#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatStructureOptEData:

Collaboration diagram for protocols::optimize_weights::PNatStructureOptEData:

Public Member Functions
	PNatStructureOptEData ()

virtual	~PNatStructureOptEData ()

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 num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, 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_total_residue (Size total_residue)

void	add_native (SingleStructureDataOP native)

void	add_decoy (SingleStructureDataOP decoy)

void	n_top_natives_to_score (Size n_top)

Size	n_top_natives_to_score () const

void	set_normalize_decoy_stddev (bool setting)

void	set_initial_decoy_stddev (Real setting)

Real	nativeness (Real rms) const

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

virtual	~OptEPositionData ()

void	tag (std::string const &tag_in)

std::string const &	tag () const

Static Public Member Functions
static void	set_nativeness_low (Real nativeness_rms_low)

static void	set_nativeness_high (Real nativeness_rms_low)

static Real	nativeness_low ()

static Real	nativeness_high ()

Protected Attributes
Size	total_residue_

SingleStructureDataOPs	natives_

SingleStructureDataOPs	decoys_

Size	n_top_natives_to_score_

Size	n_high_entropy_decoys_

bool	normalize_decoy_stddev_

Real	initial_decoy_stddev_

Real	nativeness_sum_

Static Protected Attributes
static Real	nativeness_rms_low_

static Real	nativeness_rms_high_

static Real const	high_entropy_rms_cutoff_

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::PNatStructureOptEData::PNatStructureOptEData ( )

Referenced by memory_use().

protocols::optimize_weights::PNatStructureOptEData::~PNatStructureOptEData ( )

virtual

Member Function Documentation

void protocols::optimize_weights::PNatStructureOptEData::add_decoy ( SingleStructureDataOP decoy)

References decoys_, high_entropy_rms_cutoff_, and n_high_entropy_decoys_.

void protocols::optimize_weights::PNatStructureOptEData::add_native ( SingleStructureDataOP native)

References n_top_natives_to_score_, nativeness(), nativeness_sum_, and natives_.

Real protocols::optimize_weights::PNatStructureOptEData::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.

Reimplemented in protocols::optimize_weights::PNatLigPoseOptEData.

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

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

References decoys_, natives_, and PNatStructureOptEData().

void protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score ( Size n_top)

References n_top_natives_to_score_.

Size protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score ( ) const

References n_top_natives_to_score_.

Real protocols::optimize_weights::PNatStructureOptEData::nativeness ( Real rms) const

References nativeness_rms_high_, and nativeness_rms_low_.

Referenced by add_native(), and process_score().

Real protocols::optimize_weights::PNatStructureOptEData::nativeness_high ( )

static

References nativeness_rms_high_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::add_structure_based_on_rms().

Real protocols::optimize_weights::PNatStructureOptEData::nativeness_low ( )

static

References nativeness_rms_low_.

void protocols::optimize_weights::PNatStructureOptEData::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.

Reimplemented in protocols::optimize_weights::PNatLigPoseOptEData.

References process_score().

Real protocols::optimize_weights::PNatStructureOptEData::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	num_ref_dofs,
		int const	num_total_dofs,
		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 decoys_, high_entropy_rms_cutoff_, initial_decoy_stddev_, n_high_entropy_decoys_, n_top_natives_to_score_, nativeness(), nativeness_sum_, natives_, normalize_decoy_stddev_, protocols::optimize_weights::prob_native_structure, core::scoring::rms, protocols::optimize_weights::OptEPositionData::tag(), and total_residue_.

Referenced by get_score(), and print_score().

void protocols::optimize_weights::PNatStructureOptEData::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.

References decoys_, natives_, and protocols::optimize_weights::OptEPositionData::update_range().

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

void protocols::optimize_weights::PNatStructureOptEData::set_initial_decoy_stddev ( Real setting)

References initial_decoy_stddev_.

void protocols::optimize_weights::PNatStructureOptEData::set_nativeness_high ( Real nativeness_rms_low)

static

References nativeness_rms_high_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data().

void protocols::optimize_weights::PNatStructureOptEData::set_nativeness_low ( Real nativeness_rms_low)

static

References nativeness_rms_low_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data().

void protocols::optimize_weights::PNatStructureOptEData::set_normalize_decoy_stddev ( bool setting)

References normalize_decoy_stddev_.

void protocols::optimize_weights::PNatStructureOptEData::set_total_residue ( Size total_residue)

References total_residue_.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

References decoys_, and natives_.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PNatLigPoseOptEData.

References protocols::optimize_weights::prob_native_structure.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Member Data Documentation

SingleStructureDataOPs protocols::optimize_weights::PNatStructureOptEData::decoys_

protected

Referenced by add_decoy(), protocols::optimize_weights::PNatLigPoseOptEData::do_score(), memory_use(), process_score(), range(), and size().

Real const protocols::optimize_weights::PNatStructureOptEData::high_entropy_rms_cutoff_

staticprotected

Referenced by add_decoy(), and process_score().

Real protocols::optimize_weights::PNatStructureOptEData::initial_decoy_stddev_

protected

Referenced by process_score(), and set_initial_decoy_stddev().

Size protocols::optimize_weights::PNatStructureOptEData::n_high_entropy_decoys_

protected

Referenced by add_decoy(), and process_score().

Size protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score_

protected

Referenced by add_native(), n_top_natives_to_score(), and process_score().

Real protocols::optimize_weights::PNatStructureOptEData::nativeness_rms_high_

staticprotected

Referenced by nativeness(), nativeness_high(), and set_nativeness_high().

Real protocols::optimize_weights::PNatStructureOptEData::nativeness_rms_low_

staticprotected

Referenced by nativeness(), nativeness_low(), and set_nativeness_low().

Real protocols::optimize_weights::PNatStructureOptEData::nativeness_sum_

protected

Referenced by add_native(), and process_score().

SingleStructureDataOPs protocols::optimize_weights::PNatStructureOptEData::natives_

protected

Referenced by add_native(), protocols::optimize_weights::PNatLigPoseOptEData::do_score(), memory_use(), process_score(), range(), and size().

bool protocols::optimize_weights::PNatStructureOptEData::normalize_decoy_stddev_

protected

Referenced by process_score(), and set_normalize_decoy_stddev().

Size protocols::optimize_weights::PNatStructureOptEData::total_residue_

protected

Referenced by process_score(), and set_total_residue().

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

Static Public Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation