interaction_graph

Bindings for protocols::flexpack::interaction_graph namespace

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge

Bases: EdgeBase

acknowledge_partial_state_assignment(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

C++: protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

alt_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy() const –> float

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → int

C++: protocols::flexpack::interaction_graph::FlexbbEdge::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

cur_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy() const –> float

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_nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → bool

C++: protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg() const –> bool

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

note_state_substitution_accepted(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

Copy alt data to current data after a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted() –> void

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

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

reset_alternate_states_for_uncommited_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

After a rejected state substitution, the FlexbbNode will call this function

to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution() –> 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_alt_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate

states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_

C++: protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

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

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

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

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

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbIGFactory

Bases: pybind11_object

static create_flexbb_interaction_graph(task: pyrosetta.rosetta.core.pack.task.PackerTask, flexrots: protocols::flexpack::rotamer_set::FlexbbRotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → protocols::flexpack::interaction_graph::FlexbbInteractionGraph

C++: protocols::flexpack::interaction_graph::FlexbbIGFactory::create_flexbb_interaction_graph(const class core::pack::task::PackerTask &, const class protocols::flexpack::rotamer_set::FlexbbRotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> class std::shared_ptr<class protocols::flexpack::interaction_graph::FlexbbInteractionGraph>

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph

Bases: InteractionGraphBase

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

class Subsitution

Bases: pybind11_object

Members:

SC_ONLY

BOTH_SC_AND_BB

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

property name

property value

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

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

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

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

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

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

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

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

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

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

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

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

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

commit_considered_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rotamer_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → float

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::commit_considered_backbone_move(class ObjexxFCL::FArray1<int> &) –> float

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

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

consider_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb_id: int, delta_energy: float, prev_flexseg_energy: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_backbone_move(int, float &, float &, bool &, int &) –> void

consider_bbmove_w_state_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_flexseg: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_bbmove_w_state_substitution(int, int, float &, float &, bool &, int &) –> void

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

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

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

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

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::count_dynamic_memory() const –> unsigned int

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

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

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

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

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

Iterates over all edges and calls declare_energies_final() on

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

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

test: have we arrived at the edge list end?

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

find_edge(*args, **kwargs)

Overloaded function.

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

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

Find an edge and return a nonconst pointer to it.

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

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

flexseg_members(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

get_accessible_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, move_mode: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states(enum protocols::flexpack::interaction_graph::FlexbbInteractionGraph::Subsitution, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_backbone_currently_assigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bbid: int) → bool

Is the backbone conformation (in the global enumertion of backbone conformations) already

assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_currently_assigned(int) const –> bool

get_backbone_list(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bblist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state(int, 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.InteractionGraphBase) → int

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

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

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

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

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

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

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

get_enforce_bb_contiguity(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → bool

FlexbbNodes will ask: am I allowed to have a state that breaks the backbone?

There are brief periods when the backbone is “broken” as the graph assigns new states to nodes on the same flexible segment.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_enforce_bb_contiguity() const –> bool

get_flexseg_bb_offset(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg_id: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset(int) const –> int

get_flexseg_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb(int) const –> int

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_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types() 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_states_per_backbone_for_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node(int, int) const –> int

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

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

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

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

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

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

increment_count_nodes_in_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → None

Owner keeps a count of the number of nodes undergoing a

simultaneous rotamer substitution as the backbone moves.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg() –> void

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.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node1: int, node2: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg(int, int) const –> bool

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

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

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

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

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

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

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

iterate across edges and nodes and allow them to prepare

for simulated annealing

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

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

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

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

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

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

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

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

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

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

set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

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

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

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

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

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

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

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

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

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

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

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

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) → None

Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode

Bases: NodeBase

add_to_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energy(int, float) –> void

alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alt_bb() const –> int

alternate_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state() const –> int

alternate_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

alternate_state_is_being_considered(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered() const –> bool

alternate_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy() const –> float

alternate_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_total_energy() const –> float

alternate_state_two_body_energies(*args, **kwargs)

Overloaded function.

1. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) -> pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

2. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, ind: int) -> float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies(int) const –> float

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

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

closest_state_on_alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb() const –> const class ObjexxFCL::FArray2D<int> &

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::count_dynamic_memory() const –> unsigned int

count_energy_to_node_in_my_fragtotalE(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, edge_index: int) → bool

Convention for acumulating energies between flexsegmates during a backbone move:

The smaller-indexed node counts the interaction, the larger-indexed node does not.

C++: protocols::flexpack::interaction_graph::FlexbbNode::count_energy_to_node_in_my_fragtotalE(int) const –> bool

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

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

curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_bb() const –> int

curr_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy() const –> float

curr_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy() const –> float

curr_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies() –> const class utility::vector1<float, class std::allocator<float> > &

current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state() const –> int

current_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

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

edge_connects_flexsegmate(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate() const –> const class utility::vector1<bool, class std::allocator<bool> > &

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 *

getNumStatesPerAAPerBB(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa: int) → pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::getNumStatesPerAAPerBB(int) –> class ObjexxFCL::FArray1A<int>

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_all_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_all_states(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

get_backbone_for_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state() const –> int

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_bb_for_state(int) const –> int

get_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::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_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones() 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_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa_type: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_aa_type_for_bb(int, int) const –> int

get_num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb(int) const –> int

get_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_one_body_energy(int) const –> float

get_state_offset_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_state_offset_for_bb(int) const –> int

get_states_on_curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state_list: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_states_on_curr_bb(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

inform_edges_of_alt_state_before_bbjump(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump() –> bool

num_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

Read access to private data to both derived classes and the world

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types() const –> int

num_bbconfs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_bbconfs() const –> int

num_states_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::one_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

prepare_for_simulated_annealing(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::print_internal_energies() –> void

set_amino_acid_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_closest_states_on_other_bbs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(const class ObjexxFCL::FArray2D<int> &) –> void

set_num_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nbbconfs: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones(int) –> void

set_num_states_per_backbone(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(const class utility::vector1<int, class std::allocator<int> > &) –> void

state_has_same_backbone_as_current(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_has_same_backbone_as_current(int) const –> bool

state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_info(int) const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

state_offsets_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

state_offsets_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

state_unassigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums() –> void

update_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_one_body_energy(int, float) –> void

write_current_state_to_state_array(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nodes_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array(class ObjexxFCL::FArray1<int> &) –> void

zero_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

Bases: SparseMatrixIndex

assign(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex, : pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::operator=(const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

get_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → int

C++: core::pack::interaction_graph::SparseMatrixIndex::get_aa_type() const –> int

get_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → int

C++: protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb() const –> int

get_state_ind_for_this_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex) → int

C++: core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type() const –> int

set_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, aa: int) → None

C++: core::pack::interaction_graph::SparseMatrixIndex::set_aa_type(int) –> void

set_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex, bb: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::set_bb(int) –> void

set_state_ind_for_this_aa_type(self: pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex, state_ind: int) → None

C++: core::pack::interaction_graph::SparseMatrixIndex::set_state_ind_for_this_aa_type(int) –> void

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge

Bases: OTFFlexbbEdge

acknowledge_partial_state_assignment(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

C++: protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

acknowledge_state_zeroed(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge, node_index: int) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_state_zeroed(int) –> void

acknowledge_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge, node_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(int) –> void

alt_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy() const –> float

compute_altbbconf_alternate_state_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy() –> float

compute_samebbconf_alternate_state_energy_first_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node() –> float

compute_samebbconf_alternate_state_energy_second_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node() –> float

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge) → int

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::count_dynamic_memory() const –> unsigned int

count_static_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge) → int

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::count_static_memory() const –> unsigned int

cur_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy() const –> float

declare_energies_final(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge) → None

Virtual functions from EdgeBase

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::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_alt_stateE(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_alt_stateE() –> 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_nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → bool

C++: protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg() const –> bool

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

note_long_range_interactions_exist(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist() –> void

note_state_substitution_accepted(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

Copy alt data to current data after a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted() –> void

otfedge_note_substitution_accepted(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::otfedge_note_substitution_accepted() –> void

prepare_for_simulated_annealing(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::prepare_for_simulated_annealing() –> void

print_alt_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies() const –> void

reset_alternate_states_for_uncommited_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

After a rejected state substitution, the FlexbbNode will call this function

to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution() –> 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.protocols.flexpack.interaction_graph.OTFFlexbbEdge, node_not_necessarily_glycine: int, state: int, other_bb: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values(int, int, int, float, float, float, float) –> void

set_ProCorrection_values(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge, node_not_necessarily_proline: int, state: int, other_bb: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_ProCorrection_values(int, int, int, float, float, float, float) –> void

set_alt_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate

states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_

C++: protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

set_edge_weight(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge, weight: float) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph

Bases: OTFFlexbbInteractionGraph

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

class Subsitution

Bases: pybind11_object

Members:

SC_ONLY

BOTH_SC_AND_BB

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

property name

property value

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

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

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

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

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

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

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

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

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

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

blanket_assign_state_0(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rotamer_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → float

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::commit_considered_backbone_move(class ObjexxFCL::FArray1<int> &) –> float

commit_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution() –> float

consider_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, bb_id: int, delta_energy: float, prev_flexseg_energy: float, valid_motion: bool, num_nodes_changing_state: int) → None

Virtual functions from FlexbbInteractionGraph

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(int, float &, float &, bool &, int &) –> void

consider_bbmove_w_state_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_flexseg: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution(int, int, float &, float &, bool &, int &) –> void

consider_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_node: float) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::count_dynamic_memory() const –> unsigned int

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

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

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

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

debug_note_accepted_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution() –> void

debug_note_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, alt_rotamer: pyrosetta.rosetta.core.conformation.Residue, index: int) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(const class core::conformation::Residue &, int) –> void

debug_note_projected_deltaE_of_considered_substitution(*args, **kwargs)

Overloaded function.

1. debug_note_projected_deltaE_of_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, deltaE: float, node_alt_total: float) -> None

2. debug_note_projected_deltaE_of_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, deltaE: float, node_alt_total: float, require_match: bool) -> None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(float, float, bool) –> void

debug_note_rejected_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_rejected_substitution() –> void

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

Iterates over all edges and calls declare_energies_final() on

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

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

test: have we arrived at the edge list end?

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

find_edge(*args, **kwargs)

Overloaded function.

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

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

Find an edge and return a nonconst pointer to it.

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

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

flexseg_members(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

get_accessible_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, move_mode: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states(enum protocols::flexpack::interaction_graph::FlexbbInteractionGraph::Subsitution, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_backbone_currently_assigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bbid: int) → bool

Is the backbone conformation (in the global enumertion of backbone conformations) already

assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_currently_assigned(int) const –> bool

get_backbone_list(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bblist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state(int, 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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_current_state_assignment() –> float

get_energy_sum_for_vertex_group(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, group_id: int) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_sum_for_vertex_group(int) –> float

get_enforce_bb_contiguity(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → bool

FlexbbNodes will ask: am I allowed to have a state that breaks the backbone?

There are brief periods when the backbone is “broken” as the graph assigns new states to nodes on the same flexible segment.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_enforce_bb_contiguity() const –> bool

get_flexseg_bb_offset(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg_id: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset(int) const –> int

get_flexseg_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb(int) const –> int

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_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types() 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_states_per_backbone_for_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node(int, 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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, node: int, state: int) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_one_body_energy_for_node_state(int, int) –> float

get_pose(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

Edges request the pose and the score function at the time of their creation.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_scorefxn(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_count_nodes_in_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → None

Owner keeps a count of the number of nodes undergoing a

simultaneous rotamer substitution as the backbone moves.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg() –> void

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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

Virtual functions from InteractionGraphBase

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node1: int, node2: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg(int, int) const –> bool

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int) → None

Informs the edge connecting nodes 1 and 2 that they require long range interactions.

Note – the edge must already exist.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

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

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

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

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

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

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

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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int, node_not_necessarily_glycine: int, state: int, other_bb: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_GlyCorrection_values_for_edge(int, int, int, int, int, float, float, float, float) –> void

set_ProCorrection_values_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int, node_not_necessarily_proline: int, state: int, other_bb: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_ProCorrection_values_for_edge(int, 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.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, deltaE: float) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_errorfull_deltaE_threshold(float) –> void

set_network_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, node_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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_pose(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

Pose must be set before any edges are added to the graph.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Score function must be set before any edges are added to the graph.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

set_state_for_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph, node_ind: int, new_state: int) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node(int, int) –> float

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode

Bases: OTFFlexbbNode

acknowledge_neighbors_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, which_edge: int, alternate_energy: float) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::acknowledge_neighbors_substitution(int, float) –> void

add_to_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energy(int, float) –> void

alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alt_bb() const –> int

alternate_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state() const –> int

alternate_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

alternate_state_is_being_considered(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered() const –> bool

alternate_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy() const –> float

alternate_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_total_energy() const –> float

alternate_state_two_body_energies(*args, **kwargs)

Overloaded function.

1. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) -> pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

2. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, ind: int) -> float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies(int) const –> float

assign_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, new_state: int) → float

assign a new state to this node and return the change in energy induced

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_state(int) –> float

assign_zero_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → None

Virtual functions from NodeBase not covered by FlexbbNode

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state() –> void

bounding_radius_for_rotamers(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, aatype: int, bb: int) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers(int, int) const –> double

closest_state_on_alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb() const –> const class ObjexxFCL::FArray2D<int> &

commit_alt_bb_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, state_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(class ObjexxFCL::FArray1<int> &) –> void

commit_considered_substitution(*args, **kwargs)

Overloaded function.

1. commit_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) -> None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution() –> void

2. commit_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, state_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) -> None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(class ObjexxFCL::FArray1<int> &) –> void

complete_partial_state_assignment(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → None

See description of partially_assign_state.

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment() –> void

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → int

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::count_dynamic_memory() const –> unsigned int

count_energy_to_node_in_my_fragtotalE(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, edge_index: int) → bool

Convention for acumulating energies between flexsegmates during a backbone move:

The smaller-indexed node counts the interaction, the larger-indexed node does not.

C++: protocols::flexpack::interaction_graph::FlexbbNode::count_energy_to_node_in_my_fragtotalE(int) const –> bool

count_static_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → int

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::count_static_memory() const –> unsigned int

curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_bb() const –> int

curr_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy() const –> float

curr_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy() const –> float

curr_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies() –> const class utility::vector1<float, class std::allocator<float> > &

current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state() const –> int

current_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

declare_all_rotamers_initialized(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized() –> void

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

edge_connects_flexsegmate(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate() const –> const class utility::vector1<bool, class std::allocator<bool> > &

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 *

getNumStatesPerAAPerBB(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa: int) → pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::getNumStatesPerAAPerBB(int) –> class ObjexxFCL::FArray1A<int>

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_all_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_all_states(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

get_backbone_for_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state() const –> int

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_bb_for_state(int) const –> int

get_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_current_state() const –> int

get_frag_energy_for_alt_bb_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state() –> float

get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → float

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total() –> 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_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones() 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_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa_type: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_aa_type_for_bb(int, int) const –> int

get_num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb(int) const –> int

get_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_one_body_energy(int) const –> float

get_state_offset_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_state_offset_for_bb(int) const –> int

get_states_on_curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state_list: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_states_on_curr_bb(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

inform_edges_of_alt_state_before_bbjump(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump() –> bool

num_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

Read access to private data to both derived classes and the world

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types() const –> int

num_bbconfs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_bbconfs() const –> int

num_states_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::one_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

partially_assign_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, new_state: int) → None

For assinging network states to the interaction graph: when substituting

two adjacent nodes i and j from states r and s to states r’ and s’, this function, along with its partner function, complete_partial_state_assignment, guarantees that neither the energies r’ with s nor s’ with r are computed which would be wasteful. This function is meant to be called by the owning interaction graph and not meant to be called by the outside world.

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state(int) –> void

prepare_for_altbb_move_to_closest_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, alt_bb: int) → bool

Set the alternate state to be the one on the alternate backbone

most similar to the currently assigned state. Traverse incident edges and inform them of the alternate state being considered at this node. Return true if the alternate state is valid.

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state(int) –> bool

prepare_for_altbb_move_to_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, alt_state: int) → bool

Traverse incident edges and inform them of the alternate

state being considered at this node. Return true if the alternate state is valid.

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(int) –> bool

prepare_for_simulated_annealing(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::print_internal_energies() –> void

project_deltaE_for_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode, alternate_state: int, prev_energy_for_node: float) → float

Other functions

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(int, float &) –> float

resolve_uncommitted_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution() –> void

rotamer(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, index: int) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer(int) const –> const class core::conformation::Residue &

rotamer_is_glycine(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine(int) const –> bool

rotamer_is_proline(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline(int) const –> bool

set_amino_acid_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_closest_states_on_other_bbs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(const class ObjexxFCL::FArray2D<int> &) –> void

set_num_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nbbconfs: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones(int) –> void

set_num_states_per_backbone(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_rotamer(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer(int, class std::shared_ptr<const class core::conformation::Residue>) –> void

state_has_same_backbone_as_current(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_has_same_backbone_as_current(int) const –> bool

state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_info(int) const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

state_offsets_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

state_offsets_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

state_unassigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums() –> void

update_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_one_body_energy(int, float) –> void

write_current_state_to_state_array(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nodes_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array(class ObjexxFCL::FArray1<int> &) –> void

zero_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge

Bases: FlexbbEdge

acknowledge_partial_state_assignment(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

C++: protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

alt_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy() const –> float

compute_altbbconf_alternate_state_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy() –> float

compute_samebbconf_alternate_state_energy_first_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node() –> float

compute_samebbconf_alternate_state_energy_second_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node() –> float

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → int

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::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

cur_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → float

C++: protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy() const –> float

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_nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → bool

C++: protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg() const –> bool

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

note_long_range_interactions_exist(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist() –> void

note_state_substitution_accepted(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

Copy alt data to current data after a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted() –> void

otfedge_note_substitution_accepted(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::otfedge_note_substitution_accepted() –> void

prepare_for_simulated_annealing(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing() –> void

print_alt_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies() const –> void

reset_alternate_states_for_uncommited_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge) → None

After a rejected state substitution, the FlexbbNode will call this function

to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution

C++: protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution() –> 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.protocols.flexpack.interaction_graph.OTFFlexbbEdge, node_not_necessarily_glycine: int, state: int, other_bb: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values(int, int, int, float, float, float, float) –> void

set_ProCorrection_values(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge, node_not_necessarily_proline: int, state: int, other_bb: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_ProCorrection_values(int, int, int, float, float, float, float) –> void

set_alt_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge, node_index: int, new_state: int, state_info: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex) → None

Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate

states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_

C++: protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state(int, int, const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &) –> void

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

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

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

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

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph

Bases: FlexbbInteractionGraph

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

class Subsitution

Bases: pybind11_object

Members:

SC_ONLY

BOTH_SC_AND_BB

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

property name

property value

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

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

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

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

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

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

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

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

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

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

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

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

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

commit_considered_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rotamer_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → float

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::commit_considered_backbone_move(class ObjexxFCL::FArray1<int> &) –> float

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

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

consider_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb_id: int, delta_energy: float, prev_flexseg_energy: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_backbone_move(int, float &, float &, bool &, int &) –> void

consider_bbmove_w_state_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_flexseg: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_bbmove_w_state_substitution(int, int, float &, float &, bool &, int &) –> void

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

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

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

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

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::count_dynamic_memory() const –> unsigned int

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

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

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

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

debug_note_accepted_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution() –> void

debug_note_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, alt_rotamer: pyrosetta.rosetta.core.conformation.Residue, index: int) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(const class core::conformation::Residue &, int) –> void

debug_note_projected_deltaE_of_considered_substitution(*args, **kwargs)

Overloaded function.

1. debug_note_projected_deltaE_of_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, deltaE: float, node_alt_total: float) -> None

2. debug_note_projected_deltaE_of_considered_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, deltaE: float, node_alt_total: float, require_match: bool) -> None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(float, float, bool) –> void

debug_note_rejected_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_rejected_substitution() –> void

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

Iterates over all edges and calls declare_energies_final() on

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

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

test: have we arrived at the edge list end?

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

find_edge(*args, **kwargs)

Overloaded function.

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

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

Find an edge and return a nonconst pointer to it.

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

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

flexseg_members(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

get_accessible_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, move_mode: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states(enum protocols::flexpack::interaction_graph::FlexbbInteractionGraph::Subsitution, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_backbone_currently_assigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bbid: int) → bool

Is the backbone conformation (in the global enumertion of backbone conformations) already

assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_currently_assigned(int) const –> bool

get_backbone_list(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bblist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state(int, 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.InteractionGraphBase) → int

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

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

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

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

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

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

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

get_enforce_bb_contiguity(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → bool

FlexbbNodes will ask: am I allowed to have a state that breaks the backbone?

There are brief periods when the backbone is “broken” as the graph assigns new states to nodes on the same flexible segment.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_enforce_bb_contiguity() const –> bool

get_flexseg_bb_offset(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg_id: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset(int) const –> int

get_flexseg_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb(int) const –> int

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_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types() 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_states_per_backbone_for_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node(int, int) const –> int

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

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

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

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

get_pose(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → pyrosetta.rosetta.core.pose.Pose

Edges request the pose and the score function at the time of their creation.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_scorefxn(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_count_nodes_in_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → None

Owner keeps a count of the number of nodes undergoing a

simultaneous rotamer substitution as the backbone moves.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg() –> void

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.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, : pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node1: int, node2: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg(int, int) const –> bool

note_long_range_interactions_exist_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int) → None

Informs the edge connecting nodes 1 and 2 that they require long range interactions.

Note – the edge must already exist.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::note_long_range_interactions_exist_for_edge(int, int) –> void

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

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

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

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

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

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

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

iterate across edges and nodes and allow them to prepare

for simulated annealing

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

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

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

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

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

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

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

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

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

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

set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

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

set_GlyCorrection_values_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int, node_not_necessarily_glycine: int, state: int, other_bb: int, bb_nonglybb_E: float, bb_glybb_E: float, sc_nonglybb_E: float, sc_glybb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_GlyCorrection_values_for_edge(int, int, int, int, int, float, float, float, float) –> void

set_ProCorrection_values_for_edge(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, node1: int, node2: int, node_not_necessarily_proline: int, state: int, other_bb: int, bb_nonprobb_E: float, bb_probb_E: float, sc_nonprobb_E: float, sc_probb_E: float) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_ProCorrection_values_for_edge(int, int, int, int, int, float, float, float, float) –> void

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

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

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

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

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

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

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

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

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

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

set_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.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

Pose must be set before any edges are added to the graph.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_pose(const class core::pose::Pose &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Score function must be set before any edges are added to the graph.

C++: protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode

Bases: FlexbbNode

add_to_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, energies: pyrosetta.rosetta.ObjexxFCL.FArray1_float_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energies(class ObjexxFCL::FArray1<float> &) –> void

add_to_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energy(int, float) –> void

alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alt_bb() const –> int

alternate_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state() const –> int

alternate_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

alternate_state_is_being_considered(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered() const –> bool

alternate_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy() const –> float

alternate_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_total_energy() const –> float

alternate_state_two_body_energies(*args, **kwargs)

Overloaded function.

1. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) -> pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

2. alternate_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, ind: int) -> float

C++: protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies(int) const –> float

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

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

bounding_radius_for_rotamers(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, aatype: int, bb: int) → float

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers(int, int) const –> double

closest_state_on_alt_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb() const –> const class ObjexxFCL::FArray2D<int> &

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode) → int

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::count_dynamic_memory() const –> unsigned int

count_energy_to_node_in_my_fragtotalE(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, edge_index: int) → bool

Convention for acumulating energies between flexsegmates during a backbone move:

The smaller-indexed node counts the interaction, the larger-indexed node does not.

C++: protocols::flexpack::interaction_graph::FlexbbNode::count_energy_to_node_in_my_fragtotalE(int) const –> bool

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

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

curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_bb() const –> int

curr_state_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy() const –> float

curr_state_total_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy() const –> float

curr_state_two_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies() –> const class utility::vector1<float, class std::allocator<float> > &

current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state() const –> int

current_state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::current_state_info() const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

declare_all_rotamers_initialized(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized() –> void

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

edge_connects_flexsegmate(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate() const –> const class utility::vector1<bool, class std::allocator<bool> > &

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 *

getNumStatesPerAAPerBB(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa: int) → pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::getNumStatesPerAAPerBB(int) –> class ObjexxFCL::FArray1A<int>

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_all_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_all_states(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

get_backbone_for_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state() const –> int

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_bb_for_state(int) const –> int

get_current_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::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_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones() 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_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, aa_type: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_aa_type_for_bb(int, int) const –> int

get_num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb(int) const –> int

get_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → float

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_one_body_energy(int) const –> float

get_state_offset_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, bbconf: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_state_offset_for_bb(int) const –> int

get_states_on_curr_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state_list: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::get_states_on_curr_bb(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, int) const –> void

inform_edges_of_alt_state_before_bbjump(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump() –> bool

num_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

Read access to private data to both derived classes and the world

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types() const –> int

num_bbconfs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_bbconfs() const –> int

num_states_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

num_states_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_float

C++: protocols::flexpack::interaction_graph::FlexbbNode::one_body_energies() const –> const class utility::vector1<float, class std::allocator<float> > &

prepare_for_simulated_annealing(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::prepare_for_simulated_annealing() –> void

print(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::print() const –> void

print_internal_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::print_internal_energies() –> void

rotamer(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, index: int) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer(int) const –> const class core::conformation::Residue &

rotamer_is_glycine(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine(int) const –> bool

rotamer_is_proline(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline(int) const –> bool

set_amino_acid_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_closest_states_on_other_bbs(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(const class ObjexxFCL::FArray2D<int> &) –> void

set_num_distinct_backbones(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nbbconfs: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones(int) –> void

set_num_states_per_backbone(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, : pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_rotamer(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode, state: int, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer(int, class std::shared_ptr<const class core::conformation::Residue>) –> void

state_has_same_backbone_as_current(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_has_same_backbone_as_current(int) const –> bool

state_info(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int) → pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_info(int) const –> const class protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex &

state_offsets_for_aa_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb() –> const class ObjexxFCL::FArray2D<int> &

state_offsets_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → pyrosetta.rosetta.utility.vector1_int

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_bb() –> const class utility::vector1<int, class std::allocator<int> > &

state_unassigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → bool

C++: protocols::flexpack::interaction_graph::FlexbbNode::state_unassigned() const –> bool

update_internal_energy_sums(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums() –> void

update_one_body_energy(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, state: int, energy: float) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::update_one_body_energy(int, float) –> void

write_current_state_to_state_array(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode, nodes_states: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array(class ObjexxFCL::FArray1<int> &) –> void

zero_one_body_energies(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode) → None

C++: protocols::flexpack::interaction_graph::FlexbbNode::zero_one_body_energies() –> void

class pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph

Bases: FlexbbInteractionGraph

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

class Subsitution

Bases: pybind11_object

Members:

SC_ONLY

BOTH_SC_AND_BB

BOTH_SC_AND_BB = <Subsitution.BOTH_SC_AND_BB: 1>

SC_ONLY = <Subsitution.SC_ONLY: 0>

property name

property value

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

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

add_to_nodes_one_body_energy(*args, **kwargs)

Overloaded function.

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

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

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

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

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

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

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

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

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

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

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

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

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

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

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

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

commit_considered_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rotamer_on_node: pyrosetta.rosetta.ObjexxFCL.FArray1_int_t) → float

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::commit_considered_backbone_move(class ObjexxFCL::FArray1<int> &) –> float

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

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

consider_backbone_move(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb_id: int, delta_energy: float, prev_flexseg_energy: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_backbone_move(int, float &, float &, bool &, int &) –> void

consider_bbmove_w_state_substitution(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node_ind: int, new_state: int, delta_energy: float, prev_energy_for_flexseg: float, valid_motion: bool, num_nodes_changing_state: int) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_bbmove_w_state_substitution(int, int, float &, float &, bool &, int &) –> void

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

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

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

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

count_dynamic_memory(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::count_dynamic_memory() const –> unsigned int

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

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

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

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

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

Iterates over all edges and calls declare_energies_final() on

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

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

test: have we arrived at the edge list end?

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

find_edge(*args, **kwargs)

Overloaded function.

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

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

Find an edge and return a nonconst pointer to it.

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

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

flexseg_members(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

get_accessible_states(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, move_mode: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution, rotlist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states(enum protocols::flexpack::interaction_graph::FlexbbInteractionGraph::Subsitution, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_backbone_currently_assigned(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bbid: int) → bool

Is the backbone conformation (in the global enumertion of backbone conformations) already

assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_currently_assigned(int) const –> bool

get_backbone_list(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bblist: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_bb_for_state(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, state: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state(int, 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.InteractionGraphBase) → int

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

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

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

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

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

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

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

get_enforce_bb_contiguity(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → bool

FlexbbNodes will ask: am I allowed to have a state that breaks the backbone?

There are brief periods when the backbone is “broken” as the graph assigns new states to nodes on the same flexible segment.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_enforce_bb_contiguity() const –> bool

get_flexseg_bb_offset(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, flexseg_id: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset(int) const –> int

get_flexseg_for_bb(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb(int) const –> int

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_aa_types(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types() 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_states_per_backbone_for_node(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node: int, bb: int) → int

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node(int, int) const –> int

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

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

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

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

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

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

increment_count_nodes_in_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph) → None

Owner keeps a count of the number of nodes undergoing a

simultaneous rotamer substitution as the backbone moves.

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg() –> void

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.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → None

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(const class core::pack_basic::RotamerSetsBase &) –> void

nodes_from_same_flexseg(self: pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph, node1: int, node2: int) → bool

C++: protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg(int, int) const –> bool

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

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

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

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

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

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

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

iterate across edges and nodes and allow them to prepare

for simulated annealing

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

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

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

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

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

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

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

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

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

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

set the Graph’s (single) edge list iterator to the beginning of the edge list

for a particular node

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

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

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

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

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

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

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

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

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

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

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

set_onebody_energies_multithreaded(self: pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase, node_index: int, rotset: core::pack::rotamer_set::RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, thread_assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) → None

Compute and store the onebody energy for all rotamers at a position. Safe for

a multithreaded context.

Requires that the number of states was already set.

Vikram K. Mulligan (vmulligan.org).

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

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

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

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

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

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

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

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

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

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

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