#include <NestedEnergyTermOptEData.hh>

Inheritance diagram for protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData:

Collaboration diagram for protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData:

Public Member Functions
	NestedEnergyTermDDGMutationOptEData ()

virtual	~NestedEnergyTermDDGMutationOptEData ()

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). More...

virtual OptEPositionDataType	type () const

virtual Size	memory_use () const

void	set_wt_unfolded_energies_emap (EnergyMap e)

void	set_mut_unfolded_energies_emap (EnergyMap e)

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

virtual	~DDGMutationOptEData ()

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)

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

Private Attributes
EnergyMap	wt_unfolded_energies_emap_

EnergyMap	mut_unfolded_energies_emap_

Additional Inherited Members
Public Types inherited from protocols::optimize_weights::DDGMutationOptEData
typedef core::chemical::AA	AA

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::DDGMutationOptEData
Real	experimental_ddG_

AA	wt_aa_

AA	mut_aa_

SingleStructureDataOPs	wts_

SingleStructureDataOPs	muts_

Constructor & Destructor Documentation

protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::NestedEnergyTermDDGMutationOptEData ( )

NestedEnergyTermDDGMutationOptEData::NestedEnergyTermDDGMutationOptEData()

protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::~NestedEnergyTermDDGMutationOptEData ( )

virtual

NestedEnergyTermDDGMutationOptEData::~NestedEnergyTermDDGMutationOptEData()

Member Function Documentation

Real protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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

NestedEnergyTermDDGMutationOptEData::get_score()

This get_score() method needs to contain some extra logic for the unfolded state energy term. Right now, the value under unfolded energy is 0.0, because that's what the EnergyMethod is coded to return. But, as in the NatAA class above, we need use the unweighted, unfolded energies and the current weight set to come up with a unfolded energy.

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::DDGMutationOptEData.

References core::TR().

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

virtual

NestedEnergyTermDDGMutationOptEData::memory_use()

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

Reimplemented from protocols::optimize_weights::DDGMutationOptEData.

void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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

NestedEnergyTermDDGMutationOptEData::print_score()

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::DDGMutationOptEData.

Real protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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).

NestedEnergyTermDDGMutationOptEData::process_score()

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

References protocols::comparative_modeling::features::A, protocols::optimize_weights::ddG_mutation_correlation, protocols::optimize_weights::ddG_mutation_correlation_with_unfolded_energy, core::scoring::fa_rep, core::scoring::name_from_score_type(), core::TR(), core::scoring::unfolded, and core::scoring::rna::X.

void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_mut_unfolded_energies_emap ( EnergyMap e)

inline

References mut_unfolded_energies_emap_.

void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_wt_unfolded_energies_emap ( EnergyMap e)

inline

References wt_unfolded_energies_emap_.

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

virtual

NestedEnergyTermDDGMutationOptEData::type()

Reimplemented from protocols::optimize_weights::DDGMutationOptEData.

References protocols::optimize_weights::ddG_mutation_correlation_with_unfolded_energy.

Member Data Documentation

EnergyMap protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::mut_unfolded_energies_emap_

private

Referenced by set_mut_unfolded_energies_emap().

EnergyMap protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::wt_unfolded_energies_emap_

private

Referenced by set_wt_unfolded_energies_emap().

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

src/protocols/optimize_weights/NestedEnergyTermOptEData.hh
src/protocols/optimize_weights/NestedEnergyTermOptEData.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation