Sample backbone torsions using loop hash. More...

#include <LoopHashPerturber.hh>

Inheritance diagram for protocols::loop_modeler::perturbers::LoopHashPerturber:

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

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

private

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
	)

Find a backbone segment from the loop hash library.

References bb_segs_, extract_fragment(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), last_loop_transform_, lh_library_, and use_radial_lookup_.

Referenced by perturb_subset().

std::string protocols::loop_modeler::perturbers::LoopHashPerturber::get_name ( ) const

inlineoverridevirtual

Implements protocols::kinematic_closure::perturbers::Perturber.

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

Implements protocols::kinematic_closure::perturbers::Perturber.

References core::chemical::aa_from_oneletter_code(), bb_segs_, get_backbone_segments(), get_random_backbone_segments(), core::pose::get_resnum_list(), protocols::ligand_docking::ga_ligand_dock::mutate(), core::chemical::name_from_aa(), perturb_sequence_, random_mode_, seqposes_no_mutate_str_, protocols::loops::start, and protocols::loops::stop.

Referenced by perturb_subset_with_balance().

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

Reimplemented from protocols::kinematic_closure::perturbers::Perturber.

References perturb_subset().

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

Referenced by get_backbone_segments(), get_random_backbone_segments(), and perturb_subset().

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

Referenced by extract_fragment(), get_backbone_segments(), get_random_backbone_segments(), and LoopHashPerturber().

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

Referenced by perturb_subset(), and seqposes_no_mutate_str().

bool protocols::loop_modeler::perturbers::LoopHashPerturber::use_radial_lookup_ = true

private

Referenced by get_backbone_segments(), and use_radial_lookup().

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

src/protocols/loop_modeler/perturbers/LoopHashPerturber.hh
src/protocols/loop_modeler/perturbers/LoopHashPerturber.cc

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation