#include <PNatLigPoseOptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatLigPoseOptEData:

Collaboration diagram for protocols::optimize_weights::PNatLigPoseOptEData:

Public Member Functions
	PNatLigPoseOptEData ()

virtual	~PNatLigPoseOptEData ()

virtual Real	do_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, bool const print) const

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

virtual OptEPositionDataType	type () const

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

virtual	~PNatStructureOptEData ()

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 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

Private Attributes
Real	kT_

Real	multiplier_

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

Static Public Member Functions inherited from protocols::optimize_weights::PNatStructureOptEData
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 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...

Protected Attributes inherited from protocols::optimize_weights::PNatStructureOptEData
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 inherited from protocols::optimize_weights::PNatStructureOptEData
static Real	nativeness_rms_low_

static Real	nativeness_rms_high_

static Real const	high_entropy_rms_cutoff_

Detailed Description

Definition at line 33 of file PNatLigPoseOptEData.hh.

Constructor & Destructor Documentation

protocols::optimize_weights::PNatLigPoseOptEData::PNatLigPoseOptEData ( )

Definition at line 54 of file PNatLigPoseOptEData.cc.

protocols::optimize_weights::PNatLigPoseOptEData::~PNatLigPoseOptEData ( )

virtual

Definition at line 63 of file PNatLigPoseOptEData.cc.

Member Function Documentation

Real protocols::optimize_weights::PNatLigPoseOptEData::do_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,
		bool const	print
	)		const

virtual

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Definition at line 67 of file PNatLigPoseOptEData.cc.

References protocols::optimize_weights::PNatStructureOptEData::decoys_, kT_, multiplier_, protocols::optimize_weights::PNatStructureOptEData::natives_, protocols::optimize_weights::OptEPositionData::tag(), core::scoring::total_score, type(), and core::scoring::rna::X.

Referenced by get_score(), and print_score().

virtual Real protocols::optimize_weights::PNatLigPoseOptEData::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

inlinevirtual

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::PNatStructureOptEData.

Definition at line 61 of file PNatLigPoseOptEData.hh.

References do_score().

virtual void protocols::optimize_weights::PNatLigPoseOptEData::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

inlinevirtual

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::PNatStructureOptEData.

Definition at line 77 of file PNatLigPoseOptEData.hh.

References do_score().

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

virtual

Reimplemented from protocols::optimize_weights::PNatStructureOptEData.

Definition at line 196 of file PNatLigPoseOptEData.cc.

References protocols::optimize_weights::prob_native_ligand_pose.

Referenced by do_score().

Member Data Documentation

Real protocols::optimize_weights::PNatLigPoseOptEData::kT_

private

Definition at line 149 of file PNatLigPoseOptEData.hh.

Referenced by do_score().

Real protocols::optimize_weights::PNatLigPoseOptEData::multiplier_

private

Definition at line 150 of file PNatLigPoseOptEData.hh.

Referenced by do_score().

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

src/protocols/optimize_weights/PNatLigPoseOptEData.hh
src/protocols/optimize_weights/PNatLigPoseOptEData.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation