loop_graph

Bindings for core::scoring::loop_graph namespace

class pyrosetta.rosetta.core.scoring.loop_graph.Loop

Bases: pybind11_object

Directed edge between one position in the pose to another position. Records takeoff_pos & landing_pos (in full_model numbering). Also records ‘domain’, i.e. if there are multiple poses in a collection,

which pose.

assign(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop, src: pyrosetta.rosetta.core.scoring.loop_graph.Loop) → pyrosetta.rosetta.core.scoring.loop_graph.Loop

C++: core::scoring::loop_graph::Loop::operator=(const class core::scoring::loop_graph::Loop &) –> class core::scoring::loop_graph::Loop &

landing_domain(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop) → int

C++: core::scoring::loop_graph::Loop::landing_domain() const –> unsigned long

landing_pos(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop) → int

C++: core::scoring::loop_graph::Loop::landing_pos() const –> unsigned long

set_landing_domain(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop, setting: int) → None

C++: core::scoring::loop_graph::Loop::set_landing_domain(const unsigned long &) –> void

set_landing_pos(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop, setting: int) → None

C++: core::scoring::loop_graph::Loop::set_landing_pos(const unsigned long &) –> void

set_takeoff_domain(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop, setting: int) → None

C++: core::scoring::loop_graph::Loop::set_takeoff_domain(const unsigned long &) –> void

set_takeoff_pos(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop, setting: int) → None

C++: core::scoring::loop_graph::Loop::set_takeoff_pos(const unsigned long &) –> void

takeoff_domain(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop) → int

C++: core::scoring::loop_graph::Loop::takeoff_domain() const –> unsigned long

takeoff_pos(self: pyrosetta.rosetta.core.scoring.loop_graph.Loop) → int

C++: core::scoring::loop_graph::Loop::takeoff_pos() const –> unsigned long

class pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle, : pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle) → pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle

C++: core::scoring::loop_graph::LoopCycle::operator=(const class core::scoring::loop_graph::LoopCycle &) –> class core::scoring::loop_graph::LoopCycle &

find_index_for_loop_landing_at_domain(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle, takeoff_domain: int) → int

C++: core::scoring::loop_graph::LoopCycle::find_index_for_loop_landing_at_domain(const unsigned long &) const –> unsigned long

loop(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle, n: int) → pyrosetta.rosetta.core.scoring.loop_graph.Loop

C++: core::scoring::loop_graph::LoopCycle::loop(const unsigned long) const –> const class core::scoring::loop_graph::Loop &

loops(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle) → pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop

C++: core::scoring::loop_graph::LoopCycle::loops() const –> const class utility::vector1<class core::scoring::loop_graph::Loop, class std::allocator<class core::scoring::loop_graph::Loop> > &

size(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle) → int

C++: core::scoring::loop_graph::LoopCycle::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, : pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) → pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph

C++: core::scoring::loop_graph::LoopGraph::operator=(const class core::scoring::loop_graph::LoopGraph &) –> class core::scoring::loop_graph::LoopGraph &

check_loop_cycles_are_disjoint(*args, **kwargs)

Overloaded function.

  1. check_loop_cycles_are_disjoint(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) -> None

  2. check_loop_cycles_are_disjoint(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, verbose: bool) -> None

C++: core::scoring::loop_graph::LoopGraph::check_loop_cycles_are_disjoint(const bool) –> void

has_just_simple_cycles(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) → bool

C++: core::scoring::loop_graph::LoopGraph::has_just_simple_cycles() const –> bool

loop_cycles(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) → pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle

C++: core::scoring::loop_graph::LoopGraph::loop_cycles() const –> const class utility::vector1<class core::scoring::loop_graph::LoopCycle, class std::allocator<class core::scoring::loop_graph::LoopCycle> > &

loop_score_evaluator(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, n: int) → core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator

C++: core::scoring::loop_graph::LoopGraph::loop_score_evaluator(const unsigned long) const –> class std::shared_ptr<const class core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator>

loop_suites(*args, **kwargs)

Overloaded function.

  1. loop_suites(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

  2. loop_suites(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, include_free_loops: bool) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Returns a vector of loop_suites

If include_free_loops is turned off, loops with

takeoff_domain == 0 or landing_domain == 0 will not be included

C++: core::scoring::loop_graph::LoopGraph::loop_suites(bool) const –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

missing_residues(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_char

C++: core::scoring::loop_graph::LoopGraph::missing_residues(const class core::pose::Pose &) const –> class utility::vector1<char, class std::allocator<char> >

nmissing(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: core::scoring::loop_graph::LoopGraph::nmissing(const class core::pose::Pose &) const –> unsigned long

num_current_pose_loops(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) → int

C++: core::scoring::loop_graph::LoopGraph::num_current_pose_loops() const –> unsigned long

set_error_out_on_complex_cycles(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, setting: bool) → None

C++: core::scoring::loop_graph::LoopGraph::set_error_out_on_complex_cycles(const bool &) –> void

set_use_6D_potential(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, setting: bool) → None

C++: core::scoring::loop_graph::LoopGraph::set_use_6D_potential(const bool &) –> void

total_energy(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph) → float

C++: core::scoring::loop_graph::LoopGraph::total_energy() const –> double

update(*args, **kwargs)

Overloaded function.

  1. update(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. update(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> None

C++: core::scoring::loop_graph::LoopGraph::update(class core::pose::Pose &, const bool) –> void

update_loops(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::scoring::loop_graph::LoopGraph::update_loops(const class core::pose::Pose &) –> void

update_loops_and_cycles(self: pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph, pose_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::scoring::loop_graph::LoopGraph::update_loops_and_cycles(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.scoring.loop_graph.get_6D_trans_rot_potential_evaluator(loop_cycle: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle, loop_fixed_cost: float, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator

C++: core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(const class core::scoring::loop_graph::LoopCycle &, const double &, const class core::pose::Pose &) –> class std::shared_ptr<const class core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator>

pyrosetta.rosetta.core.scoring.loop_graph.get_loop_atom(*args, **kwargs)

Overloaded function.

  1. get_loop_atom(res: int, pose: pyrosetta.rosetta.core.pose.Pose, atom_id: pyrosetta.rosetta.core.id.AtomID, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, takeoff: bool) -> None

C++: core::scoring::loop_graph::get_loop_atom(const unsigned long, const class core::pose::Pose &, class core::id::AtomID &, class numeric::xyzVector<double> &, const bool) –> void

  1. get_loop_atom(res: int, pose: pyrosetta.rosetta.core.pose.Pose, atom_name: str, atom_id: pyrosetta.rosetta.core.id.AtomID, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::scoring::loop_graph::get_loop_atom(const unsigned long, const class core::pose::Pose &, const std::string &, class core::id::AtomID &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.core.scoring.loop_graph.get_loop_close_potential(pose: pyrosetta.rosetta.core.pose.Pose, loop_cycle: pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle, loop_fixed_cost: float, use_6D_potential: bool) → pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator

C++: core::scoring::loop_graph::get_loop_close_potential(const class core::pose::Pose &, const class core::scoring::loop_graph::LoopCycle &, const double &, const bool) –> class std::shared_ptr<const class core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator>