

Vikram K. Mulligan (vmullig.edu).

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

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

Accept the considered substitution.

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

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

Consider a change in state at a particular node.

The node index.

The index of the state to which we’re considering setting the node.

The computed change in energy that would result from the substitution.

The energy prior to the substituion, returned by this function.

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

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

Get the total energy from the current states of the nodes in the network.

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

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

Get the number of nodes in the graph.

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

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

Get the number of states for a given node.

The index of the node.

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

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

Get the total number of states for all nodes in the graph.

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

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

Utility signal.

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

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

Set error threshold.

Error threshold value to set.

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

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

Set the states for the entire network.

A Fortran-style 1-array of state indices for all nodes in the network.

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

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

Explicit state modification: set node “node_ind” to state “new_state”.

The index of the node.

The index of the state to which we’re setting the node.

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

property subgraphs

class pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge

Bases: SimpleEdge

calc_long_range(*args, **kwargs)

Overloaded function.

1. calc_long_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) -> bool

C++: core::pack::interaction_graph::SimpleEdge::calc_long_range() –> bool

2. calc_long_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, setting: bool) -> None

C++: core::pack::interaction_graph::SimpleEdge::calc_long_range(bool) –> void

calc_short_range(*args, **kwargs)

Overloaded function.

1. calc_short_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) -> bool

C++: core::pack::interaction_graph::SimpleEdge::calc_short_range() –> bool

2. calc_short_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, setting: bool) -> None

C++: core::pack::interaction_graph::SimpleEdge::calc_short_range(bool) –> void

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::commit_change() –> void

compute_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, use_current_node1: bool, use_current_node2: bool) → None

C++: core::pack::interaction_graph::SimpleEdge::compute_energy(bool, bool) –> void

copy_from(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge, : pyrosetta.rosetta.utility.graph.Edge) → None

C++: core::pack::interaction_graph::NPDHBSimpleEdge::copy_from(const class utility::graph::Edge *) –> void

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

C++: core::pack::interaction_graph::NPDHBSimpleEdge::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::NPDHBSimpleEdge::count_static_memory() const –> unsigned long

get_current_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → float

C++: core::pack::interaction_graph::SimpleEdge::get_current_energy() const –> double

get_first_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int

returns the index of the lower node

C++: utility::graph::Edge::get_first_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → int

returns the index of the one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → pyrosetta.rosetta.utility.graph.Node

returns a non-const pointer to one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_node(unsigned long) –> class utility::graph::Node *

get_proposed_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → float

C++: core::pack::interaction_graph::SimpleEdge::get_proposed_energy() const –> double

get_second_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int

returns the index of the upper node

C++: utility::graph::Edge::get_second_node_ind() const –> unsigned long

is_loop(self: pyrosetta.rosetta.utility.graph.Edge) → bool

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

C++: utility::graph::Edge::is_loop() const –> bool

same_edge(self: pyrosetta.rosetta.utility.graph.Edge, node1: int, node2: int) → bool

Is this the same edge as another edge (node1,node2)? Note:

this graph does not work for multi-graphs. Edges must be unique.

C++: utility::graph::Edge::same_edge(unsigned long, unsigned long) const –> bool

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.Edge, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

called only by class Graph, this function gives the Edge the data it needs

to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::Edge::set_pos_in_owners_list(class utility::graph::EdgeListIterator) –> void

update_current_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::update_current_energy() –> void

update_proposed_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::update_proposed_energy() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph

Bases: SimpleInteractionGraph

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.

add_edge(*args, **kwargs)

Overloaded function.

1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) -> pyrosetta.rosetta.utility.graph.Edge

add an edge between two vertices. Invokes “create_edge” from the derived class.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

2. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, example_edge: pyrosetta.rosetta.utility.graph.Edge) -> pyrosetta.rosetta.utility.graph.Edge

add an edge to this graph copying the data from an edge in another graph.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(const class utility::graph::Edge *) –> class utility::graph::Edge *

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

O(V^3). Computes all pairs shortest paths using Warshall’s algorithm

and writes all the path distances to the two-dimensional table.

C++: utility::graph::Graph::all_pairs_shortest_paths() const –> class ObjexxFCL::FArray2D<int>

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

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

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, node_id: int) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::commit_change(unsigned long) –> void

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, node_id: int, new_state: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → float

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::consider_substitution(unsigned long, class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> double

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) → None

copy the edge connectivity from a source graph with a potentially

unknown type.

C++: utility::graph::Graph::copy_connectivity(const class utility::graph::Graph &) –> void

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

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_static_memory() const –> unsigned long

delete_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, : pyrosetta.rosetta.utility.graph.Edge) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::delete_edge(class utility::graph::Edge *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Graph) → None

delete all the edges present in the graph

C++: utility::graph::Graph::drop_all_edges() –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Graph, node: int) → None

delete all the edges for a single vertex in the graph

C++: utility::graph::Graph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the edge connecting nodes node1 and node2, if that edge exists

in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Graph::find_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the focused edge

C++: utility::graph::Graph::focused_edge() –> class utility::graph::Edge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Graph) → int

returns a count of all the memory used by every vertex and edge in a graph

by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Graph::getTotalMemoryUsage() const –> unsigned long

get_alternate_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_alternate_for_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

get_current_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_current_for_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

get_edge_exists(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → bool

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Graph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_node(self: pyrosetta.rosetta.utility.graph.Graph, index: int) → pyrosetta.rosetta.utility.graph.Node

C++: utility::graph::Graph::get_node(unsigned long) –> class utility::graph::Node *

get_npdhb_simple_node(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, ind: int) → pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::get_npdhb_simple_node(unsigned long) –> class core::pack::interaction_graph::NPDHBSimpleNode *

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Graph

C++: utility::graph::Graph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Graph>

get_simple_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, ind: int) → pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node(unsigned long) –> class core::pack::interaction_graph::SimpleNode *

hbond_database(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database() const –> const class core::scoring::hbonds::HBondDatabase &

hbond_options(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → pyrosetta.rosetta.core.scoring.hbonds.HBondOptions

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options() const –> const class core::scoring::hbonds::HBondOptions &

hbonding_to_res(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → pyrosetta.rosetta.utility.vector1_char

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res() –> class utility::vector1<char, class std::allocator<char> > &

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialization where the graph adds its own edges

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::initialize(const class core::pose::Pose &) –> void

npd_hb_weight(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, eval_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, intra_res: bool) → float

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hb_weight(enum core::scoring::hbonds::HBEvalType, bool) –> double

npd_hbond_set(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → core::scoring::hbonds::NPDHBondSet

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set() const –> const class core::scoring::hbonds::NPDHBondSet &

num_edges(self: pyrosetta.rosetta.utility.graph.Graph) → int

C++: utility::graph::Graph::num_edges() const –> unsigned long

num_nodes(self: pyrosetta.rosetta.utility.graph.Graph) → int

the number of nodes in the graph

C++: utility::graph::Graph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None

send an edge list to the stream os.

C++: utility::graph::Graph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None

describe this graph in dimacs form to the stream os.

C++: utility::graph::Graph::output_dimacs(std::ostream &) const –> void

pose(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SimpleInteractionGraph::pose() const –> const class core::pose::Pose &

pose_cop(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SimpleInteractionGraph::pose_cop() const –> class std::shared_ptr<const class core::pose::Pose>

print_vertices(self: pyrosetta.rosetta.utility.graph.Graph) → None

send summary information to the screen for all vertices in the graph

C++: utility::graph::Graph::print_vertices() const –> void

reject_change(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, node_id: int, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::reject_change(unsigned long, class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

return_hbond_to_queue(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, hbond: core::pack::interaction_graph::NPDHBond) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::return_hbond_to_queue(const class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond> &) –> void

scorefunction(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::SimpleInteractionGraph::scorefunction() const –> const class core::scoring::ScoreFunction &

set_num_nodes(self: pyrosetta.rosetta.utility.graph.Graph, num_nodes: int) → None

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Graph::set_num_nodes(unsigned long) –> void

set_pose_no_initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize(const class core::pose::Pose &) –> void

set_scorefunction(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction(const class core::scoring::ScoreFunction &) –> void

setup_after_edge_addition(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → None

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::setup_after_edge_addition() –> void

setup_for_scoring_for_residue_energy_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::pack::interaction_graph::SimpleInteractionGraph::setup_for_scoring_for_residue_energy_methods() –> const class std::list<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

total_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → float

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy() –> double

unused_hbond(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph) → core::pack::interaction_graph::NPDHBond

C++: core::pack::interaction_graph::NPDHBSimpleInteractionGraph::unused_hbond() –> class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond>

class pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode

Bases: SimpleNode

acknowledge_neighbors_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::acknowledge_neighbors_substitution() –> void

add_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_ptr: utility::graph::Edge, : pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

adds edge pointer to edge list; returns an iterator to the new

list element

C++: utility::graph::Node::add_edge(class utility::graph::Edge *, class utility::graph::EdgeListIterator &) –> void

alt_sc_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::alt_sc_centroid() const –> const class numeric::xyzVector<double> &

alt_sc_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::alt_sc_radius() const –> double

bb_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::bb_centroid() const –> const class numeric::xyzVector<double> &

bb_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::bb_radius() const –> double

calc_curr_hbond_weights(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::calc_curr_hbond_weights() –> void

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → None

Copy the alternate_residue_ pointer to the current_residue_ pointer;

copy the alternate energies to the current energies for this node and its incident edges.

C++: core::pack::interaction_graph::SimpleNode::commit_change() –> void

commit_change_no_res_pointer_update(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

Copy the alternate energies to the current energies for this node

and its incident edges.

C++: core::pack::interaction_graph::NPDHBSimpleNode::commit_change_no_res_pointer_update() –> void

commit_change_npd(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

Copy the alternate_residue_ pointer to the current_residue_ pointer;

copy the alternate energies to the current energies for this node and its incident edges.

C++: core::pack::interaction_graph::NPDHBSimpleNode::commit_change_npd() –> void

compute_alt_weights_for_hbonds(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, curr_state: bool) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds(bool) –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its edge list

C++: utility::graph::Node::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its edge list

C++: utility::graph::Node::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_from(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, : pyrosetta.rosetta.utility.graph.Node) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::copy_from(const class utility::graph::Node *) –> void

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

C++: core::pack::interaction_graph::NPDHBSimpleNode::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::NPDHBSimpleNode::count_static_memory() const –> unsigned long

curr_sc_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::curr_sc_centroid() const –> const class numeric::xyzVector<double> &

curr_sc_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::curr_sc_radius() const –> double

current_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::current_one_body_energy() const –> double

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Node) → None

deletes all edges incident upon this node

C++: utility::graph::Node::drop_all_edges() –> void

drop_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

removes an edge iterator from the node’s edge list. Only called by Edge class.

C++: utility::graph::Node::drop_edge(class utility::graph::EdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its edge list

C++: utility::graph::Node::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its edge list

C++: utility::graph::Node::edge_list_end() –> class utility::graph::EdgeListIterator

find_curr_hbonds_to_upper_neighbors(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors() –> void

find_edge(self: pyrosetta.rosetta.utility.graph.Node, other_node_index: int) → utility::graph::Edge

C++: utility::graph::Node::find_edge(unsigned long) –> class utility::graph::Edge *

find_hbs_for_nbrs_alt_state_step1(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, changing_nbr: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(class core::pack::interaction_graph::NPDHBSimpleNode *) –> void

find_hbs_for_nbrs_alt_state_step2(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, changing_nbr: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → float

C++: core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step2(class core::pack::interaction_graph::NPDHBSimpleNode *) –> double

get_alternate(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the pointer to the alternate state (might be 0)

C++: core::pack::interaction_graph::SimpleNode::get_alternate() const –> class std::shared_ptr<const class core::conformation::Residue>

get_alternate_ref(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the alternate state – must not be 0

C++: core::pack::interaction_graph::SimpleNode::get_alternate_ref() const –> const class core::conformation::Residue &

get_curr_upper_hbond_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → float

Compute the total energy for the current state assignment

C++: core::pack::interaction_graph::NPDHBSimpleNode::get_curr_upper_hbond_energies() –> double

get_current(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the pointer to the current state (might be 0)

C++: core::pack::interaction_graph::SimpleNode::get_current() const –> class std::shared_ptr<const class core::conformation::Residue>

get_current_ref(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the current state – must not be 0

C++: core::pack::interaction_graph::SimpleNode::get_current_ref() const –> const class core::conformation::Residue &

get_node_index(self: pyrosetta.rosetta.utility.graph.Node) → int

the index for this node

C++: utility::graph::Node::get_node_index() const –> unsigned long

get_npdhb_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → float

Compute the change in NPDHBond energy for the given (previously supplied!)

rotamer substitution

C++: core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution() –> double

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of upper neighbors – which “self” neighborness is counted if a loop edge

is present

C++: utility::graph::Node::get_num_edges_to_larger_indexed_nodes() const –> unsigned long

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of lower neighbors

C++: utility::graph::Node::get_num_edges_to_smaller_indexed_nodes() const –> unsigned long

loop_incident(self: pyrosetta.rosetta.utility.graph.Node) → bool

NOTE TO SELF: remove loop support

C++: utility::graph::Node::loop_incident() const –> bool

lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::lower_edge_list_begin() –> class utility::graph::EdgeListIterator

lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its lower-edge list

C++: utility::graph::Node::lower_edge_list_end() –> class utility::graph::EdgeListIterator

moved(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → bool

Is this node considering a state substitution?

C++: core::pack::interaction_graph::SimpleNode::moved() const –> bool

num_edges(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of edges incident on this node, which may include a loop edge

C++: utility::graph::Node::num_edges() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of neighbors counting “self” as a neighbor.

C++: utility::graph::Node::num_neighbors_counting_self() const –> unsigned long

num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of neighbors counting “self” as neighbor. Defaults to

num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

C++: utility::graph::Node::num_neighbors_counting_self_static() const –> unsigned long

one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::one_body_energy() const –> double

prepare_for_neighbors_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, changing_nbr: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::prepare_for_neighbors_substitution(class core::pack::interaction_graph::NPDHBSimpleNode *) –> void

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

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

proposed_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::proposed_one_body_energy() const –> double

reject_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Reset state on this node so that its incident edges will no longer

think it is considering an alternate conformation.

C++: core::pack::interaction_graph::SimpleNode::reject_change(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

reject_change_npd(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Reset state on this node so that its incident edges will no longer

think it is considering an alternate conformation.

C++: core::pack::interaction_graph::NPDHBSimpleNode::reject_change_npd(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

reset_hbs(self: pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode) → None

C++: core::pack::interaction_graph::NPDHBSimpleNode::reset_hbs() –> void

set_alternate(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Set the alternate residue COP and follow by computing the energy

for this residue with its neighbors and storing those computed energies on this node’s edges as their “proposed” energies

C++: core::pack::interaction_graph::SimpleNode::set_alternate(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_alternate_no_E_update(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Passive mode behavior: set the current residue pointer without updating

the alternate one body or proposed two body energies.

C++: core::pack::interaction_graph::SimpleNode::set_alternate_no_E_update(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_current(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Set the current residue COP, and follow by computing the energy

for this residue with its neighbors and storing those computed energies on this node’s edges as their “current” energies.

C++: core::pack::interaction_graph::SimpleNode::set_current(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_current_no_E_update(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Passive mode behavior: set the current residue pointer without updating

the current one body or two body energies.

C++: core::pack::interaction_graph::SimpleNode::set_current_no_E_update(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node, neighbor: int) → None

manually change the number of neighbors for a Node. Used

for symmetry scoring

C++: utility::graph::Node::set_num_neighbors_counting_self_static(unsigned long) –> void

update_energies_after_passive_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → None

C++: core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change() –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::upper_edge_list_begin() –> class utility::graph::EdgeListIterator

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its upper-edge list

C++: utility::graph::Node::upper_edge_list_end() –> class utility::graph::EdgeListIterator

class pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond

Bases: pybind11_object

property acc_atm_

property acc_rsd_

property acc_wt_

property acc_wt_alt_

property don_atm_

property don_rsd_

property don_wt_

property don_wt_alt_

property energy_

property sfxn_wt_

class pyrosetta.rosetta.core.pack.interaction_graph.NodeBase

Bases: pybind11_object

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::NodeBase::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_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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge

Bases: FixedBBEdge

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

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

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

C++: core::pack::interaction_graph::OnTheFlyEdge::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

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.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_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.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

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

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_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_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

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.OnTheFlyInteractionGraph

Bases: FixedBBInteractionGraph

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

2. 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

3. 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.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

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

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::count_dynamic_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

2. 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.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.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.OnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::OnTheFlyInteractionGraph::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_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.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.InteractionGraphBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::InteractionGraphBase::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.OnTheFlyNode

Bases: FixedBBNode

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

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

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.OnTheFlyNode) → int

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

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

C++: core::pack::interaction_graph::OnTheFlyNode::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

2. 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_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_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

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

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

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

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

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.NodeBase) → bool

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

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.PDEdge

Bases: PrecomputedPairEnergiesEdge

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.PDEdge, 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::PDEdge::acknowledge_state_change(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, float &) –> void

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

updates bookkeeping information when one of the two nodes enters its

“unassigned” state.

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

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDEdge, 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::PDEdge::acknowledge_substitution(int, const float, int, const class core::pack::interaction_graph::SparseMatrixIndex &) –> void

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

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

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

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

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::PDEdge::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.PDEdge, node1aa: int, node2aa: int) → None

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

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

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

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

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

static get_alternate_state_energy_first_node(first_node_alt_state: int, second_node_orig_state: int, second_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, first_node_state_offset_minus_1: int, second_node_curr_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → float

C++: core::pack::interaction_graph::PDEdge::get_alternate_state_energy_first_node(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, int, int, int, class ObjexxFCL::FArray1<float> &) –> float

static get_alternate_state_energy_second_node(first_node_orig_state: int, second_node_alt_state: int, first_node_orig_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alternate_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, second_node_alt_state_num_states_per_aatype: int, aa_neighbor_offset: int, edge_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → float

C++: core::pack::interaction_graph::PDEdge::get_alternate_state_energy_second_node(int, int, const class core::pack::interaction_graph::SparseMatrixIndex &, const class core::pack::interaction_graph::SparseMatrixIndex &, int, int, class ObjexxFCL::FArray1<float> &) –> float

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

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

get_edge_table_ptr(self: pyrosetta.rosetta.core.pack.interaction_graph.PDEdge) → float

C++: core::pack::interaction_graph::PDEdge::get_edge_table_ptr() –> 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_offsets_for_aatypes(self: pyrosetta.rosetta.core.pack.interaction_graph.PDEdge) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

Returns the array of offsets into the sparse two-body energy table

for amino-acid neighbors. Used in transferring information from edges onto nodes for cache efficiency.

C++: core::pack::interaction_graph::PDEdge::get_offsets_for_aatypes() –> const class ObjexxFCL::FArray2D<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_second_node_num_states_per_aa(self: pyrosetta.rosetta.core.pack.interaction_graph.PDEdge) → pyrosetta.rosetta.utility.vector1_int

returns an FArray of the number of states for each amino acid type for the

higher-indexed node

C++: core::pack::interaction_graph::PDEdge::get_second_node_num_states_per_aa() –> const class utility::vector1<int, class std::allocator<int> > &

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

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

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

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

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

C++: core::pack::interaction_graph::PDEdge::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.PDEdge) → None

C++: core::pack::interaction_graph::PDEdge::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.PDEdge, weight: float) → None

C++: core::pack::interaction_graph::PDEdge::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.PDEdge, sparse_conn_info: pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t) → None

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph

Bases: PrecomputedPairEnergiesInteractionGraph

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

Override the InteractionGraphBase class’s implementation of this function

to return ‘true’.

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

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

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

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

C++: core::pack::interaction_graph::PDInteractionGraph::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

2. 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

3. 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

3. 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.PDInteractionGraph) → None

C++: core::pack::interaction_graph::PDInteractionGraph::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(*args, **kwargs)

Overloaded function.

1. commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph) -> float

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

2. commit_considered_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) -> float

C++: core::pack::interaction_graph::PDInteractionGraph::commit_considered_substitution(const class ObjexxFCL::FArray2D<float> &) –> float

consider_substitution(*args, **kwargs)

Overloaded function.

1. consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) -> None

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

2. consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, node_ind: int, new_state: int, deltaE_unweighted: float, prevE_unweighted: float, deltaE_weighted: float, prevE_weighted: float, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) -> None

C++: core::pack::interaction_graph::PDInteractionGraph::consider_substitution(int, int, float &, float &, float &, float &, const class ObjexxFCL::FArray2D<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.PDInteractionGraph) → int

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

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

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph, node1: int, node2: int, node1aa: int, node2aa: int) → pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph) → int

older scheme for memory accounting – replace this asap

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

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph) → float

@ brief O(1) total energy report. Protected read access for derived classes.

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

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

a user may define subsets of the vertex set for which they would like to

know the internal energy sum.

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph) → int

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph, node: int, state: int) → float

C++: core::pack::interaction_graph::PDInteractionGraph::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

get_weighted_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → float

C++: core::pack::interaction_graph::PDInteractionGraph::get_weighted_energy(const class ObjexxFCL::FArray2D<float> &) const –> float

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.PDInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph) → None

outputs the current state for each node, useful for debugging

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDInteractionGraph, : float) → None

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

set_network_state(*args, **kwargs)

Overloaded function.

1. set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) -> float

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

2. set_network_state(self: pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) -> float

C++: core::pack::interaction_graph::PDInteractionGraph::set_network_state(class ObjexxFCL::FArray1<int> &, const class ObjexxFCL::FArray2D<float> &) –> 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.PDInteractionGraph, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::PDInteractionGraph::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.PDNode

Bases: PrecomputedPairEnergiesNode

aatype_for_state(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, state: int) → int

return the amino acid type for a particular state – this indexing is of course completely

arbitrary

C++: core::pack::interaction_graph::PDNode::aatype_for_state(int) const –> int

acknowledge_neighbors_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, edge_to_altered_neighbor: int, new_edge_energy: float, other_node_new_state: int, other_node_new_state_sparse_info: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → None

C++: core::pack::interaction_graph::PDNode::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.PDNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

adds all the energies in energies to the one-body energies for this node

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

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

adds energy to the one-body energy for state state

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

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

assigns node a new_state

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

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

assigns node’s state to it’s zero, or “unassigned” state.

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

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

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

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

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

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

C++: core::pack::interaction_graph::PDNode::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.PDNode) → int

returns the state the node is currently assigned

C++: core::pack::interaction_graph::PDNode::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_num_states_for_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, aa_type: int) → int

C++: core::pack::interaction_graph::PDNode::get_num_states_for_aa_type(int) const –> int

get_num_states_for_aa_types(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode) → pyrosetta.rosetta.utility.vector1_int

returns an FArray & with the number of states for each amino acid type

C++: core::pack::interaction_graph::PDNode::get_num_states_for_aa_types() const –> const class utility::vector1<int, class std::allocator<int> > &

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

returns the one body energy for a state

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

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

returns the one body energy for the state the node is currently assigned

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

get_sparse_mat_info_for_curr_state(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode) → pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::PDNode::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.PDNode, state: int) → pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

C++: core::pack::interaction_graph::PDNode::get_sparse_mat_info_for_state(int) const –> const class core::pack::interaction_graph::SparseMatrixIndex &

get_weighted_energy_with_higher_indexed_nodes(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → float

C++: core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes(const class ObjexxFCL::FArray2D<float> &) const –> float

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

prepares node for simulated annealing

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

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

prints a description of the node and all of it’s one-body energies

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

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

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

project_deltaE_for_substitution(*args, **kwargs)

Overloaded function.

1. project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, alternate_state: int, prev_node_energy: float) -> float

returns the change in energy that would be induced by switching this node

from its current state into another state

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

2. project_deltaE_for_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, alternate_state: int, deltaE_unweighted: float, prevE_unweighted: float, deltaE_weighted: float, prevE_weighted: float, weights: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) -> None

returns the change in weighted energy that would be induced

by switching this node from its current state into another state

C++: core::pack::interaction_graph::PDNode::project_deltaE_for_substitution(int, float &, float &, float &, float &, const class ObjexxFCL::FArray2D<float> &) –> void

set_amino_acid_types(self: pyrosetta.rosetta.core.pack.interaction_graph.PDNode, : pyrosetta.rosetta.std.vector_int) → None

sets the amino acid type for each state

C++: core::pack::interaction_graph::PDNode::set_amino_acid_types(const class std::vector<int, class std::allocator<int> > &) –> void

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

Is the current state unassigned (set to the zero or null state)?

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

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

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

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

set all the one-body energies for this node

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

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

update energy to the one-body energy for state

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

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

Set all onebody energies to zero.

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

class pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge

Bases: FixedBBEdge

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

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

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

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

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

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

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.PrecomputedPairEnergiesEdge, first_state: int, second_state: int) → float

Get the two-body energy for two states of the nodes connected to this edge.

Must be implmented by derived classes.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::interaction_graph::PrecomputedPairEnergiesEdge::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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph

Bases: FixedBBInteractionGraph

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

2. 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

3. 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

3. 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.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

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.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

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.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(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.InteractionGraphBase, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::InteractionGraphBase::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.InteractionGraphBase, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::InteractionGraphBase::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.PrecomputedPairEnergiesNode

Bases: FixedBBNode

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.NodeBase, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

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

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

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

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

C++: core::pack::interaction_graph::NodeBase::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_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.PrecomputedPairEnergiesNode, state: int) → float

Get the one-body energy for a state of this node.

Must be implmented by derived classes.

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator

Bases: AnnealableGraphBase

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

Are there any nodes unassigned?

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

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

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

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

State initialization: set all nodes to state zero.

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

clean_up_after_packing(self: pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, 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.

This version calls the clean_up_residuearrayannealableenergy_after_packing() function in the associated energy methods.

Vikram K. Mulligan (vmullig.edu).

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

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

Set the node that we were considering to the state that we were considering (i.e. commit the change).

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

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

Consider setting a particular node to a particular state.

Index of the node to be potentially modified.

Index of the state that we might set this node to.

The change in energy that would result from the substitution, returned by this function.

The previous energy for this node, prior to the substitution, returned by this function.

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

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

Get the energy fo the current state.

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

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

Get the number of nodes.

This lies a little bit. It only returns the number of independent nodes.

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

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

Get the number of states for a specific node.

Index of the node.

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

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

Get the total number of states for all nodes.

This lies a little bit. It only returns the total number of states for the independent nodes.

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

has_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator) → bool

Do any energy methods have a nonzero weight?

C++: core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::has_methods() –> bool

initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : pyrosetta.rosetta.utility.graph.Graph) → None

C++: core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(const class core::scoring::ScoreFunction &, class core::pose::Pose &, class core::pack::rotamer_set::RotamerSets &, class std::shared_ptr<const class utility::graph::Graph>) –> void

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

Utility signal.

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

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

Set error threshold.

Error threshold value to set.

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

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

Set states for all nodes across the network.

Fortran-style 1-array of state indices for all nodes in the network.

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

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

Explicit state modification: set a particular node to a particular state.

Index of the node to modify.

Index of the state that we’re setting this node TO.

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

class pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType

Bases: pybind11_object

Members:

whole_whole

whole_sc

sc_whole

sc_sc

property name

sc_sc = <ResiduePairEvalType.sc_sc: 3>

sc_whole = <ResiduePairEvalType.sc_whole: 2>

property value

whole_sc = <ResiduePairEvalType.whole_sc: 1>

whole_whole = <ResiduePairEvalType.whole_whole: 0>

class pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots

Bases: pybind11_object

Handles sphere-sphere overlap calculations for the HPatchInteractionGraph.

One big change from the r++ version of this class is that this class now includes all of the information that was previously stored in the RotamerCoords class. Since I’m not storing atoms in trie ordering (perhaps I’ll add this later), there is no need to have a separate class for the rotamer coordinates.

RotamerDots hold DotSphere objects for the atoms of a given Residue (or really, of the current state on some interaction graph Node). Default use of the class will result in RotamerDots objects keeping DotSpheres for every atom of a residue. For the hpatch interaction graph, though, we only care about the SASA of the heavy atoms. No need to include the hydrogens when looking for hydrophobic patches. By not keeping track of the hydrogens, we save a huge amount of time on computing updates to the SASA score because hydrogen atoms generally make up half of a protein. So I’m adding a boolean flag to the non-default constructor which toggles whether we’re tracking SASA of all atoms, or just the heavy atoms.

Two other big changes being made to this class are that 1) the class will now keep track of two kinds of SASA and 2) it will no longer keep score or score_is_current variables. The two kinds of SASA the class will keep track of are the standard SASA, and a SASA with polar atom radii extended. The expanded polar SASA will only be kept if a boolean flag is set at construct time. If not, it will just calculate standard SASA and that’s it. The second change is that this class is now only keeping track of SASA. RotamerDots objects will not be responsible for calculating a score.

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

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

copy(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, rhs: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → None

C++: core::pack::interaction_graph::RotamerDots::copy(const class core::pack::interaction_graph::RotamerDots &) –> void

decrement_from_cached(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, cached_dot_overlap: core::pack::interaction_graph::RotamerDotsCache) → None

C++: core::pack::interaction_graph::RotamerDots::decrement_from_cached(const class core::pack::interaction_graph::RotamerDotsCache &) –> void

static dot_coord(index: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::RotamerDots::dot_coord(unsigned long) –> class numeric::xyzVector<double>

get_atom_coords_xyz(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, atom_index: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::RotamerDots::get_atom_coords_xyz(unsigned long) const –> class numeric::xyzVector<double>

get_atom_counts(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere

C++: core::pack::interaction_graph::RotamerDots::get_atom_counts() –> const class utility::vector1<class core::pack::interaction_graph::DotSphere, class std::allocator<class core::pack::interaction_graph::DotSphere> > &

get_atom_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, atom_index: int) → float

C++: core::pack::interaction_graph::RotamerDots::get_atom_radius(unsigned long) const –> double

get_atom_sasa(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, atom_index: int) → float

C++: core::pack::interaction_graph::RotamerDots::get_atom_sasa(unsigned long) const –> double

get_num_atoms(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → int

C++: core::pack::interaction_graph::RotamerDots::get_num_atoms() const –> unsigned long

get_num_covered_total(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → int

C++: core::pack::interaction_graph::RotamerDots::get_num_covered_total() const –> unsigned long

get_num_uncovered(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, atom: int) → int

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

get_radii(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → pyrosetta.rosetta.utility.vector1_double

C++: core::pack::interaction_graph::RotamerDots::get_radii() const –> const class utility::vector1<double, class std::allocator<double> > *

get_res_res_overlap(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, other_res: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, res1_covered_by_res2: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t, res2_covered_by_res1: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t, atom_atom_overlaps_cache: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) → None

C++: core::pack::interaction_graph::RotamerDots::get_res_res_overlap(const class core::pack::interaction_graph::RotamerDots &, class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &, class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) const –> void

get_sasa(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → float

C++: core::pack::interaction_graph::RotamerDots::get_sasa() const –> double

increment_both(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, other: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → None

C++: core::pack::interaction_graph::RotamerDots::increment_both(class core::pack::interaction_graph::RotamerDots &) –> void

increment_both_and_cache(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, other_rotamer: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, others_dots_covered_by_this: core::pack::interaction_graph::RotamerDotsCache, this_dots_covered_by_other: core::pack::interaction_graph::RotamerDotsCache, atom_atom_overlaps_cache: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) → None

C++: core::pack::interaction_graph::RotamerDots::increment_both_and_cache(class core::pack::interaction_graph::RotamerDots &, class core::pack::interaction_graph::RotamerDotsCache &, class core::pack::interaction_graph::RotamerDotsCache &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) –> void

increment_from_cached(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, cached_dot_overlap: core::pack::interaction_graph::RotamerDotsCache) → None

C++: core::pack::interaction_graph::RotamerDots::increment_from_cached(const class core::pack::interaction_graph::RotamerDotsCache &) –> void

increment_self_overlap(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → None

C++: core::pack::interaction_graph::RotamerDots::increment_self_overlap() –> void

increment_this_and_cache(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, other: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, this_overlap_on_other: core::pack::interaction_graph::RotamerDotsCache, atom_atom_overlaps_cache: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) → None

C++: core::pack::interaction_graph::RotamerDots::increment_this_and_cache(const class core::pack::interaction_graph::RotamerDots &, class core::pack::interaction_graph::RotamerDotsCache &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) –> void

invert_to_boolmasks(*args, **kwargs)

Overloaded function.

1. invert_to_boolmasks(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, inv_dots: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t) -> None

C++: core::pack::interaction_graph::RotamerDots::invert_to_boolmasks(class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &) const –> void

2. invert_to_boolmasks(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, inv_dots: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t, ats_to_update: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::interaction_graph::RotamerDots::invert_to_boolmasks(class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

max_atom_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → float

C++: core::pack::interaction_graph::RotamerDots::max_atom_radius() –> double

name3(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → str

C++: core::pack::interaction_graph::RotamerDots::name3() const –> std::string

overlaps(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, other: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → bool

C++: core::pack::interaction_graph::RotamerDots::overlaps(const class core::pack::interaction_graph::RotamerDots &) const –> bool

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

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

radius_for_attype(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots, attype_index: int) → float

C++: core::pack::interaction_graph::RotamerDots::radius_for_attype(const unsigned long) –> double

rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::RotamerDots::rotamer() const –> class std::shared_ptr<const class core::conformation::Residue>

seqpos(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots) → int

C++: core::pack::interaction_graph::RotamerDots::seqpos() const –> unsigned long

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

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache

Bases: pybind11_object

A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes.

During packing, when a first class node has to respond to another Node changing state, it’s faster to decrement the coverage the previous state produced and increment the coverage the new state produces than to completely recalculate how the new state overlaps the node. But instead of holding that coverage information in a RotamerDots object (which does alot of other things), hold it in this cache class instead.

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

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

get_atom_counts(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache) → pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere

C++: core::pack::interaction_graph::RotamerDotsCache::get_atom_counts() const –> const class utility::vector1<class core::pack::interaction_graph::DotSphere, class std::allocator<class core::pack::interaction_graph::DotSphere> > &

increment_count(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache, covered: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t) → None

C++: core::pack::interaction_graph::RotamerDotsCache::increment_count(class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &) –> void

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

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

resize(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache, num_atoms: int) → None

C++: core::pack::interaction_graph::RotamerDotsCache::resize(unsigned long) –> void

write_to_compact_array(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache, compact: pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t) → None

C++: core::pack::interaction_graph::RotamerDotsCache::write_to_compact_array(class utility::vector1<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> >, class std::allocator<class utility::vector1<class ObjexxFCL::ubyte, class std::allocator<class ObjexxFCL::ubyte> > > > &) const –> void

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData

Bases: SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t

A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class.

The RotamerDots class keeps track of the SASA of some rotamer using DotSphere objects and lots of get overlap calls on atoms. The SASA of a given atom (or residue) depends on what radii are used for the atoms. Different program use different sets of radii, and for the hpatch score, the polar atom radii are expanded. Previously RotamerDots objects would have a static vector member variable that represented the particular set of radii being used. It would also have a second static vector member variable that represented the expanded polar version of the radii. So, no matter how many instances of RotamerDots objects we created, we only maintained two vectors for the radii. Now, we want to make the RotamerDots class only use one set of radii for the hpatch score: the expanded polar radii. The super easy solution would be to remove all the logic that keeps track of SASA when using the standard radii and make the RotamerDots class only calculate that kind of SASA. But, there will probably be more uses in the future for a RotamerDots class that can calculate SASA with a standard set of radii than with the expanded polar ones. So, that’s where this class comes in. It will read in database files, depending on which set of radii are requested and provide access to that data in some way.

Let’s say we have to create RotamerDots objects for two different sets of SASA radii. When those objects are constructed a pointer to the right set of radii will have to be set. Definitely don’t want to copy/store the radii to each instance. If I make it a pointer to this class, then it would only work for one set of radii. So at RotamerDots construct time we have to ask this class to give us a pointer to the set of radii that are requested. Then only one instance of this class exists, and all RotamerDots objects have pointers set to the radii they care about. What would this change in the RotamerDots API? The get_radius() function would dereference the pointer and index into the vector to get the right radius. This structure is similar to how the ChemicalManager works. But, in that class, the functions return AtomTypeSet objects.

get_NACCESS_SASA_radii(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) → pyrosetta.rosetta.utility.vector1_double

return a pointer to the SASA radii used by NACCESS

C++: core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii() const –> const class utility::vector1<double, class std::allocator<double> > *

get_NACCESS_SASA_radii_with_expanded_polars(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) → pyrosetta.rosetta.utility.vector1_double

return a pointer to the SASA radii used by NACCESS, with polar atom radii expanded

C++: core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars() const –> const class utility::vector1<double, class std::allocator<double> > *

get_ROSETTA_SASA_radii(self: pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData) → pyrosetta.rosetta.utility.vector1_double

return a pointer to the standard Rosetta SASA radii

C++: core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii() const –> const class utility::vector1<double, class std::allocator<double> > *

static get_instance() → core::pack::interaction_graph::RotamerDotsRadiusData

C++: utility::SingletonBase<core::pack::interaction_graph::RotamerDotsRadiusData>::get_instance() –> class core::pack::interaction_graph::RotamerDotsRadiusData *

class pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge

Bases: Edge

calc_long_range(*args, **kwargs)

Overloaded function.

1. calc_long_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) -> bool

C++: core::pack::interaction_graph::SimpleEdge::calc_long_range() –> bool

2. calc_long_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, setting: bool) -> None

C++: core::pack::interaction_graph::SimpleEdge::calc_long_range(bool) –> void

calc_short_range(*args, **kwargs)

Overloaded function.

1. calc_short_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) -> bool

C++: core::pack::interaction_graph::SimpleEdge::calc_short_range() –> bool

2. calc_short_range(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, setting: bool) -> None

C++: core::pack::interaction_graph::SimpleEdge::calc_short_range(bool) –> void

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::commit_change() –> void

compute_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, use_current_node1: bool, use_current_node2: bool) → None

C++: core::pack::interaction_graph::SimpleEdge::compute_energy(bool, bool) –> void

copy_from(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge, : pyrosetta.rosetta.utility.graph.Edge) → None

C++: core::pack::interaction_graph::SimpleEdge::copy_from(const class utility::graph::Edge *) –> void

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

C++: core::pack::interaction_graph::SimpleEdge::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::SimpleEdge::count_static_memory() const –> unsigned long

get_current_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → float

C++: core::pack::interaction_graph::SimpleEdge::get_current_energy() const –> double

get_first_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int

returns the index of the lower node

C++: utility::graph::Edge::get_first_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → int

returns the index of the one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → pyrosetta.rosetta.utility.graph.Node

returns a non-const pointer to one node given the index of the other.

node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_node(unsigned long) –> class utility::graph::Node *

get_proposed_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → float

C++: core::pack::interaction_graph::SimpleEdge::get_proposed_energy() const –> double

get_second_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int

returns the index of the upper node

C++: utility::graph::Edge::get_second_node_ind() const –> unsigned long

is_loop(self: pyrosetta.rosetta.utility.graph.Edge) → bool

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

C++: utility::graph::Edge::is_loop() const –> bool

same_edge(self: pyrosetta.rosetta.utility.graph.Edge, node1: int, node2: int) → bool

Is this the same edge as another edge (node1,node2)? Note:

this graph does not work for multi-graphs. Edges must be unique.

C++: utility::graph::Edge::same_edge(unsigned long, unsigned long) const –> bool

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.Edge, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

called only by class Graph, this function gives the Edge the data it needs

to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::Edge::set_pos_in_owners_list(class utility::graph::EdgeListIterator) –> void

update_current_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::update_current_energy() –> void

update_proposed_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge) → None

C++: core::pack::interaction_graph::SimpleEdge::update_proposed_energy() –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph

Bases: Graph

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.

add_edge(*args, **kwargs)

Overloaded function.

1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) -> pyrosetta.rosetta.utility.graph.Edge

add an edge between two vertices. Invokes “create_edge” from the derived class.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

2. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, example_edge: pyrosetta.rosetta.utility.graph.Edge) -> pyrosetta.rosetta.utility.graph.Edge

add an edge to this graph copying the data from an edge in another graph.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(const class utility::graph::Edge *) –> class utility::graph::Edge *

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

O(V^3). Computes all pairs shortest paths using Warshall’s algorithm

and writes all the path distances to the two-dimensional table.

C++: utility::graph::Graph::all_pairs_shortest_paths() const –> class ObjexxFCL::FArray2D<int>

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

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

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id: int) → None

C++: core::pack::interaction_graph::SimpleInteractionGraph::commit_change(unsigned long) –> void

consider_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id: int, new_state: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → float

C++: core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(unsigned long, class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> double

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) → None

copy the edge connectivity from a source graph with a potentially

unknown type.

C++: utility::graph::Graph::copy_connectivity(const class utility::graph::Graph &) –> void

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

C++: core::pack::interaction_graph::SimpleInteractionGraph::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::SimpleInteractionGraph::count_static_memory() const –> unsigned long

delete_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, : pyrosetta.rosetta.utility.graph.Edge) → None

C++: core::pack::interaction_graph::SimpleInteractionGraph::delete_edge(class utility::graph::Edge *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Graph) → None

delete all the edges present in the graph

C++: utility::graph::Graph::drop_all_edges() –> void

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Graph, node: int) → None

delete all the edges for a single vertex in the graph

C++: utility::graph::Graph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Graph::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the edge connecting nodes node1 and node2, if that edge exists

in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Graph::find_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the focused edge

C++: utility::graph::Graph::focused_edge() –> class utility::graph::Edge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Graph) → int

returns a count of all the memory used by every vertex and edge in a graph

by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Graph::getTotalMemoryUsage() const –> unsigned long

get_alternate_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_alternate_for_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

get_current_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_current_for_node(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

get_edge_exists(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) → bool

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Graph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_node(self: pyrosetta.rosetta.utility.graph.Graph, index: int) → pyrosetta.rosetta.utility.graph.Node

C++: utility::graph::Graph::get_node(unsigned long) –> class utility::graph::Node *

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Graph) → pyrosetta.rosetta.utility.graph.Graph

C++: utility::graph::Graph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Graph>

get_simple_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, ind: int) → pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode

C++: core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node(unsigned long) –> class core::pack::interaction_graph::SimpleNode *

initialize(*args, **kwargs)

Overloaded function.

1. initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Initialization where the graph adds its own edges; use set_pose_no_initialize

if the edges should be added externally. Assumes that the pose does not change its sequence.

C++: core::pack::interaction_graph::SimpleInteractionGraph::initialize(const class core::pose::Pose &) –> void

2. initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Initialization where the graph creates a packer-neighbor graph from the input

packer task so that edges between residues that might become larger than they are in the input Pose (e.g., GLY –> ARG mutation) can be added to the graph.

C++: core::pack::interaction_graph::SimpleInteractionGraph::initialize(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

num_edges(self: pyrosetta.rosetta.utility.graph.Graph) → int

C++: utility::graph::Graph::num_edges() const –> unsigned long

num_nodes(self: pyrosetta.rosetta.utility.graph.Graph) → int

the number of nodes in the graph

C++: utility::graph::Graph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None

send an edge list to the stream os.

C++: utility::graph::Graph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) → None

describe this graph in dimacs form to the stream os.

C++: utility::graph::Graph::output_dimacs(std::ostream &) const –> void

pose(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SimpleInteractionGraph::pose() const –> const class core::pose::Pose &

pose_cop(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SimpleInteractionGraph::pose_cop() const –> class std::shared_ptr<const class core::pose::Pose>

print_vertices(self: pyrosetta.rosetta.utility.graph.Graph) → None

send summary information to the screen for all vertices in the graph

C++: utility::graph::Graph::print_vertices() const –> void

reject_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, node_id: int, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

C++: core::pack::interaction_graph::SimpleInteractionGraph::reject_change(unsigned long, class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

scorefunction(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::SimpleInteractionGraph::scorefunction() const –> const class core::scoring::ScoreFunction &

set_num_nodes(self: pyrosetta.rosetta.utility.graph.Graph, num_nodes: int) → None

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Graph::set_num_nodes(unsigned long) –> void

set_pose_no_initialize(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize the graph so that all nodes take their current state from the

input Pose – this does not add any edges to the graph.

C++: core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize(const class core::pose::Pose &) –> void

set_scorefunction(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction(const class core::scoring::ScoreFunction &) –> void

setup_after_edge_addition(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → None

If set_pose_no_initialize was called, then after edges have been added. This

function will also do any bookkeeping necessary before the start of simulated annealing

C++: core::pack::interaction_graph::SimpleInteractionGraph::setup_after_edge_addition() –> void

setup_for_scoring_for_residue_energy_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::pack::interaction_graph::SimpleInteractionGraph::setup_for_scoring_for_residue_energy_methods() –> const class std::list<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

total_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → float

C++: core::pack::interaction_graph::SimpleInteractionGraph::total_energy() –> double

class pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode

Bases: Node

add_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_ptr: utility::graph::Edge, : pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

adds edge pointer to edge list; returns an iterator to the new

list element

C++: utility::graph::Node::add_edge(class utility::graph::Edge *, class utility::graph::EdgeListIterator &) –> void

alt_sc_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::alt_sc_centroid() const –> const class numeric::xyzVector<double> &

alt_sc_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::alt_sc_radius() const –> double

bb_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::bb_centroid() const –> const class numeric::xyzVector<double> &

bb_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::bb_radius() const –> double

commit_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → None

Copy the alternate_residue_ pointer to the current_residue_ pointer;

copy the alternate energies to the current energies for this node and its incident edges.

C++: core::pack::interaction_graph::SimpleNode::commit_change() –> void

commit_change_no_res_pointer_update(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → None

Copy the alternate energies to the current energies for this node

and its incident edges.

C++: core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update() –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its edge list

C++: utility::graph::Node::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its edge list

C++: utility::graph::Node::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_from(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, : pyrosetta.rosetta.utility.graph.Node) → None

C++: core::pack::interaction_graph::SimpleNode::copy_from(const class utility::graph::Node *) –> void

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

C++: core::pack::interaction_graph::SimpleNode::count_dynamic_memory() const –> unsigned long

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

C++: core::pack::interaction_graph::SimpleNode::count_static_memory() const –> unsigned long

curr_sc_centroid(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::interaction_graph::SimpleNode::curr_sc_centroid() const –> const class numeric::xyzVector<double> &

curr_sc_radius(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::curr_sc_radius() const –> double

current_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::current_one_body_energy() const –> double

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Node) → None

deletes all edges incident upon this node

C++: utility::graph::Node::drop_all_edges() –> void

drop_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None

removes an edge iterator from the node’s edge list. Only called by Edge class.

C++: utility::graph::Node::drop_edge(class utility::graph::EdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its edge list

C++: utility::graph::Node::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its edge list

C++: utility::graph::Node::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Node, other_node_index: int) → utility::graph::Edge

C++: utility::graph::Node::find_edge(unsigned long) –> class utility::graph::Edge *

get_alternate(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the pointer to the alternate state (might be 0)

C++: core::pack::interaction_graph::SimpleNode::get_alternate() const –> class std::shared_ptr<const class core::conformation::Residue>

get_alternate_ref(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the alternate state – must not be 0

C++: core::pack::interaction_graph::SimpleNode::get_alternate_ref() const –> const class core::conformation::Residue &

get_current(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the pointer to the current state (might be 0)

C++: core::pack::interaction_graph::SimpleNode::get_current() const –> class std::shared_ptr<const class core::conformation::Residue>

get_current_ref(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → pyrosetta.rosetta.core.conformation.Residue

return the current state – must not be 0

C++: core::pack::interaction_graph::SimpleNode::get_current_ref() const –> const class core::conformation::Residue &

get_node_index(self: pyrosetta.rosetta.utility.graph.Node) → int

the index for this node

C++: utility::graph::Node::get_node_index() const –> unsigned long

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of upper neighbors – which “self” neighborness is counted if a loop edge

is present

C++: utility::graph::Node::get_num_edges_to_larger_indexed_nodes() const –> unsigned long

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of lower neighbors

C++: utility::graph::Node::get_num_edges_to_smaller_indexed_nodes() const –> unsigned long

loop_incident(self: pyrosetta.rosetta.utility.graph.Node) → bool

NOTE TO SELF: remove loop support

C++: utility::graph::Node::loop_incident() const –> bool

lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::lower_edge_list_begin() –> class utility::graph::EdgeListIterator

lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its lower-edge list

C++: utility::graph::Node::lower_edge_list_end() –> class utility::graph::EdgeListIterator

moved(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → bool

Is this node considering a state substitution?

C++: core::pack::interaction_graph::SimpleNode::moved() const –> bool

num_edges(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of edges incident on this node, which may include a loop edge

C++: utility::graph::Node::num_edges() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of neighbors counting “self” as a neighbor.

C++: utility::graph::Node::num_neighbors_counting_self() const –> unsigned long

num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node) → int

the number of neighbors counting “self” as neighbor. Defaults to

num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

C++: utility::graph::Node::num_neighbors_counting_self_static() const –> unsigned long

one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::one_body_energy() const –> double

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

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

proposed_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → float

C++: core::pack::interaction_graph::SimpleNode::proposed_one_body_energy() const –> double

reject_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Reset state on this node so that its incident edges will no longer

think it is considering an alternate conformation.

C++: core::pack::interaction_graph::SimpleNode::reject_change(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_alternate(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Set the alternate residue COP and follow by computing the energy

for this residue with its neighbors and storing those computed energies on this node’s edges as their “proposed” energies

C++: core::pack::interaction_graph::SimpleNode::set_alternate(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_alternate_no_E_update(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Passive mode behavior: set the current residue pointer without updating

the alternate one body or proposed two body energies.

C++: core::pack::interaction_graph::SimpleNode::set_alternate_no_E_update(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_current(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Set the current residue COP, and follow by computing the energy

for this residue with its neighbors and storing those computed energies on this node’s edges as their “current” energies.

C++: core::pack::interaction_graph::SimpleNode::set_current(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_current_no_E_update(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode, res: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Passive mode behavior: set the current residue pointer without updating

the current one body or two body energies.

C++: core::pack::interaction_graph::SimpleNode::set_current_no_E_update(class std::shared_ptr<const class core::conformation::Residue>, class basic::datacache::BasicDataCache &) –> void

set_num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node, neighbor: int) → None

manually change the number of neighbors for a Node. Used

for symmetry scoring

C++: utility::graph::Node::set_num_neighbors_counting_self_static(unsigned long) –> void

update_energies_after_passive_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode) → None

C++: core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change() –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::upper_edge_list_begin() –> class utility::graph::EdgeListIterator

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the end of its upper-edge list

C++: utility::graph::Node::upper_edge_list_end() –> class utility::graph::EdgeListIterator

class pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex

Bases: pybind11_object

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

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

get_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → int

C++: core::pack::interaction_graph::SparseMatrixIndex::get_aa_type() const –> int

get_state_ind_for_this_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → int

C++: core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type() const –> int

set_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, aa: int) → None

C++: core::pack::interaction_graph::SparseMatrixIndex::set_aa_type(int) –> void

set_state_ind_for_this_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, state_ind: int) → None

C++: core::pack::interaction_graph::SparseMatrixIndex::set_state_ind_for_this_aa_type(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy

Bases: ContextDependentOneBodyEnergy

Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms.

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

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

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

C++: core::pack::interaction_graph::SurfaceEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, p: core::pose::Pose) → bool

Use the dof_derivative interface for this energy method when

calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.

C++: core::scoring::methods::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

defines_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

C++: core::scoring::methods::OneBodyEnergy::defines_score_for_residue(const class core::conformation::Residue &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) → float

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → None

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::interaction_graph::SurfaceEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?

Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

indicate_required_context_graphs(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::pack::interaction_graph::SurfaceEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the cd_1b element of the EnergyMethodType enumeration; this method

should NOT be overridden by derived classes.

C++: core::scoring::methods::ContextDependentOneBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

residue_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::interaction_graph::SurfaceEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work necessary before evaluating the derivatives for this residue

C++: core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None

if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

1. setup_for_packing() is called for all energy methods

2. rotamers are built

3. setup_for_packing_with_rotsets() is called for all energy methods

4. prepare_rotamers_for_packing() is called for all energy methods

5. The energy methods are asked to score all rotamers and rotamer pairs

6. Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::SurfaceEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) → None

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → int

Return the version of the energy method

C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator

Bases: EnergyMethodCreator

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

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

create_energy_method(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new SurfaceEnergy

C++: core::pack::interaction_graph::SurfaceEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: core::pack::interaction_graph::SurfaceEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential

Bases: SingletonBase_core_pack_interaction_graph_SurfacePotential_t

With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These “potential” classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don’t put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn’t use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I’ve decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run.

average_residue_hASA(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, aa_type: pyrosetta.rosetta.core.chemical.AA, num_nbs: int) → float

C++: core::pack::interaction_graph::SurfacePotential::average_residue_hASA(enum core::chemical::AA, unsigned long) –> double

compute_pose_hpatch_score(*args, **kwargs)

Overloaded function.

1. compute_pose_hpatch_score(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, pose: pyrosetta.rosetta.core.pose.Pose) -> float

return the hpatch score for an entire pose

C++: core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(const class core::pose::Pose &) –> double

2. compute_pose_hpatch_score(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, pose: pyrosetta.rosetta.core.pose.Pose, total_hpatch_energy_: float, patch_scores_: pyrosetta.rosetta.std.map_unsigned_long_std_pair_double_double_t_std_allocator_std_pair_const_unsigned_long_std_pair_double_double_t, atoms_in_patches_: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t) -> None

C++: core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(const class core::pose::Pose &, double &, class std::map<unsigned long, struct std::pair<double, double>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, struct std::pair<double, double> > > > &, class std::map<unsigned long, class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > > > > &) –> void

compute_pose_surface_energy(*args, **kwargs)

Overloaded function.

1. compute_pose_surface_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, pose: pyrosetta.rosetta.core.pose.Pose, surface_energy_: float) -> None

C++: core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(const class core::pose::Pose &, double &) –> void

2. compute_pose_surface_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, pose: pyrosetta.rosetta.core.pose.Pose, total_surface_energy_: float, residue_surface_energy_: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(const class core::pose::Pose &, double &, class utility::vector1<double, class std::allocator<double> > &) –> void

compute_residue_surface_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector, resid: int, num_neighbors_: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &, unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

static get_instance() → core::pack::interaction_graph::SurfacePotential

C++: utility::SingletonBase<core::pack::interaction_graph::SurfacePotential>::get_instance() –> class core::pack::interaction_graph::SurfacePotential *

hASA_patch_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, patch_area: float, num_nbs: int) → float

C++: core::pack::interaction_graph::SurfacePotential::hASA_patch_energy(double, unsigned long) –> double

hpatch_score(self: pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential, patch_area: float) → float

C++: core::pack::interaction_graph::SurfacePotential::hpatch_score(double) –> double

class pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge

Bases: SymmOnTheFlyEdge

acknowledge_partial_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_ind: int, new_state: int, bumped_recent_history_index: int, new_state_recent_history_index: int) → None

C++: core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_partial_state_change(int, int, int, int) –> void

acknowledge_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_ind: int, new_state: int, bumped_recent_history_index: int, new_state_recent_history_index: int, new_energy: float) → None

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

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

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

acknowledge_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, substituted_node_index: int, curr_state_energy: float, nodes_new_state: int, bumped_recent_history_index: int, new_state_recent_history_index: int, neighbors_curr_state: int) → None

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

add_GlyCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_glycine: int, state: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_GlyCorrection_values(int, int, float, float, float, float) –> void

add_ProCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline: int, state: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_ProCorrection_values(int, int, float, float, float, float) –> void

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

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

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

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

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

C++: core::pack::interaction_graph::SymmLinearMemEdge::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

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

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

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

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

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

get_energy_for_alt_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, store_rpes: bool, changing_node_index: int, alternate_state: int, alternate_state_recent_history_index: int, other_node_curr_state: int, other_node_state_recent_history_index: int) → float

C++: core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state(bool, int, int, int, 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_glycine_correction_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, : int, : int) → bool

fullfilling base class virtual member request – however, this function does not quite

make sense for a symmetric otf ig, so this is just stubbed out to return true.

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

get_symmlinmem_ig_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge) → core::pack::interaction_graph::SymmLinearMemoryInteractionGraph

C++: core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_ig_owner() –> class core::pack::interaction_graph::SymmLinearMemoryInteractionGraph *

get_symmlinmem_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode

C++: core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_node(int) –> class core::pack::interaction_graph::SymmLinearMemNode *

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

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

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

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge) → None

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

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

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

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

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

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

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

reset_state_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge, node_index: int, state: int, recent_history_id: int) → None

C++: core::pack::interaction_graph::SymmLinearMemEdge::reset_state_energies(int, int, int) –> void

residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int, whichnode_restypegroup: int, othernode_restypegroup: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair(int, int, int, int) const –> unsigned char

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.SymmLinearMemEdge, weight: float) → None

C++: core::pack::interaction_graph::SymmLinearMemEdge::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_residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(int, int) –> void

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode

Bases: SymmOnTheFlyNode

acknowledge_last_substititon_not_committed(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → None

update bookkeeping info to acknolwedge that the last alternative state considered was not

in fact chosen for the currently assigned state.

C++: core::pack::interaction_graph::SymmLinearMemNode::acknowledge_last_substititon_not_committed() –> void

acknowledge_neighbors_partial_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_to_altered_neighbor: int, other_node_new_state: int, other_state_recent_history_index: int) → None

C++: core::pack::interaction_graph::SymmLinearMemNode::acknowledge_neighbors_partial_state_substitution(int, int, int) –> void

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

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

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

set to a particular state – updates the energies internally

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

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

set to state 0

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

bb_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the backbone on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::bb_bounding_sphere(int) const –> struct std::pair<class numeric::xyzVector<double>, double>

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

proceed to change the currently assigned state to the alternative state considered in

the last call to project_deltaE_for_substitution

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

complete_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → None

second half of the entire-graph state assignment.

C++: core::pack::interaction_graph::SymmLinearMemNode::complete_state_assignment() –> void

compute_pair_energy_for_alternate_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_making_energy_request: int) → float

comupute the interaction energy between the alternate state being considered on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_alternate_state(int) –> float

compute_pair_energy_for_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, edge_making_energy_request: int) → float

comupute the interaction energy between the currently assigned state on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_current_state(int) –> float

compute_rotamer_pair_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request: int, state_this: int, state_other: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(int, int, int) const –> float

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

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

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

C++: core::pack::interaction_graph::SymmLinearMemNode::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.SymmOnTheFlyNode) -> bool

C++: core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain() const –> bool

2. distinguish_backbone_and_sidechain(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting: bool) -> None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::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_adjacent_otf_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_adjacent_otf_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

get_adjacent_symmlinmem_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode

C++: core::pack::interaction_graph::SymmLinearMemNode::get_adjacent_symmlinmem_node(int) –> class core::pack::interaction_graph::SymmLinearMemNode *

get_asu_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the asymmetric unit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_asu_rotamer(int) const –> const class core::conformation::Residue &

get_curr_state_recent_state_id(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → int

return the “recent state id” for the currently assigned state

C++: core::pack::interaction_graph::SymmLinearMemNode::get_curr_state_recent_state_id() const –> int

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

return the index of the currently assigned state

C++: core::pack::interaction_graph::SymmLinearMemNode::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_incident_otf_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge: int) → core::pack::interaction_graph::SymmOnTheFlyEdge

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_incident_otf_edge(int) –> class core::pack::interaction_graph::SymmOnTheFlyEdge *

get_incident_symmlinmem_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, index: int) → core::pack::interaction_graph::SymmLinearMemEdge

C++: core::pack::interaction_graph::SymmLinearMemNode::get_incident_symmlinmem_edge(int) –> class core::pack::interaction_graph::SymmLinearMemEdge *

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_res_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of distinct ResidueType objects pointed to by all of the

rotamrs for this node.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_res_types() const –> int

get_num_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of ResidueType groups, as defined by the RotamerSet’s logic

for grouping different ResidueType objects which have the same “name3” and the same neighbor radius.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_restype_groups() 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_restype_group(*args, **kwargs)

Overloaded function.

1. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> pyrosetta.rosetta.utility.vector1_int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group() –> class utility::vector1<int, class std::allocator<int> > &

2. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) -> int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group(int) –> int

get_on_the_fly_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → core::pack::interaction_graph::SymmOnTheFlyInteractionGraph

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_on_the_fly_owner() –> class core::pack::interaction_graph::SymmOnTheFlyInteractionGraph *

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

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

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

return the one-body energy for the currently assigned state

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

get_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → int

C++: core::pack::interaction_graph::SymmLinearMemNode::get_recent_history_size() const –> int

get_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the requested subunit. This reference

is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(int, int) const –> const class core::conformation::Residue &

get_state_offset_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_state_offset_for_restype_group(int) const –> int

get_symmlinmem_ig_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → core::pack::interaction_graph::SymmLinearMemoryInteractionGraph

C++: core::pack::interaction_graph::SymmLinearMemNode::get_symmlinmem_ig_owner() –> class core::pack::interaction_graph::SymmLinearMemoryInteractionGraph *

get_totalE(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode) → float

return the total energy for this node; includes full energies to neighboring residues

C++: core::pack::interaction_graph::SymmLinearMemNode::get_totalE() const –> float

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, new_state: int) → None

first half of an entire-graph state assignment that avoids unnecessary energy updates

as produced in assign_state. Adjust all node’s states first, then update all energies.

C++: core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state(int) –> void

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

symmlinmem ig does not have to do anything before sim annealing begins

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

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

write internal energy and bookkeeping data to standard out

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

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

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

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

compute the change in energy induced by substituting the currently assigned state with

some alternative state

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

sc_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the sidechain of a given state on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::sc_bounding_sphere(int, int) const –> struct std::pair<class numeric::xyzVector<double>, double>

set_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_one_body_energy(int, float) –> void

set_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode, num_states_to_maintain_in_recent_history: int) → None

C++: core::pack::interaction_graph::SymmLinearMemNode::set_recent_history_size(int) –> void

set_rotamers(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>) –> void

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

state 0 represents the unasigned state

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

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

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

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

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

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

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

zero_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::zero_one_body_energy(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph

Bases: SymmOnTheFlyInteractionGraph

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

active_score_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::active_score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

add_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, node_not_neccessarily_proline: 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::SymmOnTheFlyInteractionGraph::add_GlyCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

add_ProCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, 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::SymmOnTheFlyInteractionGraph::add_ProCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

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

2. 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

3. 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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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 &

asymmetric_unit(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::asymmetric_unit() const –> unsigned long

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmLinearMemoryInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmLinearMemoryInteractionGraph) → int

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

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmOnTheFlyInteractionGraph, node: int) -> bool

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.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.SymmLinearMemoryInteractionGraph) → int

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmLinearMemoryInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_num_restype_groups() const –> int

get_num_rpe_calculations_count(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_on_the_fly_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_on_the_fly_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

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

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

get_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph) → int

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_recent_history_size() const –> unsigned long

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.SymmOnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

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

non_const_pose(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

debugging only – modify the pose during simulated annealing, if you’re so inclined

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::non_const_pose() –> class core::pose::Pose &

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

note_rpe_calculated(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → None

to be called by owned OTF node only

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_rpe_calculated() const –> void

note_short_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(int, int) –> 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.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::pose() const –> const class core::pose::Pose &

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmLinearMemoryInteractionGraph) → None

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmOnTheFlyInteractionGraph) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::reset_rpe_calculations_count() –> void

score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::score_function() const –> const class core::scoring::ScoreFunction &

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.SymmLinearMemoryInteractionGraph, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.pose.Pose) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_recent_history_size(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph, recent_history_size: int) → None

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_recent_history_size(unsigned long) –> void

set_residues_adjacent_for_subunit_pair_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, asu_node_index: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_residues_adjacent_for_subunit_pair_for_edge(int, int, int, int) –> void

set_score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function(const class core::scoring::ScoreFunction &) –> 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.SymmLinearMemoryInteractionGraph, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::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

setup_for_scoring_for_residue_energy_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::setup_for_scoring_for_residue_energy_methods() const –> const class std::list<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

symm_info(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symm_info() const –> const class core::conformation::symmetry::SymmetryInfo &

symmetric_transform(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Return the homogeneous transform to translate and rotate coordinates

originally in the asymmetric unit into a given destination subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform(unsigned long) const –> const class numeric::HomogeneousTransform<double> &

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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::zero_one_body_energy_for_node_state(int, int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge

Bases: SymmOnTheFlyEdge

acknowledge_partial_state_change(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge, node_ind: int, new_state: int) → None

C++: core::pack::interaction_graph::SymmMinimalistEdge::acknowledge_partial_state_change(int, int) –> void

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

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

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

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

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

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

add_GlyCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_glycine: int, state: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_GlyCorrection_values(int, int, float, float, float, float) –> void

add_ProCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline: int, state: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_ProCorrection_values(int, int, float, float, float, float) –> void

alt_state_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge) → float

C++: core::pack::interaction_graph::SymmMinimalistEdge::alt_state_energy() const –> float

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

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

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

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

curr_state_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge) → float

C++: core::pack::interaction_graph::SymmMinimalistEdge::curr_state_energy() const –> float

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

C++: core::pack::interaction_graph::SymmMinimalistEdge::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

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

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

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

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

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

get_energy_for_alt_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge, changing_node_index: int) → float

C++: core::pack::interaction_graph::SymmMinimalistEdge::get_energy_for_alt_state(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_glycine_correction_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, : int, : int) → bool

fullfilling base class virtual member request – however, this function does not quite

make sense for a symmetric otf ig, so this is just stubbed out to return true.

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

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

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

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

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge) → None

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

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

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

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

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

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

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

residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int, whichnode_restypegroup: int, othernode_restypegroup: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair(int, int, int, int) const –> unsigned char

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.SymmMinimalistEdge, weight: float) → None

C++: core::pack::interaction_graph::SymmMinimalistEdge::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_residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(int, int) –> void

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph

Bases: SymmOnTheFlyInteractionGraph

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

active_score_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::active_score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

add_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, node_not_neccessarily_proline: 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::SymmOnTheFlyInteractionGraph::add_GlyCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

add_ProCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, 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::SymmOnTheFlyInteractionGraph::add_ProCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

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

2. 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

3. 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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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 &

asymmetric_unit(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::asymmetric_unit() const –> unsigned long

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmMinimalistInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmMinimalistInteractionGraph) → int

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

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmOnTheFlyInteractionGraph, node: int) -> bool

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.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.SymmMinimalistInteractionGraph) → int

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmMinimalistInteractionGraph) → float

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

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_num_restype_groups() const –> int

get_num_rpe_calculations_count(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_on_the_fly_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_on_the_fly_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.SymmOnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

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

non_const_pose(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

debugging only – modify the pose during simulated annealing, if you’re so inclined

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::non_const_pose() –> class core::pose::Pose &

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

note_rpe_calculated(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → None

to be called by owned OTF node only

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_rpe_calculated() const –> void

note_short_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(int, int) –> 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.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::pose() const –> const class core::pose::Pose &

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmMinimalistInteractionGraph) → None

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmOnTheFlyInteractionGraph) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::reset_rpe_calculations_count() –> void

score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::score_function() const –> const class core::scoring::ScoreFunction &

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.SymmMinimalistInteractionGraph, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.pose.Pose) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_residues_adjacent_for_subunit_pair_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, asu_node_index: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_residues_adjacent_for_subunit_pair_for_edge(int, int, int, int) –> void

set_score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function(const class core::scoring::ScoreFunction &) –> 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.SymmMinimalistInteractionGraph, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::SymmMinimalistInteractionGraph::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

setup_for_scoring_for_residue_energy_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::setup_for_scoring_for_residue_energy_methods() const –> const class std::list<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

symm_info(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symm_info() const –> const class core::conformation::symmetry::SymmetryInfo &

symmetric_transform(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Return the homogeneous transform to translate and rotate coordinates

originally in the asymmetric unit into a given destination subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform(unsigned long) const –> const class numeric::HomogeneousTransform<double> &

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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::zero_one_body_energy_for_node_state(int, int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode

Bases: SymmOnTheFlyNode

acknowledge_last_substititon_not_committed(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode) → None

update bookkeeping info to acknolwedge that the last alternative state considered was not

in fact chosen for the currently assigned state.

C++: core::pack::interaction_graph::SymmMinimalistNode::acknowledge_last_substititon_not_committed() –> void

acknowledge_neighbors_partial_state_substitution(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_to_altered_neighbor: int, other_node_new_state: int) → None

C++: core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_partial_state_substitution(int, int) –> void

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

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

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

set to a particular state – updates the energies internally

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

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

set to state 0

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

bb_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the backbone on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::bb_bounding_sphere(int) const –> struct std::pair<class numeric::xyzVector<double>, double>

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

proceed to change the currently assigned state to the alternative state considered in

the last call to project_deltaE_for_substitution

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

complete_state_assignment(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode) → None

second half of the entire-graph state assignment.

C++: core::pack::interaction_graph::SymmMinimalistNode::complete_state_assignment() –> void

compute_pair_energy_for_alternate_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_making_energy_request: int) → float

comupute the interaction energy between the alternate state being considered on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::SymmMinimalistNode::compute_pair_energy_for_alternate_state(int) –> float

compute_pair_energy_for_current_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, edge_making_energy_request: int) → float

comupute the interaction energy between the currently assigned state on this residue and

the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

C++: core::pack::interaction_graph::SymmMinimalistNode::compute_pair_energy_for_current_state(int) –> float

compute_rotamer_pair_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request: int, state_this: int, state_other: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(int, int, int) const –> float

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

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

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

C++: core::pack::interaction_graph::SymmMinimalistNode::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.SymmOnTheFlyNode) -> bool

C++: core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain() const –> bool

2. distinguish_backbone_and_sidechain(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting: bool) -> None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::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_adjacent_otf_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_adjacent_otf_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

get_adjacent_symmin_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode

C++: core::pack::interaction_graph::SymmMinimalistNode::get_adjacent_symmin_node(int) –> class core::pack::interaction_graph::SymmMinimalistNode *

get_asu_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the asymmetric unit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_asu_rotamer(int) const –> const class core::conformation::Residue &

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

return the index of the currently assigned state

C++: core::pack::interaction_graph::SymmMinimalistNode::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_incident_otf_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge: int) → core::pack::interaction_graph::SymmOnTheFlyEdge

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_incident_otf_edge(int) –> class core::pack::interaction_graph::SymmOnTheFlyEdge *

get_incident_symmin_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, index: int) → core::pack::interaction_graph::SymmMinimalistEdge

C++: core::pack::interaction_graph::SymmMinimalistNode::get_incident_symmin_edge(int) –> class core::pack::interaction_graph::SymmMinimalistEdge *

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_res_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of distinct ResidueType objects pointed to by all of the

rotamrs for this node.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_res_types() const –> int

get_num_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of ResidueType groups, as defined by the RotamerSet’s logic

for grouping different ResidueType objects which have the same “name3” and the same neighbor radius.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_restype_groups() 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_restype_group(*args, **kwargs)

Overloaded function.

1. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> pyrosetta.rosetta.utility.vector1_int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group() –> class utility::vector1<int, class std::allocator<int> > &

2. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) -> int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group(int) –> int

get_on_the_fly_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → core::pack::interaction_graph::SymmOnTheFlyInteractionGraph

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_on_the_fly_owner() –> class core::pack::interaction_graph::SymmOnTheFlyInteractionGraph *

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

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

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

return the one-body energy for the currently assigned state

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

get_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the requested subunit. This reference

is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(int, int) const –> const class core::conformation::Residue &

get_state_offset_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_state_offset_for_restype_group(int) const –> int

get_symmin_ig_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode) → core::pack::interaction_graph::SymmMinimalistInteractionGraph

C++: core::pack::interaction_graph::SymmMinimalistNode::get_symmin_ig_owner() –> class core::pack::interaction_graph::SymmMinimalistInteractionGraph *

get_totalE(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode) → float

return the total energy for this node; includes full energies to neighboring residues

C++: core::pack::interaction_graph::SymmMinimalistNode::get_totalE() const –> float

partial_assign_state(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode, new_state: int) → None

first half of an entire-graph state assignment that avoids unnecessary energy updates

as produced in assign_state. Adjust all node’s states first, then update all energies.

C++: core::pack::interaction_graph::SymmMinimalistNode::partial_assign_state(int) –> void

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

symmin ig does not have to do anything before sim annealing begins

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

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

write internal energy and bookkeeping data to standard out

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

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

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

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

compute the change in energy induced by substituting the currently assigned state with

some alternative state

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

sc_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the sidechain of a given state on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::sc_bounding_sphere(int, int) const –> struct std::pair<class numeric::xyzVector<double>, double>

set_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_one_body_energy(int, float) –> void

set_rotamers(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>) –> void

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

state 0 represents the unasigned state

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

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

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

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

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

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

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

zero_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::zero_one_body_energy(int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge

Bases: FixedBBEdge

add_GlyCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_glycine: int, state: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_GlyCorrection_values(int, int, float, float, float, float) –> void

add_ProCorrection_values(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_not_necessarily_proline: int, state: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::add_ProCorrection_values(int, int, float, float, float, float) –> void

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

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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

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

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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_glycine_correction_for_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, node_ind: int, state: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge, : int, : int) → bool

fullfilling base class virtual member request – however, this function does not quite

make sense for a symmetric otf ig, so this is just stubbed out to return true.

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

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

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::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.SymmOnTheFlyEdge) → None

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

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

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

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

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

residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int, whichnode_restypegroup: int, othernode_restypegroup: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair(int, int, int, int) const –> unsigned char

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_residues_adjacent_for_subunit_pair(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge, which_node: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(int, int) –> void

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

fullfilling base class virtual member request – however, this funciton does not quite

make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

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

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

class pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph

Bases: FixedBBInteractionGraph

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

active_score_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::active_score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

add_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, node_not_neccessarily_proline: 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::SymmOnTheFlyInteractionGraph::add_GlyCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

add_ProCorrection_values_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, 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::SymmOnTheFlyInteractionGraph::add_ProCorrection_values_for_edge(int, int, int, int, float, float, float, float) –> void

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

2. 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

3. 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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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 &

asymmetric_unit(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::asymmetric_unit() const –> unsigned long

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::count_dynamic_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.SymmOnTheFlyInteractionGraph, node: int) -> bool

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.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.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_num_restype_groups() const –> int

get_num_rpe_calculations_count(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → int

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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_on_the_fly_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node_index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_on_the_fly_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

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

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.SymmOnTheFlyInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

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

non_const_pose(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

debugging only – modify the pose during simulated annealing, if you’re so inclined

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::non_const_pose() –> class core::pose::Pose &

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

note_rpe_calculated(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → None

to be called by owned OTF node only

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_rpe_calculated() const –> void

note_short_range_interactions_exist_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(int, int) –> 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.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::pose() const –> const class core::pose::Pose &

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.InteractionGraphBase) → None

C++: core::pack::interaction_graph::InteractionGraphBase::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.SymmOnTheFlyInteractionGraph) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::reset_rpe_calculations_count() –> void

score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::score_function() const –> const class core::scoring::ScoreFunction &

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.InteractionGraphBase, deltaE: float) → None

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

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

C++: core::pack::interaction_graph::InteractionGraphBase::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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int, one_body_energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.pose.Pose) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_residues_adjacent_for_subunit_pair_for_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, node1: int, node2: int, asu_node_index: int, other_node_subunit: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_residues_adjacent_for_subunit_pair_for_edge(int, int, int, int) –> void

set_score_function(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function(const class core::scoring::ScoreFunction &) –> 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.InteractionGraphBase, node_ind: int, new_state: int) → float

C++: core::pack::interaction_graph::InteractionGraphBase::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

setup_for_scoring_for_residue_energy_methods(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::setup_for_scoring_for_residue_energy_methods() const –> const class std::list<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

symm_info(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph) → pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symm_info() const –> const class core::conformation::symmetry::SymmetryInfo &

symmetric_transform(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph, dst_subunit: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Return the homogeneous transform to translate and rotate coordinates

originally in the asymmetric unit into a given destination subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform(unsigned long) const –> const class numeric::HomogeneousTransform<double> &

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.SymmOnTheFlyInteractionGraph, node_ind: int, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::zero_one_body_energy_for_node_state(int, int) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

Bases: FixedBBNode

add_to_one_body_energies(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, energy1b: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

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

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

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

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

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

bb_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the backbone on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::bb_bounding_sphere(int) const –> struct std::pair<class numeric::xyzVector<double>, double>

compute_rotamer_pair_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge_making_energy_request: int, state_this: int, state_other: int) → float

C++: core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(int, int, int) const –> float

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

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

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

C++: core::pack::interaction_graph::SymmOnTheFlyNode::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.SymmOnTheFlyNode) -> bool

C++: core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain() const –> bool

2. distinguish_backbone_and_sidechain(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, setting: bool) -> None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::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_adjacent_otf_node(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, index: int) → pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_adjacent_otf_node(int) –> class core::pack::interaction_graph::SymmOnTheFlyNode *

get_asu_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the asymmetric unit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_asu_rotamer(int) const –> const class core::conformation::Residue &

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_incident_otf_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, edge: int) → core::pack::interaction_graph::SymmOnTheFlyEdge

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_incident_otf_edge(int) –> class core::pack::interaction_graph::SymmOnTheFlyEdge *

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_res_types(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of distinct ResidueType objects pointed to by all of the

rotamrs for this node.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_res_types() const –> int

get_num_restype_groups(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → int

the number of ResidueType groups, as defined by the RotamerSet’s logic

for grouping different ResidueType objects which have the same “name3” and the same neighbor radius.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_restype_groups() 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_restype_group(*args, **kwargs)

Overloaded function.

1. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) -> pyrosetta.rosetta.utility.vector1_int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group() –> class utility::vector1<int, class std::allocator<int> > &

2. get_num_states_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) -> int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group(int) –> int

get_on_the_fly_owner(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode) → core::pack::interaction_graph::SymmOnTheFlyInteractionGraph

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_on_the_fly_owner() –> class core::pack::interaction_graph::SymmOnTheFlyInteractionGraph *

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

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

get_rotamer(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → pyrosetta.rosetta.core.conformation.Residue

Returns a reference to the rotamer object in the requested subunit. This reference

is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(int, int) const –> const class core::conformation::Residue &

get_state_offset_for_restype_group(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, restype_group: int) → int

C++: core::pack::interaction_graph::SymmOnTheFlyNode::get_state_offset_for_restype_group(int) const –> int

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

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

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

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

sc_bounding_sphere(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, subunit: int) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, float]

Returns a bounding sphere for the sidechain of a given state on a particular subunit.

C++: core::pack::interaction_graph::SymmOnTheFlyNode::sc_bounding_sphere(int, int) const –> struct std::pair<class numeric::xyzVector<double>, double>

set_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int, energy: float) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_one_body_energy(int, float) –> void

set_rotamers(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, rotamers: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(class std::shared_ptr<const class core::pack::rotamer_set::RotamerSet>) –> void

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

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

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

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

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

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

zero_one_body_energy(self: pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode, state: int) → None

C++: core::pack::interaction_graph::SymmOnTheFlyNode::zero_one_body_energy(int) –> void

pyrosetta.rosetta.core.pack.interaction_graph.compute_alt_weights_for_npd_hbonds(res: pyrosetta.rosetta.core.conformation.Residue, atom_hbonds: pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t, tmp_energies: pyrosetta.rosetta.utility.vector1_double, temp_weights: pyrosetta.rosetta.utility.vector1_double) → None

Compute the don_wt_alt_s and the acc_wt_alt_s from the perspective of the

input residue given the (complete) arrays of NPDHBondOPs for each atom.

Used by both the NPDHBondNode and the NPDHBondBackgroundNode, and so defined in the .cc file.

C++: core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond>, class std::allocator<class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond> > >, class std::allocator<class utility::vector1<class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond>, class std::allocator<class std::shared_ptr<struct core::pack::interaction_graph::NPDHBond> > > > > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.exposed_hydrophobic_data

Bases: pybind11_object

property exhphobe_index_

property fc_bg_

property node_index_

pyrosetta.rosetta.core.pack.interaction_graph.generate_pose_from_packer_description(pose: pyrosetta.rosetta.core.pose.Pose, packer_problem_description: str) → None

Given the description of a packer problem as generated by get_annealable_graph_summary(), pull out

and re-generate the pose.

The contents of the pose are destroyed and replaced by the pose from the description in this operation.

C++: core::pack::interaction_graph::generate_pose_from_packer_description(class core::pose::Pose &, const std::string &) –> void

pyrosetta.rosetta.core.pack.interaction_graph.get_annealable_graph_summary(*args, **kwargs)

Overloaded function.

1. get_annealable_graph_summary(igstream: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, rot_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, anngraph: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> None

2. get_annealable_graph_summary(igstream: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, rot_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, anngraph: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, short_version: bool) -> None

Given an interaction graph, get a summary describing it fully.

This is intended to be a machine-readable summary that facilitates a Rosetta interface to external annealers or optimizers.

The output stream for the summary.

The pose, for reference.

The RotamerSets object containing the set of sets of rotamers for each position.

The pre-computed interaction graph.

If true, only the interaction graph summary is returned. If false, information needed to reconstruct the pose

is also included. False by default.

Vikram K. Mulligan (vmulligan.org)

C++: core::pack::interaction_graph::get_annealable_graph_summary(std::ostream &, const class core::pose::Pose &, const class core::pack::rotamer_set::RotamerSets &, const class std::shared_ptr<const class core::pack::interaction_graph::AnnealableGraphBase> &, const bool) –> void

class pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct

Bases: pybind11_object

for storing three peices of associated data describing the recent history structure on a LinearMemNode.

property more_ancient_ptr

property more_recent_ptr

property state_in_rh

pyrosetta.rosetta.core.pack.interaction_graph.set_externally_generated_packer_solution(pose: pyrosetta.rosetta.core.pose.Pose, packer_problem_description: str, packer_solution_description: str) → None

Given a description of a packer problem, a description of the solution, and a pose to put a result in, generate

a pose representing the solution.

The contents of the pose are destroyed by this operation, and replaced by the pose described in the packer problem and the rotamers described in the solutions!

The pose, cleared and rebuilt by this operation.

A description of the packer problem, including blocks for the original pose, the rotamers, and the energies, as generated by get_annealable_graph_summary().

A solution to the packer problem, in the format of a series of lines, one for each packable position, consisting of <seqpos #> <rotamer #>.

Vikram K. Mulligan (vmulligan.org)

C++: core::pack::interaction_graph::set_externally_generated_packer_solution(class core::pose::Pose &, const std::string &, const std::string &) –> void