#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatAAOptEPositionData:

Collaboration diagram for protocols::optimize_weights::PNatAAOptEPositionData:

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
	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

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_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

Protected Member Functions
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...

Private Attributes
Size	position_

AA	native_aa_

Size	neighbor_count_

PNatAAOptERotamerDataOPs	data_

Member Typedef Documentation

typedef core::chemical::AA protocols::optimize_weights::PNatAAOptEPositionData::AA

Constructor & Destructor Documentation

protocols::optimize_weights::PNatAAOptEPositionData::PNatAAOptEPositionData ( )

protocols::optimize_weights::PNatAAOptEPositionData::~PNatAAOptEPositionData ( )

virtual

Member Function Documentation

void protocols::optimize_weights::PNatAAOptEPositionData::add_rotamer_line_data ( PNatAAOptERotamerDataOP rot_in)

inline

References data_.

PNatAAOptERotamerDataOPs& protocols::optimize_weights::PNatAAOptEPositionData::data ( )

inline

References data_.

PNatAAOptERotamerDataOPs const& protocols::optimize_weights::PNatAAOptEPositionData::data ( ) const

inline

References data_.

Real protocols::optimize_weights::PNatAAOptEPositionData::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

Does actual work for OptE minimization

Determine the metric for optimization of energy weights. Original source is Brian Kuhlman's FORTRAN weight training program. Since the goal is to maximize site-by-site sequence recovery, the metric is decomposable by positions, and this does the work for one position. First, a pass is made through all the rotamers at the position, and the lowest energy rotamer for each amino acid is identified. Next, a rough partition function is constructed. The score to be minimized is the negative log of the probabilty of selecting a native aa rotamer (needn't be the native conformation).

Limitations:

Assumes that the choices available at each position are the 20 canonical amino acids - no DNA base recovery, no pTyr.
Doesn't have Chris Saunder's compositional constraints. This would require implementation of a direction-set ( aka powell ) minimizer, as his optimization metric doesn't yield gradients.

Parameters

num_energy_dofs Basically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData.

References core::chemical::num_canonical_aas.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

AA protocols::optimize_weights::PNatAAOptEPositionData::native_aa ( ) const

inline

References native_aa_.

Size protocols::optimize_weights::PNatAAOptEPositionData::neighbor_count ( ) const

inline

References neighbor_count_.

Size protocols::optimize_weights::PNatAAOptEPositionData::position ( ) const

inline

References position_.

void protocols::optimize_weights::PNatAAOptEPositionData::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::PSSMOptEPositionData.

References protocols::sic_dock::neighbor_count(), core::chemical::num_canonical_aas, and core::scoring::rna::X.

void protocols::optimize_weights::PNatAAOptEPositionData::process_rotamers	(	optimization::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,
		optimization::Multivec &	ref_deriv_weight
	)		const

protected

used by derived class as well – finds the energies for the best rotamer for each amino acid

void protocols::optimize_weights::PNatAAOptEPositionData::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.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

References core::chemical::aa_unk.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

References core::chemical::aa_from_name().

PNatAAOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_begin ( ) const

inline

References data_.

PNatAAOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatAAOptEPositionData::rotamer_data_end ( ) const

inline

References data_.

void protocols::optimize_weights::PNatAAOptEPositionData::set_native_aa ( AA nat_in)

inline

References native_aa_.

void protocols::optimize_weights::PNatAAOptEPositionData::set_neighbor_count ( Size nb_in)

inline

References neighbor_count_.

void protocols::optimize_weights::PNatAAOptEPositionData::set_position ( Size pos_in)

inline

References position_.

virtual Size protocols::optimize_weights::PNatAAOptEPositionData::size ( ) const

inlinevirtual

Implements protocols::optimize_weights::OptEPositionData.

References data_.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

References protocols::optimize_weights::prob_native_amino_acid.

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

References rot(), and core::io::serialization::size().

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

virtual

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PSSMOptEPositionData, and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData.

References protocols::sic_dock::neighbor_count(), and rot().

Member Data Documentation

PNatAAOptERotamerDataOPs protocols::optimize_weights::PNatAAOptEPositionData::data_

private

Referenced by add_rotamer_line_data(), data(), rotamer_data_begin(), rotamer_data_end(), and size().

AA protocols::optimize_weights::PNatAAOptEPositionData::native_aa_

private

Referenced by native_aa(), and set_native_aa().

Size protocols::optimize_weights::PNatAAOptEPositionData::neighbor_count_

private

Referenced by neighbor_count(), and set_neighbor_count().

Size protocols::optimize_weights::PNatAAOptEPositionData::position_

private

Referenced by position(), and set_position().

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

src/protocols/optimize_weights/OptEData.hh
src/protocols/optimize_weights/OptEData.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation