perturbers

Bindings for protocols::loop_modeler::perturbers namespace

class pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber

Bases: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber

Sample backbone torsions using loop hash

extract_fragment(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, frag_index: int, loop_size: int) Tuple[pyrosetta.rosetta.protocols.loophash.BackboneSegment, str]

Extract the fragment information into a pair

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::extract_fragment(unsigned long, unsigned long) –> struct std::pair<class protocols::loophash::BackboneSegment, std::string >

get_backbone_segments(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, pose: pyrosetta.rosetta.core.pose.Pose, loophash_fragment_start: int, loophash_fragment_end: int) None

Find a backbone segment from the loop hash library

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::get_backbone_segments(const class core::pose::Pose &, unsigned long, unsigned long) –> void

get_name(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber) str

Perturber::get_name

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::get_name() const –> std::string

get_random_backbone_segments(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, pose: pyrosetta.rosetta.core.pose.Pose, loophash_fragment_start: int, loophash_fragment_end: int) None

Find a random backbone segment from the loop hash library

The selected fragment need not to match the leap

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::get_random_backbone_segments(const class core::pose::Pose &, unsigned long, unsigned long) –> void

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_sequence(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, value: bool) None

Set if perturb sequence

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_sequence(bool) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) None

Perturber::perturb_subset()

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) None

Perturber::perturb_subset_with_balance()

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) None
Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

random_mode(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, value: bool) None

Set if use random mode

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::random_mode(bool) –> void

seqposes_no_mutate_str(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, value: str) None

Set the sequence positions that should not be mutated

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::seqposes_no_mutate_str(std::string) –> void

use_radial_lookup(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, value: bool) None

Set if use radial loopup

C++: protocols::loop_modeler::perturbers::LoopHashPerturber::use_radial_lookup(bool) –> void