#include <NestedEnergyTermOptEData.hh>

Public Member Functions
	NestedEnergyTermPNatAAOptEPositionData ()

virtual	~NestedEnergyTermPNatAAOptEPositionData ()

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
	Does actual work for OptE minimization Special implementation of get_score that includes logic to handle unfolded state energy calculation. See header file and OptEData.hh for more information. More...

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
	Special implementation of print_score that includes logic to handle unfolded state energy calculation. More...

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
	To be sure we create the right types when writing/reading from files, need to add a special OptEPositionData type that gets returned here. More...

virtual void	write_to_file (std::ofstream &outfile) const
	Add a special for loop to print out the unfolded state energy EnergyMap values. More...

virtual void	read_from_file (std::ifstream &infile)

virtual void	write_to_binary_file (std::ofstream &outfile) const
	Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently. More...

virtual void	read_from_binary_file (std::ifstream &infile)
	Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently. More...

void	set_unfolded_energy_emap_vector (utility::vector1< EnergyMap > emap_vector)

utility::vector1< EnergyMap > &	unfolded_energy_emap_vector ()

virtual Size	memory_use () const

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

virtual	~PNatAAOptEPositionData ()

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 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

void	set_position (Size pos_in)

Size	position () const

void	set_native_aa (AA nat_in)

AA	native_aa () const

void	set_neighbor_count (Size nb_in)

Size	neighbor_count () const

void	add_rotamer_line_data (PNatAAOptERotamerDataOP rot_in)

PNatAAOptERotamerDataOPs &	data ()

PNatAAOptERotamerDataOPs const &	data () const

PNatAAOptERotamerDataOPs::const_iterator	rotamer_data_begin () const

PNatAAOptERotamerDataOPs::const_iterator	rotamer_data_end () 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
utility::vector1< EnergyMap >	unfolded_energy_emap_vector_
	used by derived class as well – finds the energies for the best rotamer for each amino acid More...

Additional Inherited Members
Public Types inherited from protocols::optimize_weights::PNatAAOptEPositionData
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

Protected Member Functions inherited from protocols::optimize_weights::PNatAAOptEPositionData
void	process_rotamers (Multivec const &vars, Size const num_energy_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list, Size const aa_range, utility::vector1< Real > const &dummy_set, utility::vector1< Real > &best_energy_by_aa, utility::vector1< utility::vector1< Real > > &unweighted_E_dof, Multivec &ref_deriv_weight) const
	used by derived class as well – finds the energies for the best rotamer for each amino acid More...

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...

Constructor & Destructor Documentation

protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::NestedEnergyTermPNatAAOptEPositionData ( )

NestedEnergyTermPNatAAOptEPositionData::NestedEnergyTermPNatAAOptEPositionData()

protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::~NestedEnergyTermPNatAAOptEPositionData ( )

virtual

NestedEnergyTermPNatAAOptEPositionData::~NestedEnergyTermPNatAAOptEPositionData()

Member Function Documentation

Real protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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

Does actual work for OptE minimization Special implementation of get_score that includes logic to handle unfolded state energy calculation. See header file and OptEData.hh for more information.

NestedEnergyTermPNatAAOptEPositionData::get_score()

References core::scoring::TR.

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

virtual

NestedEnergyTermPNatAAOptEPositionData::memory_use()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References size(), and protocols::analysis::total.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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

Special implementation of print_score that includes logic to handle unfolded state energy calculation.

NestedEnergyTermPNatAAOptEPositionData::print_score()

Real protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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).

NestedEnergyTermPNatAAOptEPositionData::process_score()

References cutoff, F, core::scoring::hbond_lr_bb, I, optE::inv_kT_nataa, core::scoring::name_from_score_type(), protocols::sic_dock::neighbor_count(), core::chemical::num_canonical_aas, core::scoring::omega, option, tag, protocols::loops::tt, type, and protocols::comparative_modeling::features::X.

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

virtual

Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently.

NestedEnergyTermPNatAAOptEPositionData::read_from_binary_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

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

virtual

NestedEnergyTermPNatAAOptEPositionData::read_from_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References core::chemical::aa_from_name(), from_string(), getline(), core::chemical::num_canonical_aas, core::scoring::pair, score, core::scoring::ScoreTypeManager::score_type_from_name(), protocols::sparta::section(), ss, and string_split().

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::set_unfolded_energy_emap_vector ( utility::vector1< EnergyMap > emap_vector )

inline

References unfolded_energy_emap_vector_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data().

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

virtual

To be sure we create the right types when writing/reading from files, need to add a special OptEPositionData type that gets returned here.

NestedEnergyTermPNatAAOptEPositionData::type()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References protocols::optimize_weights::prob_native_amino_acid_with_unfolded_energy.

utility::vector1< EnergyMap >& protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::unfolded_energy_emap_vector ( )

inline

References unfolded_energy_emap_vector_.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_binary_file ( std::ofstream & outfile ) const

virtual

Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently.

NestedEnergyTermPNatAAOptEPositionData::write_to_binary_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file ( std::ofstream & outfile ) const

virtual

Add a special for loop to print out the unfolded state energy EnergyMap values.

NestedEnergyTermPNatAAOptEPositionData::write_to_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References core::scoring::n_score_types, core::scoring::name_from_score_type(), protocols::sic_dock::neighbor_count(), core::chemical::num_canonical_aas, rot(), and type.