#include <DDGBindOptEData.hh>

Inheritance diagram for protocols::optimize_weights::DDGBindOptEData:

Collaboration 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...

virtual	~DDGBindOptEData ()

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
	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...

virtual OptEPositionDataType	type () const

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

virtual Size	size () const

virtual Size	memory_use () const

virtual void	write_to_file (std::ofstream &) const

virtual void	read_from_file (std::ifstream &)

virtual void	write_to_binary_file (std::ofstream &) const

virtual void	read_from_binary_file (std::ifstream &)

void	set_experimental_ddg_bind (Real exp_ddg_bind)

void	add_mutation (std::pair< 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 ()

virtual	~OptEPositionData ()

void	tag (std::string const &tag_in)

std::string const &	tag () const

Private Attributes
Real	experimental_ddG_bind_

utility::vector1< std::pair < 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...

Detailed Description

Definition at line 30 of file DDGBindOptEData.hh.

Member Typedef Documentation

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

Definition at line 34 of file DDGBindOptEData.hh.

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

Definition at line 35 of file DDGBindOptEData.hh.

Constructor & Destructor Documentation

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

Initialize all of the member variables to 0.

DDGBindOptEData::DDGBindOptEData()

Definition at line 50 of file DDGBindOptEData.cc.

Referenced by memory_use().

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

virtual

DDGBindOptEData::~DDGBindOptEData()

Definition at line 57 of file DDGBindOptEData.cc.

Member Function Documentation

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

DDGBindOptEData::add_mutant_complex()

Definition at line 686 of file DDGBindOptEData.cc.

References mutant_complexes_.

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

DDGBindOptEData::add_mutant_unbounds()

Definition at line 700 of file DDGBindOptEData.cc.

References mutant_unbounds_.

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

DDGBindOptEData::add_mutation()

Definition at line 672 of file DDGBindOptEData.cc.

References mutations_.

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

DDGBindOptEData::add_wt_complex()

Definition at line 679 of file DDGBindOptEData.cc.

References wt_complexes_.

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

DDGBindOptEData::add_wt_unbounds()

Definition at line 693 of file DDGBindOptEData.cc.

References wt_unbounds_.

Real protocols::optimize_weights::DDGBindOptEData::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 &	free_score_list,
		ScoreTypes const &	fixed_score_list
	)		const

virtual

DDGBindOptEData::get_score()

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 64 of file DDGBindOptEData.cc.

References process_score().

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

virtual

DDGBindOptEData::memory_use()

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

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 317 of file DDGBindOptEData.cc.

References DDGBindOptEData(), mutant_complexes_, mutant_unbounds_, 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,
		Size const	num_energy_dofs,
		int const	num_ref_dofs,
		int const	num_total_dofs,
		EnergyMap const &	fixed_terms,
		ScoreTypes const &	free_score_list,
		ScoreTypes const &	fixed_score_list
	)		const

virtual

DDGBindOptEData::print_score()

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 83 of file DDGBindOptEData.cc.

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,
		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.

DDGBindOptEData::process_score()

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Definition at line 109 of file DDGBindOptEData.cc.

References protocols::comparative_modeling::features::A, protocols::optimize_weights::ddG_bind_correlation, experimental_ddG_bind_, mutant_complexes_, mutant_unbounds_, mutations_, protocols::optimize_weights::OptEPositionData::tag(), wt_complexes_, wt_unbounds_, and core::scoring::rna::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

virtual

DDGBindOptEData::range()

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.

Definition at line 286 of file DDGBindOptEData.cc.

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

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

inlinevirtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 68 of file DDGBindOptEData.hh.

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

inlinevirtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 66 of file DDGBindOptEData.hh.

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

DDGBindOptEData::set_experimental_ddg_bind()

Definition at line 665 of file DDGBindOptEData.cc.

References experimental_ddG_bind_.

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

virtual

DDGBindOptEData::size()

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 307 of file DDGBindOptEData.cc.

References mutant_complexes_, mutant_unbounds_, wt_complexes_, and wt_unbounds_.

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

virtual

DDGBindOptEData::type()

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 273 of file DDGBindOptEData.cc.

References protocols::optimize_weights::ddG_bind_correlation.

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

inlinevirtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 67 of file DDGBindOptEData.hh.

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

inlinevirtual

Implements protocols::optimize_weights::OptEPositionData.

Definition at line 65 of file DDGBindOptEData.hh.

Member Data Documentation

Real protocols::optimize_weights::DDGBindOptEData::experimental_ddG_bind_

private

Definition at line 80 of file DDGBindOptEData.hh.

Referenced by process_score(), and set_experimental_ddg_bind().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_complexes_

private

Definition at line 84 of file DDGBindOptEData.hh.

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

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_unbounds_

private

Definition at line 86 of file DDGBindOptEData.hh.

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

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

private

Definition at line 81 of file DDGBindOptEData.hh.

Referenced by add_mutation(), and process_score().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_complexes_

private

Definition at line 83 of file DDGBindOptEData.hh.

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

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_unbounds_

private

Definition at line 85 of file DDGBindOptEData.hh.

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

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation