#include <DDGBindOptEData.hh>

Inheritance diagram for protocols::optimize_weights::DDGBindOptEData:

Public Types
enum	DDG_Bind_File_Index { WT_COMPLEXES_LIST_FILE = 1, MUT_COMPLEXES_LIST_FILE, WT_UNBOUNDS_LIST_FILE, MUT_UNBOUNDS_LIST_FILE }

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
	DDGBindOptEData ()
	Initialize all of the member variables to 0. More...

	~DDGBindOptEData () 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 num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list) const
	One method to do the score processing which takes a boolean dictating whether to print to an ostream or not. With this function, changes to how scoring works only need to be made in one place as opposed to two (when get_score() and print_score() both had scoring logic in them). Avoiding code duplication is good. More...

OptEPositionDataType	type () const override

void	range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const override

core::Size	size () const override

core::Size	memory_use () const override

void	write_to_file (std::ofstream &) const override

void	read_from_file (std::ifstream &) override

void	write_to_binary_file (std::ofstream &) const override

void	read_from_binary_file (std::ifstream &) override

void	set_experimental_ddg_bind (Real exp_ddg_bind)

void	add_mutation (std::pair< core::Size, std::pair< AA, AA > > mutation)

void	add_wt_complex (SingleStructureDataOP wt)

void	add_mutant_complex (SingleStructureDataOP mut)

void	add_wt_unbounds (SingleStructureDataOP wt)

void	add_mutant_unbounds (SingleStructureDataOP mut)

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 Attributes
Real	experimental_ddG_bind_

utility::vector1< std::pair < core::Size, std::pair< AA, AA > > >	mutations_

SingleStructureDataOPs	wt_complexes_

SingleStructureDataOPs	mutant_complexes_

SingleStructureDataOPs	wt_unbounds_

SingleStructureDataOPs	mutant_unbounds_

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...

Member Typedef Documentation

typedef core::chemical::AA protocols::optimize_weights::DDGBindOptEData::AA

Member Enumeration Documentation

enum protocols::optimize_weights::DDGBindOptEData::DDG_Bind_File_Index

Enumerator
WT_COMPLEXES_LIST_FILE
MUT_COMPLEXES_LIST_FILE
WT_UNBOUNDS_LIST_FILE
MUT_UNBOUNDS_LIST_FILE

Constructor & Destructor Documentation

protocols::optimize_weights::DDGBindOptEData::DDGBindOptEData ( )

Initialize all of the member variables to 0.

Referenced by memory_use().

protocols::optimize_weights::DDGBindOptEData::~DDGBindOptEData ( )

overridedefault

Member Function Documentation

void protocols::optimize_weights::DDGBindOptEData::add_mutant_complex ( SingleStructureDataOP mut )

References mutant_complexes_.

void protocols::optimize_weights::DDGBindOptEData::add_mutant_unbounds ( SingleStructureDataOP mut )

References mutant_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::add_mutation ( std::pair< core::Size, std::pair< AA, AA > > mutation )

References mutations_.

void protocols::optimize_weights::DDGBindOptEData::add_wt_complex ( SingleStructureDataOP wt )

References wt_complexes_.

void protocols::optimize_weights::DDGBindOptEData::add_wt_unbounds ( SingleStructureDataOP wt )

References wt_unbounds_.

Real protocols::optimize_weights::DDGBindOptEData::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

Implements protocols::optimize_weights::OptEPositionData.

References process_score().

core::Size protocols::optimize_weights::DDGBindOptEData::memory_use ( ) const

overridevirtual

Only used for user feedback. Nothing in the code uses the result from this to allocate memory.

Implements protocols::optimize_weights::OptEPositionData.

References DDGBindOptEData(), mutant_complexes_, mutant_unbounds_, protocols::analysis::total, wt_complexes_, and wt_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::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

Implements protocols::optimize_weights::OptEPositionData.

References process_score().

Real protocols::optimize_weights::DDGBindOptEData::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	num_ref_dofs,
		int const	num_total_dofs,
		EnergyMap const &	fixed_terms,
		ScoreTypes const &	score_list,
		ScoreTypes const &	fixed_score_list
	)		const

One method to do the score processing which takes a boolean dictating whether to print to an ostream or not. With this function, changes to how scoring works only need to be made in one place as opposed to two (when get_score() and print_score() both had scoring logic in them). Avoiding code duplication is good.

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

References protocols::comparative_modeling::features::A, protocols::mean_field::arg_min(), protocols::optimize_weights::ddG_bind_correlation, experimental_ddG_bind_, core::chemical::element::F, mutant_complexes_, mutant_unbounds_, mutations_, protocols::optimize_weights::OptEPositionData::tag(), wt_complexes_, wt_unbounds_, and protocols::comparative_modeling::features::X.

Referenced by get_score(), and print_score().

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

overridevirtual

Determine the upper and lower bounds on the unweighted component energy terms at this "position" and deposit them in the passed-in EnergyMap objects. Called by the IterativeOptE driver class to print extra information to the minimization data file.

Implements protocols::optimize_weights::OptEPositionData.

References mutant_complexes_, mutant_unbounds_, protocols::optimize_weights::OptEPositionData::update_range(), wt_complexes_, and wt_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::read_from_binary_file ( std::ifstream & )

inlineoverridevirtual

Implements protocols::optimize_weights::OptEPositionData.

void protocols::optimize_weights::DDGBindOptEData::read_from_file ( std::ifstream & )

inlineoverridevirtual

Implements protocols::optimize_weights::OptEPositionData.

void protocols::optimize_weights::DDGBindOptEData::set_experimental_ddg_bind ( Real exp_ddg_bind )

References experimental_ddG_bind_.

core::Size protocols::optimize_weights::DDGBindOptEData::size ( ) const

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

References mutant_complexes_, mutant_unbounds_, wt_complexes_, and wt_unbounds_.

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

overridevirtual

Implements protocols::optimize_weights::OptEPositionData.

References protocols::optimize_weights::ddG_bind_correlation.

void protocols::optimize_weights::DDGBindOptEData::write_to_binary_file ( std::ofstream & ) const

inlineoverridevirtual

Implements protocols::optimize_weights::OptEPositionData.

void protocols::optimize_weights::DDGBindOptEData::write_to_file ( std::ofstream & ) const

inlineoverridevirtual

Implements protocols::optimize_weights::OptEPositionData.

Member Data Documentation

Real protocols::optimize_weights::DDGBindOptEData::experimental_ddG_bind_

private

Referenced by process_score(), and set_experimental_ddg_bind().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_complexes_

private

Referenced by add_mutant_complex(), memory_use(), process_score(), range(), and size().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_unbounds_

private

Referenced by add_mutant_unbounds(), memory_use(), process_score(), range(), and size().

utility::vector1< std::pair< core::Size, std::pair < AA, AA > > > protocols::optimize_weights::DDGBindOptEData::mutations_

private

Referenced by add_mutation(), and process_score().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_complexes_

private

Referenced by add_wt_complex(), memory_use(), process_score(), range(), and size().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_unbounds_

private

Referenced by add_wt_unbounds(), memory_use(), process_score(), range(), and size().

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

src/protocols/optimize_weights/DDGBindOptEData.hh
src/protocols/optimize_weights/DDGBindOptEData.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation