#include <ProteinUpstreamBuilder.hh>

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

Collaboration 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
virtual	~FullChiSampleSet ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

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

utility::vector1< Size >	n_samples_per_chi () const

Size	num_chi_samples_total () const

utility::vector1< Real > const &	chi_samples (Size chi) const

Real	chi_sample (Size chi, Size sample_id) const

HTReal const &	frame (Size chi, Size sample_id) const

Private Member Functions
void	expand_non_dunbrack_chi (Size chi, BuildSet const &build_set)

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

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

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

void	create_hts_for_chi (Size chi)

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

Private Attributes
bool const	dry_run_

Size	num_chi_samples_total_

utility::vector1< Size >	n_samples_per_chi_

utility::vector1 < utility::vector1< Real > >	chi_samples_

utility::vector1 < utility::vector1< HTReal > >	frames_

Detailed Description

Definition at line 342 of file ProteinUpstreamBuilder.hh.

Member Typedef Documentation

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

Definition at line 350 of file ProteinUpstreamBuilder.hh.

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

Definition at line 351 of file ProteinUpstreamBuilder.hh.

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

Definition at line 349 of file ProteinUpstreamBuilder.hh.

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

Definition at line 348 of file ProteinUpstreamBuilder.hh.

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

Definition at line 347 of file ProteinUpstreamBuilder.hh.

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

Definition at line 346 of file ProteinUpstreamBuilder.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 52 of file ProteinUpstreamBuilder.cc.

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

Definition at line 373 of file ProteinUpstreamBuilder.cc.

Member Function Documentation

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

inline

Definition at line 380 of file ProteinUpstreamBuilder.hh.

References chi_samples_, and dry_run_.

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

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

inline

Definition at line 373 of file ProteinUpstreamBuilder.hh.

References chi_samples_, and dry_run_.

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

private

Definition at line 716 of file ProteinUpstreamBuilder.cc.

References chi_samples_, dry_run_, frames_, and n_samples_per_chi_.

Referenced by FullChiSampleSet().

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

staticprivate

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

Definition at line 729 of file ProteinUpstreamBuilder.cc.

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

Referenced by expand_non_dunbrack_chi(), and FullChiSampleSet().

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

private

Definition at line 447 of file ProteinUpstreamBuilder.cc.

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::ResidueType::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(), and protocols::match::upstream::SampleStrategyData::strategy().

Referenced by FullChiSampleSet().

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

private

Definition at line 498 of file ProteinUpstreamBuilder.cc.

Referenced by FullChiSampleSet().

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

private

Definition at line 638 of file ProteinUpstreamBuilder.cc.

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().

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