#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::DDGMutationOptEData:

Collaboration diagram for protocols::optimize_weights::DDGMutationOptEData:

Public Types
typedef core::chemical::AA	AA

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

Public Member Functions
	DDGMutationOptEData ()

virtual	~DDGMutationOptEData ()

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_wt_aa (AA wt_aa)

void	set_mut_aa (AA mut_aa)

void	set_experimental_ddg (Real ddg)

void	add_wt (SingleStructureDataOP wt)

void	add_mutant (SingleStructureDataOP mut)

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

virtual	~OptEPositionData ()

void	tag (std::string const &tag_in)

std::string const &	tag () const

Protected Attributes
Real	experimental_ddG_

AA	wt_aa_

AA	mut_aa_

SingleStructureDataOPs	wts_

SingleStructureDataOPs	muts_

Additional Inherited Members
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 914 of file OptEData.hh.

Member Typedef Documentation

typedef core::chemical::AA protocols::optimize_weights::DDGMutationOptEData::AA

Definition at line 917 of file OptEData.hh.

Constructor & Destructor Documentation

protocols::optimize_weights::DDGMutationOptEData::DDGMutationOptEData ( )

Definition at line 3209 of file OptEData.cc.

Referenced by protocols::optimize_weights::OptEPositionDataFactory::create_position_data(), and memory_use().

protocols::optimize_weights::DDGMutationOptEData::~DDGMutationOptEData ( )

virtual

Definition at line 3216 of file OptEData.cc.

Member Function Documentation

void protocols::optimize_weights::DDGMutationOptEData::add_mutant ( SingleStructureDataOP mut)

Definition at line 3925 of file OptEData.cc.

References muts_.

void protocols::optimize_weights::DDGMutationOptEData::add_wt ( SingleStructureDataOP wt)

Definition at line 3919 of file OptEData.cc.

References wts_.

Real protocols::optimize_weights::DDGMutationOptEData::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::NestedEnergyTermDDGMutationOptEData.

Definition at line 3220 of file OptEData.cc.

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

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData.

Definition at line 3709 of file OptEData.cc.

References DDGMutationOptEData(), muts_, and wts_.

void protocols::optimize_weights::DDGMutationOptEData::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::NestedEnergyTermDDGMutationOptEData.

Definition at line 3322 of file OptEData.cc.

References process_score().

Real protocols::optimize_weights::DDGMutationOptEData::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

Definition at line 3343 of file OptEData.cc.

References protocols::optimize_weights::ddG_mutation_correlation, experimental_ddG_, core::scoring::fa_rep, mut_aa_, muts_, protocols::optimize_weights::OptEPositionData::tag(), wt_aa_, and wts_.

Referenced by get_score(), and print_score().

void protocols::optimize_weights::DDGMutationOptEData::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 3659 of file OptEData.cc.

References muts_, protocols::optimize_weights::OptEPositionData::update_range(), and wts_.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 3704 of file OptEData.cc.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 3694 of file OptEData.cc.

void protocols::optimize_weights::DDGMutationOptEData::set_experimental_ddg ( Real ddg)