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protocols::loop_modeler::perturbers::LoopHashPerturber Class Reference

Sample backbone torsions using loop hash. More...

#include <LoopHashPerturber.hh>

Inheritance diagram for protocols::loop_modeler::perturbers::LoopHashPerturber:
Inheritance graph
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Public Member Functions

 LoopHashPerturber (protocols::loophash::LoopHashLibraryOP lh_library)
 constructor More...
 
std::string get_name () const override
 
void perturb_subset (core::pose::Pose const &pose, kinematic_closure::IndexList const &residues, kinematic_closure::ClosureProblemOP problem) override
 
void perturb_subset_with_balance (core::pose::Pose const &pose, kinematic_closure::IndexList const &residues, kinematic_closure::ClosureProblemOP problem) override
 
void get_backbone_segments (core::pose::Pose const &pose, core::Size loophash_fragment_start, core::Size loophash_fragment_end)
 Find a backbone segment from the loop hash library. More...
 
void get_random_backbone_segments (core::pose::Pose const &pose, core::Size loophash_fragment_start, core::Size loophash_fragment_end)
 Find a random backbone segment from the loop hash library The selected fragment need not to match the leap. More...
 
std::pair
< protocols::loophash::BackboneSegment,
std::string > 
extract_fragment (core::Size frag_index, core::Size loop_size)
 Extract the fragment information into a pair. More...
 
void use_radial_lookup (bool value)
 Set if use radial loopup. More...
 
void random_mode (bool value)
 Set if use random mode. More...
 
void perturb_sequence (bool value)
 Set if perturb sequence. More...
 
void seqposes_no_mutate_str (std::string value)
 Set the sequence positions that should not be mutated. More...
 
- Public Member Functions inherited from protocols::kinematic_closure::perturbers::Perturber
void perturb (Pose const &pose, ClosureProblemOP problem)
 Perturb all of the non-pivot residues. More...
 
void perturb_with_balance (Pose const &pose, ClosureProblemOP problem)
 Perturb all of the non-pivot residues such that detailed balance is obeyed. More...
 

Private Types

typedef utility::vector1
< std::pair
< protocols::loophash::BackboneSegment,
std::string > > 
BackboneSegments
 

Private Attributes

protocols::loophash::LoopHashLibraryOP lh_library_
 
bool use_radial_lookup_ = true
 
bool random_mode_ = false
 
bool perturb_sequence_ = false
 
std::string seqposes_no_mutate_str_
 
BackboneSegments bb_segs_
 
numeric::geometry::hashing::Real6 last_loop_transform_
 

Detailed Description

Sample backbone torsions using loop hash.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::loop_modeler::perturbers::LoopHashPerturber::LoopHashPerturber ( protocols::loophash::LoopHashLibraryOP  lh_library)

constructor

References lh_library_.

Member Function Documentation

std::pair< protocols::loophash::BackboneSegment, std::string > protocols::loop_modeler::perturbers::LoopHashPerturber::extract_fragment ( core::Size  frag_index,
core::Size  loop_size 
)

Extract the fragment information into a pair.

References lh_library_.

Referenced by get_backbone_segments(), and get_random_backbone_segments().

void protocols::loop_modeler::perturbers::LoopHashPerturber::get_backbone_segments ( core::pose::Pose const &  pose,
core::Size  loophash_fragment_start,
core::Size  loophash_fragment_end 
)
std::string protocols::loop_modeler::perturbers::LoopHashPerturber::get_name ( ) const
inlineoverridevirtual
void protocols::loop_modeler::perturbers::LoopHashPerturber::get_random_backbone_segments ( core::pose::Pose const &  pose,
core::Size  loophash_fragment_start,
core::Size  loophash_fragment_end 
)

Find a random backbone segment from the loop hash library The selected fragment need not to match the leap.

References bb_segs_, extract_fragment(), and lh_library_.

Referenced by perturb_subset().

void protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_sequence ( bool  value)
inline

Set if perturb sequence.

References perturb_sequence_.

void protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset ( core::pose::Pose const &  pose,
kinematic_closure::IndexList const &  residues,
kinematic_closure::ClosureProblemOP  problem 
)
overridevirtual
void protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset_with_balance ( core::pose::Pose const &  pose,
kinematic_closure::IndexList const &  residues,
kinematic_closure::ClosureProblemOP  problem 
)
overridevirtual
void protocols::loop_modeler::perturbers::LoopHashPerturber::random_mode ( bool  value)
inline

Set if use random mode.

References random_mode_.

void protocols::loop_modeler::perturbers::LoopHashPerturber::seqposes_no_mutate_str ( std::string  value)
inline

Set the sequence positions that should not be mutated.

References seqposes_no_mutate_str_.

void protocols::loop_modeler::perturbers::LoopHashPerturber::use_radial_lookup ( bool  value)
inline

Set if use radial loopup.

References use_radial_lookup_.

Member Data Documentation

BackboneSegments protocols::loop_modeler::perturbers::LoopHashPerturber::bb_segs_
private
numeric::geometry::hashing::Real6 protocols::loop_modeler::perturbers::LoopHashPerturber::last_loop_transform_
private

Referenced by get_backbone_segments().

protocols::loophash::LoopHashLibraryOP protocols::loop_modeler::perturbers::LoopHashPerturber::lh_library_
private
bool protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_sequence_ = false
private

Referenced by perturb_sequence(), and perturb_subset().

bool protocols::loop_modeler::perturbers::LoopHashPerturber::random_mode_ = false
private

Referenced by perturb_subset(), and random_mode().

std::string protocols::loop_modeler::perturbers::LoopHashPerturber::seqposes_no_mutate_str_
private
bool protocols::loop_modeler::perturbers::LoopHashPerturber::use_radial_lookup_ = true
private

The documentation for this class was generated from the following files: