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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber, lh_library: protocols::loophash::LoopHashLibrary) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_string<char>) –> 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