core::pack::dunbrack::DunbrackRotamerSampleData Class Reference

#include <DunbrackRotamer.hh>

Public Member Functions
	DunbrackRotamerSampleData ()
	DunbrackRotamerSampleData (bool is_nrchi_sample)
	~DunbrackRotamerSampleData ()
void	set_nrchi_sample (bool setting)
	Setters. More...
void	set_nchi (Size nchi)
void	set_rotwell (Size chi_index, Size rotwell)
void	set_rotwell (utility::vector1< Size > const &)
void	set_chi_mean (Size chi_index, Real mean)
void	set_chi_sd (Size chi_index, Real sd)
void	set_prob (Real probability)
void	set_nrchi_lower_boundary (Real low)
void	set_nrchi_upper_boundary (Real high)
void	set_nrchi_probability (Real nrchi_prob)
bool	nrchi_sample () const
bool	chi_is_nonrotameric (Size chi) const
Size	nchi () const
Size4 const &	rot_well () const
Real4 const &	chi_mean () const
Real4 const &	chi_sd () const
Real	probability () const
Real	nrchi_lower_boundary () const
Real	nrchi_upper_boundary () const
Real	nrchi_probability () const
void	assign_random_chi (utility::vector1< Real > &chi_angles, numeric::random::RandomGenerator &RG, core::Real factor=1.0) const
Real	chi_probability (utility::vector1< Real > const &chi_angles, core::Real factor=1.0) const

Private Attributes
bool	nrchi_sample_
Size	nchi_
	Does this sample describe a semi-rotameric residue? More...
Size4	rot_well_
	The number of chi values the library describes; Between 1 & 4. More...
Real4	chi_mean_
	The integer description of the rotamer conformation. More...
Real4	chi_sd_
	The chi angle at the center of the distribution. More...
Real	probability_
	Standard deviation from the center for each chi. More...
Real	nrchi_lower_boundary_
	The probability of finding the rotamer in this rot_well. More...
Real	nrchi_upper_boundary_
	Requires nrchi_sample_. The lower boundary of the non-rotameric chi well, in degrees. More...
Real	nrchi_probability_
	Requires nrchi_sample_. The upper boundary of the non-rotameric chi well, in degrees. More...

Constructor & Destructor Documentation

core::pack::dunbrack::DunbrackRotamerSampleData::DunbrackRotamerSampleData

(

)

core::pack::dunbrack::DunbrackRotamerSampleData::DunbrackRotamerSampleData

(

bool

is_nrchi_sample

)

core::pack::dunbrack::DunbrackRotamerSampleData::~DunbrackRotamerSampleData ( )

default

Member Function Documentation

void core::pack::dunbrack::DunbrackRotamerSampleData::assign_random_chi	(	utility::vector1< Real > &	chi_angles,
		numeric::random::RandomGenerator &	RG,
		core::Real	factor = 1.0
	)		const

References chi_mean_, chi_sd_, and nchi().

bool core::pack::dunbrack::DunbrackRotamerSampleData::chi_is_nonrotameric ( Size  chi ) const

inline

References nchi_, and nrchi_sample_.

Referenced by protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), and protocols::match::upstream::DunbrackSCSampler::samples().

Real4 const& core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean ( ) const

inline

References chi_mean_.

Referenced by core::pack::assign_random_continuous_rotamer(), protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior(), protocols::match::upstream::FullChiSampleSet::expand_samples_by_steps_wi_sdrange(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), and protocols::match::upstream::DunbrackSCSampler::samples().

Real core::pack::dunbrack::DunbrackRotamerSampleData::chi_probability	(	utility::vector1< Real > const &	chi_angles,
		core::Real	factor = 1.0
	)		const

References protocols::abinitio::abscript::angle_diff(), chi_mean_, chi_sd_, and nchi().

Real4 const& core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd ( ) const

inline

References chi_sd_.

Referenced by core::pack::assign_random_continuous_rotamer(), protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior(), and protocols::match::upstream::FullChiSampleSet::expand_samples_by_steps_wi_sdrange().

Size core::pack::dunbrack::DunbrackRotamerSampleData::nchi ( ) const

inline

References nchi_.

Referenced by assign_random_chi(), core::pack::assign_random_continuous_rotamer(), chi_probability(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), and set_nchi().

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary ( ) const

inline

References nrchi_lower_boundary_, and nrchi_sample_.

Referenced by protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), and protocols::match::upstream::DunbrackSCSampler::samples().

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_probability ( ) const

inline

References nrchi_probability_, and nrchi_sample_.

bool core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_sample ( ) const

inline

References nrchi_sample_.

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary ( ) const

inline

References nrchi_sample_, and nrchi_upper_boundary_.

Referenced by protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), and protocols::match::upstream::DunbrackSCSampler::samples().

Real core::pack::dunbrack::DunbrackRotamerSampleData::probability ( ) const

inline

References probability_.

Referenced by protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), and set_prob().

Size4 const& core::pack::dunbrack::DunbrackRotamerSampleData::rot_well ( ) const

inline

References rot_well_.

void core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_mean	(	Size	chi_index,
		Real	mean
	)

References chi_mean_, core::simple_metrics::metrics::mean, and nchi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep(), and protocols::match::upstream::DunbrackSCSampler::samples().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_chi_sd	(	Size	chi_index,
		Real	sd
	)

References chi_sd_, and nchi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi

(

Size

nchi

)

References core::pack::dunbrack::DUNBRACK_MAX_SCTOR, nchi(), and nchi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_lower_boundary

(

Real

low

)

References nrchi_lower_boundary_, and nrchi_sample_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep(), and protocols::match::upstream::DunbrackSCSampler::samples().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_probability

(

Real

nrchi_prob

)

References nrchi_probability_, and nrchi_sample_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_sample

(

bool

setting

)

Setters.

References nrchi_sample_.

void core::pack::dunbrack::DunbrackRotamerSampleData::set_nrchi_upper_boundary

(

Real

high

)

References nrchi_sample_, and nrchi_upper_boundary_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep(), and protocols::match::upstream::DunbrackSCSampler::samples().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_prob

(

Real

probability

)

References probability(), and probability_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_rotwell	(	Size	chi_index,
		Size	rotwell
	)

References nchi_, and rot_well_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep().

void core::pack::dunbrack::DunbrackRotamerSampleData::set_rotwell

(

utility::vector1< Size > const &

rotwell

)

References nchi_, nrchi_sample_, and rot_well_.

Member Data Documentation

Real4 core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean_

private

The integer description of the rotamer conformation.

Referenced by assign_random_chi(), chi_mean(), chi_probability(), and set_chi_mean().

Real4 core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd_

private

The chi angle at the center of the distribution.

Referenced by assign_random_chi(), chi_probability(), chi_sd(), and set_chi_sd().

Size core::pack::dunbrack::DunbrackRotamerSampleData::nchi_

private

Does this sample describe a semi-rotameric residue?

Referenced by chi_is_nonrotameric(), nchi(), set_chi_mean(), set_chi_sd(), set_nchi(), and set_rotwell().

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary_

private

The probability of finding the rotamer in this rot_well.

Referenced by nrchi_lower_boundary(), and set_nrchi_lower_boundary().

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_probability_

private

Requires nrchi_sample_. The upper boundary of the non-rotameric chi well, in degrees.

Referenced by nrchi_probability(), and set_nrchi_probability().

bool core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_sample_

private

Referenced by chi_is_nonrotameric(), nrchi_lower_boundary(), nrchi_probability(), nrchi_sample(), nrchi_upper_boundary(), set_nrchi_lower_boundary(), set_nrchi_probability(), set_nrchi_sample(), set_nrchi_upper_boundary(), and set_rotwell().

Real core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary_

private

Requires nrchi_sample_. The lower boundary of the non-rotameric chi well, in degrees.

Referenced by nrchi_upper_boundary(), and set_nrchi_upper_boundary().

Real core::pack::dunbrack::DunbrackRotamerSampleData::probability_

private

Standard deviation from the center for each chi.

Referenced by probability(), and set_prob().

Size4 core::pack::dunbrack::DunbrackRotamerSampleData::rot_well_

private

The number of chi values the library describes; Between 1 & 4.

Referenced by rot_well(), and set_rotwell().

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

• src/core/pack/dunbrack/DunbrackRotamer.hh
• src/core/pack/dunbrack/DunbrackRotamer.cc