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

#include <ProteinUpstreamBuilder.hh>

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_

Member Typedef Documentation

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

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

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

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

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

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

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

References core::chemical::ResidueType::atom(), core::chemical::ResidueType::chi_atoms(), chi_samples_, create_hts_for_chi(), numeric::dihedral_degrees(), 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_, n_samples_per_chi_, core::pack::dunbrack::DunbrackRotamerSampleData::nchi(), core::chemical::ResidueType::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(), protocols::match::upstream::SampleStrategyData::strategy(), and utility_exit_with_message.

Member Function Documentation

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

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

inline

References chi_samples_, and dry_run_.

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

private

References chi_samples_, dry_run_, frames_, n_samples_per_chi_, and runtime_assert.

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.

References EX_ONE_STDDEV, NO_EXTRA_CHI_SAMPLES, option, and user.

Referenced by expand_non_dunbrack_chi(), and FullChiSampleSet().

void protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi ( 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::ResidueType::name(), 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(), utility::to_string(), and utility_exit_with_message.

Referenced by FullChiSampleSet().

void protocols::match::upstream::FullChiSampleSet::expand_samples_by_ex_behavior ( 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_, EX_FOUR_HALF_STEP_STDDEVS, EX_ONE_HALF_STEP_STDDEV, EX_ONE_STDDEV, EX_SIX_QUARTER_STEP_STDDEVS, EX_THREE_THIRD_STEP_STDDEVS, EX_TWO_FULL_STEP_STDDEVS, EX_TWO_HALF_STEP_STDDEVS, n_samples_per_chi_, NO_EXTRA_CHI_SAMPLES, core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_lower_boundary(), core::pack::dunbrack::DunbrackRotamerSampleData::nrchi_upper_boundary(), num_chi_samples_total_, and utility_exit_with_message.

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

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, runtime_assert, 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  )

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(), utility::to_string(), and utility_exit_with_message.

Referenced by FullChiSampleSet().

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

inline

References dry_run_, and frames_.

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

utility::vector1< 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().

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

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().

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().

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

private

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

utility::vector1< 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().

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