protocols::match::upstream::FullChiSampleSet Class Reference

#include <ProteinUpstreamBuilder.hh>

Inheritance diagram for protocols::match::upstream::FullChiSampleSet:

Public Types
typedef core::Size	Size
typedef core::Real	Real
typedef numeric::HomogeneousTransform< Real >	HTReal
typedef core::pack::task::ExtraRotSample	ExtraRotSample
typedef core::pack::dunbrack::DunbrackRotamerSampleData	DunbrackRotamerSampleData
typedef utility::vector1< DunbrackRotamerSampleData >	DunbrackRotamerSampleDataVector

Public Member Functions
	~FullChiSampleSet () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	FullChiSampleSet (BuildSet const &build_set, core::pack::dunbrack::DunbrackRotamerSampleData const &sample, bool dry_run)
utility::vector1< core::Size >	n_samples_per_chi () const
core::Size	num_chi_samples_total () const
utility::vector1< Real > const &	chi_samples (core::Size chi) const
Real	chi_sample (core::Size chi, core::Size sample_id) const
HTReal const &	frame (core::Size chi, core::Size sample_id) const

Private Member Functions
void	expand_non_dunbrack_chi (core::Size chi, BuildSet const &build_set)
void	expand_samples_by_ex_behavior (core::Size chi, ExtraRotSample behavior, core::pack::dunbrack::DunbrackRotamerSampleData const &sample)
void	expand_samples_by_steps_wi_sdrange (core::Size chi, SampleStrategyData const &stratdat, core::pack::dunbrack::DunbrackRotamerSampleData const &sample)
void	expand_samples_for_nrchi_wi_nrchi_bin (core::Size chi, SampleStrategyData const &stratdat, core::pack::dunbrack::DunbrackRotamerSampleData const &sample)
void	create_hts_for_chi (core::Size chi)

Static Private Member Functions
static ExtraRotSample	ex_level_from_flags (core::Size chi)
	This doesn't belong in this class – move to core. More...

Private Attributes
bool const	dry_run_
core::Size	num_chi_samples_total_
utility::vector1< core::Size >	n_samples_per_chi_
utility::vector1< utility::vector1< Real > >	chi_samples_
utility::vector1< utility::vector1< HTReal > >	frames_

Member Typedef Documentation

DunbrackRotamerSampleData

typedef core::pack::dunbrack::DunbrackRotamerSampleData protocols::match::upstream::FullChiSampleSet::DunbrackRotamerSampleData

DunbrackRotamerSampleDataVector

typedef utility::vector1< DunbrackRotamerSampleData > protocols::match::upstream::FullChiSampleSet::DunbrackRotamerSampleDataVector

ExtraRotSample

typedef core::pack::task::ExtraRotSample protocols::match::upstream::FullChiSampleSet::ExtraRotSample

HTReal

typedef numeric::HomogeneousTransform< Real > protocols::match::upstream::FullChiSampleSet::HTReal

Real

typedef core::Real protocols::match::upstream::FullChiSampleSet::Real

Size

typedef core::Size protocols::match::upstream::FullChiSampleSet::Size

Constructor & Destructor Documentation

~FullChiSampleSet()

protocols::match::upstream::FullChiSampleSet::~FullChiSampleSet ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

FullChiSampleSet()

protocols::match::upstream::FullChiSampleSet::FullChiSampleSet	(	BuildSet const &	build_set,
		core::pack::dunbrack::DunbrackRotamerSampleData const &	sample,
		bool	dry_run
	)

References core::chemical::ResidueType::chi_atoms(), chi_samples_, create_hts_for_chi(), dry_run_, ex_level_from_flags(), expand_non_dunbrack_chi(), expand_samples_by_ex_behavior(), expand_samples_by_steps_wi_sdrange(), expand_samples_for_nrchi_wi_nrchi_bin(), protocols::match::upstream::follow_EX_flags, frames_, core::chemical::ResidueType::ideal_xyz(), n_samples_per_chi_, core::chemical::ResidueType::nchi(), core::pack::dunbrack::DunbrackRotamerSampleData::nchi(), protocols::match::upstream::no_samples, protocols::match::upstream::nonrotameric_chi_sample_wi_nrchi_bin, protocols::match::upstream::nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary, protocols::match::upstream::BuildSet::restype(), protocols::match::upstream::rotameric_chi_mimic_EX_flags, protocols::match::upstream::rotameric_chi_partition_sd_range, protocols::match::upstream::rotameric_chi_step_by_value, protocols::match::upstream::rotameric_chi_step_wi_sd_range, protocols::match::upstream::SampleStrategyData::sample_level(), protocols::match::upstream::BuildSet::sample_strategy_for_chi(), and protocols::match::upstream::SampleStrategyData::strategy().

Member Function Documentation

chi_sample()

Real protocols::match::upstream::FullChiSampleSet::chi_sample ( core::Size  chi, core::Size  sample_id  ) const

inline

References chi_samples_, and dry_run_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

chi_samples()

utility::vector1< Real > const& protocols::match::upstream::FullChiSampleSet::chi_samples ( core::Size  chi ) const

inline

References chi_samples_, and dry_run_.

create_hts_for_chi()

void protocols::match::upstream::FullChiSampleSet::create_hts_for_chi ( core::Size  chi )

private

References chi_samples_, dry_run_, frames_, and n_samples_per_chi_.

Referenced by FullChiSampleSet().

ex_level_from_flags()

FullChiSampleSet::ExtraRotSample protocols::match::upstream::FullChiSampleSet::ex_level_from_flags ( core::Size  chi )

staticprivate

This doesn't belong in this class – move to core.

References core::pack::task::EX_ONE_STDDEV, and core::pack::task::NO_EXTRA_CHI_SAMPLES.

Referenced by expand_non_dunbrack_chi(), and FullChiSampleSet().

expand_non_dunbrack_chi()

void protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi ( core::Size  chi, BuildSet const &  build_set  )

private

References core::chemical::ResidueType::chi_2_proton_chi(), chi_samples_, dry_run_, ex_level_from_flags(), core::chemical::ResidueType::is_proton_chi(), n_samples_per_chi_, core::chemical::ResidueTypeBase::name(), core::pack::task::NO_EXTRA_CHI_SAMPLES, protocols::match::upstream::no_samples, num_chi_samples_total_, core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), protocols::match::upstream::BuildSet::restype(), protocols::match::upstream::BuildSet::sample_strategy_for_chi(), protocols::match::upstream::SampleStrategyData::strategy(), and core::id::to_string().

Referenced by FullChiSampleSet().

expand_samples_by_ex_behavior()

void protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior ( core::Size  chi, ExtraRotSample  behavior, core::pack::dunbrack::DunbrackRotamerSampleData const &  sample  )

private

References core::pack::dunbrack::DunbrackRotamerSampleData::chi_is_nonrotameric(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean(), chi_samples_, core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd(), dry_run_, core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, core::pack::task::EX_ONE_HALF_STEP_STDDEV, core::pack::task::EX_ONE_STDDEV, core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, core::pack::task::EX_TWO_FULL_STEP_STDDEVS, core::pack::task::EX_TWO_HALF_STEP_STDDEVS, n_samples_per_chi_, core::pack::task::NO_EXTRA_CHI_SAMPLES, core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary(), core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary(), and num_chi_samples_total_.

Referenced by FullChiSampleSet().

expand_samples_by_steps_wi_sdrange()

void protocols::match::upstream::FullChiSampleSet::expand_samples_by_steps_wi_sdrange ( core::Size  chi, SampleStrategyData const &  stratdat, core::pack::dunbrack::DunbrackRotamerSampleData const &  sample  )

private

References core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean(), chi_samples_, core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd(), dry_run_, n_samples_per_chi_, num_chi_samples_total_, protocols::match::upstream::rotameric_chi_step_wi_sd_range, protocols::match::upstream::SampleStrategyData::sd_range(), protocols::match::upstream::SampleStrategyData::step_size(), and protocols::match::upstream::SampleStrategyData::strategy().

Referenced by FullChiSampleSet().

expand_samples_for_nrchi_wi_nrchi_bin()

void protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin ( core::Size  chi, SampleStrategyData const &  stratdat, core::pack::dunbrack::DunbrackRotamerSampleData const &  sample  )

private

References core::pack::dunbrack::DunbrackRotamerSampleData::chi_is_nonrotameric(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean(), chi_samples_, dry_run_, n_samples_per_chi_, protocols::match::upstream::SampleStrategyData::n_samples_per_side_of_nrchi_bin(), core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary(), protocols::match::upstream::SampleStrategyData::nrchi_prob_minimum_for_extra_samples(), core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary(), num_chi_samples_total_, core::pack::dunbrack::DunbrackRotamerSampleData::probability(), and core::id::to_string().

Referenced by FullChiSampleSet().

frame()

HTReal const& protocols::match::upstream::FullChiSampleSet::frame ( core::Size  chi, core::Size  sample_id  ) const

inline

References dry_run_, and frames_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

n_samples_per_chi()

utility::vector1< core::Size > protocols::match::upstream::FullChiSampleSet::n_samples_per_chi ( ) const

inline

References dry_run_, and n_samples_per_chi_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

num_chi_samples_total()

core::Size protocols::match::upstream::FullChiSampleSet::num_chi_samples_total ( ) const

inline

References num_chi_samples_total_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

Member Data Documentation

chi_samples_

utility::vector1< utility::vector1< Real > > protocols::match::upstream::FullChiSampleSet::chi_samples_

private

Referenced by chi_sample(), chi_samples(), create_hts_for_chi(), expand_non_dunbrack_chi(), expand_samples_by_ex_behavior(), expand_samples_by_steps_wi_sdrange(), expand_samples_for_nrchi_wi_nrchi_bin(), and FullChiSampleSet().

dry_run_

bool const protocols::match::upstream::FullChiSampleSet::dry_run_

private

Referenced by chi_sample(), chi_samples(), create_hts_for_chi(), expand_non_dunbrack_chi(), expand_samples_by_ex_behavior(), expand_samples_by_steps_wi_sdrange(), expand_samples_for_nrchi_wi_nrchi_bin(), frame(), FullChiSampleSet(), and n_samples_per_chi().

frames_

utility::vector1< utility::vector1< HTReal > > protocols::match::upstream::FullChiSampleSet::frames_

private

Referenced by create_hts_for_chi(), frame(), and FullChiSampleSet().

n_samples_per_chi_

utility::vector1< core::Size > protocols::match::upstream::FullChiSampleSet::n_samples_per_chi_

private

Referenced by create_hts_for_chi(), expand_non_dunbrack_chi(), expand_samples_by_ex_behavior(), expand_samples_by_steps_wi_sdrange(), expand_samples_for_nrchi_wi_nrchi_bin(), FullChiSampleSet(), and n_samples_per_chi().

num_chi_samples_total_

core::Size protocols::match::upstream::FullChiSampleSet::num_chi_samples_total_

private

Referenced by expand_non_dunbrack_chi(), expand_samples_by_ex_behavior(), expand_samples_by_steps_wi_sdrange(), expand_samples_for_nrchi_wi_nrchi_bin(), and num_chi_samples_total().

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

• src/protocols/match/upstream/ProteinUpstreamBuilder.hh
• src/protocols/match/upstream/ProteinUpstreamBuilder.cc