#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatRotOptEPositionData:

Collaboration diagram for protocols::optimize_weights::PNatRotOptEPositionData:

Public Member Functions
	PNatRotOptEPositionData ()

virtual	~PNatRotOptEPositionData ()

virtual Real	get_score (Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list) const

virtual void	print_score (std::ostream &ostr, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list) const

Real	process_score (std::ostream &ostr, bool print, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const, int const, EnergyMap const &fixed_terms, ScoreTypes const &, ScoreTypes const &fixed_score_list) const

virtual void	range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const
	Return the upper and lower bound on the unweighted components at this position if they are larger (or smaller) than the unweighted values already in the two input EnergyMaps. More...

virtual Size	size () const

virtual OptEPositionDataType	type () const

virtual void	write_to_file (std::ofstream &outfile) const

virtual void	read_from_file (std::ifstream &infile)

virtual void	write_to_binary_file (std::ofstream &outfile) const

virtual void	read_from_binary_file (std::ifstream &infile)

virtual Size	memory_use () const

void	set_native_rotamer_index (utility::vector1< Size > const &native_rotamer_index)

void	set_native_rotamer_chi (utility::vector1< Real > const &native_chi)

void	set_native_chi_periodicity (utility::vector1< Real > const &native_chi_periodicity)

bool	count_rotamer_as_native (PNatRotOptERotamerDataOP rotamer) const

void	set_rotamer_well_counts (utility::vector1< Size > const &rotamer_well_counts)

void	add_rotamer_line_data (PNatRotOptERotamerDataOP rot_in)

PNatRotOptERotamerDataOPs &	data ()

PNatRotOptERotamerDataOPs const &	data () const

PNatRotOptERotamerDataOPs::const_iterator	rotamer_data_begin () const

PNatRotOptERotamerDataOPs::const_iterator	rotamer_data_end () const

core::chemical::AA	aa () const

core::chemical::AA &	aa ()

Real	phi () const

Real	psi () const

Real &	phi ()

Real &	psi ()

Public Member Functions inherited from protocols::optimize_weights::OptEPositionData
	OptEPositionData ()

virtual	~OptEPositionData ()

void	tag (std::string const &tag_in)

std::string const &	tag () const

Private Member Functions
Size	rotamer_index_2_well_id (utility::vector1< Size > const &rotamer_index) const

Size	rotamer_index_2_well_id (utility::LexicographicalIterator const &lexiter) const

bool	is_native_rotamer_well (utility::vector1< Size > const &rotamer_index) const

bool	is_native_rotamer_well (utility::LexicographicalIterator const &lexiter) const

Private Attributes
utility::vector1< Size >	native_rotamer_index_

utility::vector1< Size >	rotamer_well_counts_

int	n_wells_

core::chemical::AA	aa_

Real	phi_

Real	psi_

PNatRotOptERotamerDataOPs	data_

utility::vector1< Real >	native_chi_

utility::vector1< Real >	native_chi_periodicity_

Additional Inherited Members
Public Types inherited from protocols::optimize_weights::OptEPositionData
typedef core::Real	Real

typedef core::Size	Size

typedef core::optimization::Multivec	Multivec

typedef core::scoring::EnergyMap	EnergyMap

typedef core::scoring::ScoreTypes	ScoreTypes

Protected Member Functions inherited from protocols::optimize_weights::OptEPositionData
void	update_range (SingleStructureDataCOP structure, ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const
	Helper function for range(); updates lower/upper_bound as needed so that score_list scores from structure are included in the range. More...

Detailed Description

Definition at line 589 of file OptEData.hh.

Constructor & Destructor Documentation

protocols::optimize_weights::PNatRotOptEPositionData::PNatRotOptEPositionData ( )

Definition at line 1227 of file OptEData.cc.

Referenced by memory_use().

protocols::optimize_weights::PNatRotOptEPositionData::~PNatRotOptEPositionData ( )

virtual

Definition at line 1229 of file OptEData.cc.

Member Function Documentation

core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa ( ) const

Definition at line 2039 of file OptEData.cc.

References aa_.

core::chemical::AA & protocols::optimize_weights::PNatRotOptEPositionData::aa ( )

Definition at line 2040 of file OptEData.cc.

References aa_.

void protocols::optimize_weights::PNatRotOptEPositionData::add_rotamer_line_data ( PNatRotOptERotamerDataOP rot_in)

Definition at line 2011 of file OptEData.cc.

References data_.

bool protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native ( PNatRotOptERotamerDataOP rotamer) const

Definition at line 1980 of file OptEData.cc.

References native_chi_, native_chi_periodicity_, and rotamer_well_counts_.

Referenced by process_score().

PNatRotOptERotamerDataOPs & protocols::optimize_weights::PNatRotOptEPositionData::data ( )

Definition at line 2017 of file OptEData.cc.

References data_.

PNatRotOptERotamerDataOPs const & protocols::optimize_weights::PNatRotOptEPositionData::data ( ) const

Definition at line 2023 of file OptEData.cc.

References data_.

Real protocols::optimize_weights::PNatRotOptEPositionData::get_score	(	optimization::Multivec const &	component_weights,
		optimization::Multivec const &	vars,
		optimization::Multivec &	dE_dvars,
		Size const	num_energy_dofs,
		int const	num_ref_dofs,
		int const	num_total_dofs,
		EnergyMap const &	fixed_terms,
		ScoreTypes const &	score_list,
		ScoreTypes const &	fixed_score_list
	)		const

virtual

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1232 of file OptEData.cc.

References process_score(), and protocols::optimize_weights::TR().

bool protocols::optimize_weights::PNatRotOptEPositionData::is_native_rotamer_well ( utility::vector1< Size > const & rotamer_index) const

private

Definition at line 2077 of file OptEData.cc.

References native_rotamer_index_.

Referenced by process_score().

bool protocols::optimize_weights::PNatRotOptEPositionData::is_native_rotamer_well ( utility::LexicographicalIterator const & lexiter) const

private

Definition at line 2088 of file OptEData.cc.

References native_rotamer_index_.

Size protocols::optimize_weights::PNatRotOptEPositionData::memory_use ( ) const

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1674 of file OptEData.cc.

References data_, native_rotamer_index_, PNatRotOptEPositionData(), and rotamer_well_counts_.

Real protocols::optimize_weights::PNatRotOptEPositionData::phi ( ) const

Definition at line 2042 of file OptEData.cc.

References phi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::phi ( )

Definition at line 2044 of file OptEData.cc.

References phi_.

void protocols::optimize_weights::PNatRotOptEPositionData::print_score	(	std::ostream &	ostr,
		optimization::Multivec const &	component_weights,
		optimization::Multivec const &	vars,
		optimization::Multivec &	dE_dvars,
		Size const	num_energy_dofs,
		int const	num_ref_dofs,
		int const	num_total_dofs,
		EnergyMap const &	fixed_terms,
		ScoreTypes const &	score_list,
		ScoreTypes const &	fixed_score_list
	)		const

virtual

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1363 of file OptEData.cc.

References process_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::process_score	(	std::ostream &	ostr,
		bool	print,
		optimization::Multivec const &	component_weights,
		optimization::Multivec const &	vars,
		optimization::Multivec &	dE_dvars,
		Size const	num_energy_dofs,
		int const	,
		int const	,
		EnergyMap const &	fixed_terms,
		ScoreTypes const &	score_list,
		ScoreTypes const &	fixed_score_list
	)		const

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Definition at line 1386 of file OptEData.cc.

References aa_, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_tyr, count_rotamer_as_native(), is_native_rotamer_well(), n_wells_, native_chi_, native_rotamer_index_, phi_, protocols::optimize_weights::prob_native_rotamer, psi_, rotamer_data_begin(), rotamer_data_end(), rotamer_index_2_well_id(), rotamer_well_counts_, and protocols::optimize_weights::OptEPositionData::tag().

Referenced by get_score(), and print_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::psi ( ) const

Definition at line 2043 of file OptEData.cc.

References psi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::psi ( )

Definition at line 2045 of file OptEData.cc.

References psi_.

void protocols::optimize_weights::PNatRotOptEPositionData::range	(	ScoreTypes const &	free_score_list,
		ScoreTypes const &	fixed_score_list,
		EnergyMap &	lower_bound,
		EnergyMap &	upper_bound
	)		const

virtual

Return the upper and lower bound on the unweighted components at this position if they are larger (or smaller) than the unweighted values already in the two input EnergyMaps.

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1598 of file OptEData.cc.

References rotamer_data_begin(), and rotamer_data_end().

void protocols::optimize_weights::PNatRotOptEPositionData::read_from_binary_file ( std::ifstream & infile)

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1670 of file OptEData.cc.

void protocols::optimize_weights::PNatRotOptEPositionData::read_from_file ( std::ifstream & infile)

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1660 of file OptEData.cc.

PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_begin ( ) const

Definition at line 2029 of file OptEData.cc.

References data_.

Referenced by process_score(), and range().

PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_end ( ) const

Definition at line 2034 of file OptEData.cc.

References data_.

Referenced by process_score(), and range().

Size protocols::optimize_weights::PNatRotOptEPositionData::rotamer_index_2_well_id ( utility::vector1< Size > const & rotamer_index) const

private

Definition at line 2049 of file OptEData.cc.

References rotamer_well_counts_.

Referenced by process_score().

Size protocols::optimize_weights::PNatRotOptEPositionData::rotamer_index_2_well_id ( utility::LexicographicalIterator const & lexiter) const

private

Definition at line 2063 of file OptEData.cc.

References rotamer_well_counts_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_chi_periodicity ( utility::vector1< Real > const & native_chi_periodicity)

Definition at line 1972 of file OptEData.cc.

References native_chi_periodicity_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_chi ( utility::vector1< Real > const & native_chi)

Definition at line 1964 of file OptEData.cc.

References native_chi_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_index ( utility::vector1< Size > const & native_rotamer_index)

Definition at line 1950 of file OptEData.cc.

References native_rotamer_index_, and rotamer_well_counts_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_rotamer_well_counts ( utility::vector1< Size > const & rotamer_well_counts)

Definition at line 1997 of file OptEData.cc.

References n_wells_, and rotamer_well_counts_.

Size protocols::optimize_weights::PNatRotOptEPositionData::size ( ) const

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1641 of file OptEData.cc.

References data_.

OptEPositionDataType protocols::optimize_weights::PNatRotOptEPositionData::type ( ) const

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1648 of file OptEData.cc.

References protocols::optimize_weights::prob_native_rotamer.

void protocols::optimize_weights::PNatRotOptEPositionData::write_to_binary_file ( std::ofstream & outfile) const

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1665 of file OptEData.cc.

void protocols::optimize_weights::PNatRotOptEPositionData::write_to_file ( std::ofstream & outfile) const

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 1655 of file OptEData.cc.

Member Data Documentation

core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa_

private

Definition at line 750 of file OptEData.hh.

Referenced by aa(), and process_score().

PNatRotOptERotamerDataOPs protocols::optimize_weights::PNatRotOptEPositionData::data_

private

Definition at line 753 of file OptEData.hh.

Referenced by add_rotamer_line_data(), data(), memory_use(), rotamer_data_begin(), rotamer_data_end(), and size().

int protocols::optimize_weights::PNatRotOptEPositionData::n_wells_

private

Definition at line 749 of file OptEData.hh.

Referenced by process_score(), and set_rotamer_well_counts().

utility::vector1< Real > protocols::optimize_weights::PNatRotOptEPositionData::native_chi_

private

Definition at line 754 of file OptEData.hh.

Referenced by count_rotamer_as_native(), process_score(), and set_native_rotamer_chi().

utility::vector1< Real > protocols::optimize_weights::PNatRotOptEPositionData::native_chi_periodicity_

private

Definition at line 755 of file OptEData.hh.

Referenced by count_rotamer_as_native(), and set_native_chi_periodicity().

utility::vector1< Size > protocols::optimize_weights::PNatRotOptEPositionData::native_rotamer_index_

private

Definition at line 747 of file OptEData.hh.

Referenced by is_native_rotamer_well(), memory_use(), process_score(), and set_native_rotamer_index().

Real protocols::optimize_weights::PNatRotOptEPositionData::phi_

private

Definition at line 751 of file OptEData.hh.

Referenced by phi(), and process_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::psi_

private

Definition at line 752 of file OptEData.hh.

Referenced by process_score(), and psi().

utility::vector1< Size > protocols::optimize_weights::PNatRotOptEPositionData::rotamer_well_counts_

private

Definition at line 748 of file OptEData.hh.

Referenced by count_rotamer_as_native(), memory_use(), process_score(), rotamer_index_2_well_id(), set_native_rotamer_index(), and set_rotamer_well_counts().

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

src/protocols/optimize_weights/OptEData.hh
src/protocols/optimize_weights/OptEData.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation