protocols::optimize_weights::PNatRotOptEPositionData Class Reference

#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatRotOptEPositionData:

Public Member Functions
	PNatRotOptEPositionData ()
	~PNatRotOptEPositionData () override
Real	get_score (Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::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 override
void	print_score (std::ostream &ostr, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::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 override
Real	process_score (std::ostream &ostr, bool print, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::Size const num_energy_dofs, int const, int const, EnergyMap const &fixed_terms, ScoreTypes const &, ScoreTypes const &fixed_score_list) const
void	range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const override
	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...
core::Size	size () const override
OptEPositionDataType	type () const override
void	write_to_file (std::ofstream &outfile) const override
void	read_from_file (std::ifstream &infile) override
void	write_to_binary_file (std::ofstream &outfile) const override
void	read_from_binary_file (std::ifstream &infile) override
core::Size	memory_use () const override
void	set_native_rotamer_index (utility::vector1< core::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< core::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 ()
	~OptEPositionData () override
void	tag (std::string const &tag_in)
std::string const &	tag () const

Private Member Functions
core::Size	rotamer_index_2_well_id (utility::vector1< core::Size > const &rotamer_index) const
core::Size	rotamer_index_2_well_id (utility::LexicographicalIterator const &lexiter) const
bool	is_native_rotamer_well (utility::vector1< core::Size > const &rotamer_index) const
bool	is_native_rotamer_well (utility::LexicographicalIterator const &lexiter) const

Private Attributes
utility::vector1< core::Size >	native_rotamer_index_
utility::vector1< core::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...

Constructor & Destructor Documentation

protocols::optimize_weights::PNatRotOptEPositionData::PNatRotOptEPositionData

(

)

Referenced by memory_use().

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

overridedefault

Member Function Documentation

core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa

(

)

const

References aa_.

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

(

)

References aa_.

void protocols::optimize_weights::PNatRotOptEPositionData::add_rotamer_line_data

(

PNatRotOptERotamerDataOP

rot_in

)

References data_.

bool protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native

(

PNatRotOptERotamerDataOP

rotamer

)

const

References native_chi_, native_chi_periodicity_, rotamer_well_counts_, and protocols::environment::TOLERANCE.

Referenced by process_score().

PNatRotOptERotamerDataOPs & protocols::optimize_weights::PNatRotOptEPositionData::data

(

)

References data_.

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

(

)

const

References data_.

Real protocols::optimize_weights::PNatRotOptEPositionData::get_score ( optimization::Multivec const &  component_weights, optimization::Multivec const &  vars, optimization::Multivec &  dE_dvars, core::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

overridevirtual

Parameters

num_energy_dofs

Basically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

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

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

private

References native_rotamer_index_.

Referenced by process_score().

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

private

References native_rotamer_index_.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

References data_, native_rotamer_index_, PNatRotOptEPositionData(), rotamer_well_counts_, and protocols::analysis::total.

Real protocols::optimize_weights::PNatRotOptEPositionData::phi

(

)

const

References phi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::phi

(

)

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, core::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

overridevirtual

Parameters

num_energy_dofs

Basically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

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,
		core::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

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

References psi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::psi

(

)

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

overridevirtual

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.

References rotamer_data_begin(), and rotamer_data_end().

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_begin

(

)

const

References data_.

Referenced by process_score(), and range().

PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_end

(

)

const

References data_.

Referenced by process_score(), and range().

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

private

References rotamer_well_counts_.

Referenced by process_score().

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

private

References rotamer_well_counts_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_chi_periodicity

(

utility::vector1< Real > const &

native_chi_periodicity

)

References native_chi_periodicity_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_chi

(

utility::vector1< Real > const &

native_chi

)

References native_chi_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_index

(

utility::vector1< core::Size > const &

native_rotamer_index

)

References native_rotamer_index_, and rotamer_well_counts_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_rotamer_well_counts

(

utility::vector1< core::Size > const &

rotamer_well_counts

)

References n_wells_, and rotamer_well_counts_.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

References data_.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

References protocols::optimize_weights::prob_native_rotamer.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

Member Data Documentation

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

private

Referenced by aa(), and process_score().

PNatRotOptERotamerDataOPs protocols::optimize_weights::PNatRotOptEPositionData::data_

private

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

Referenced by process_score(), and set_rotamer_well_counts().

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

private

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

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

private

Referenced by count_rotamer_as_native(), and set_native_chi_periodicity().

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

private

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

Real protocols::optimize_weights::PNatRotOptEPositionData::phi_

private

Referenced by phi(), and process_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::psi_

private

Referenced by process_score(), and psi().

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

private

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