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.
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
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.
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
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.
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
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.
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
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
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.
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
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
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.
declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None
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.
find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase
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
- 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.
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
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
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.
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
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
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.
declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None
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.
find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase
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.
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
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
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.
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
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.
find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase
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.
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
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.
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
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
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.
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
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
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.
declare_edge_energies_final(self: pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph, node1: int, node2: int) -> None
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.
find_edge(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node1: int, node2: int) -> pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase
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 ¶