OptE mode multifunction class. More...

#include <OptEMultifunc.hh>

Public Types
typedef core::scoring::ScoreTypes	ScoreTypes

typedef core::scoring::EnergyMap	EnergyMap

typedef core::optimization::Multivec	Multivec

typedef core::Real	Real

typedef core::Size	Size

Public Member Functions
	OptEMultifunc (OptEData &opte_data_in, EnergyMap const &fixed_terms_in, int num_free_in, ScoreTypes &score_list_in, ScoreTypes &fixed_score_list_in, Multivec const &component_weights)

	OptEMultifunc (OptEData &opte_data_in, EnergyMap const &fixed_terms_in, int num_free_in, ScoreTypes const &score_list_in, ScoreTypes const &fixed_score_list_in, utility::vector1< Real > const &reference_energies_in, Multivec const &component_weights)

virtual	~OptEMultifunc ()
	Destructor. More...

virtual Real	operator() (Multivec const &vars) const
	The objective function for optE. Called in IterativeOptEDriver when optimizing the weights. Sums over all of the PositionData objects in the OptEData object, and calls get_score() on each of them. Each PositionData object implements print_score() and get_score() methods that print/return how good a weight set is for optimizing the metric that PositionData object represents. More...

virtual void	dfunc (Multivec const &vars, Multivec &dE_dvars) const
	OptE dfunc. More...

Multivec	get_dofs_from_energy_map (EnergyMap const &start_vals) const
	Does actual work for OptE minimization. More...

EnergyMap	get_energy_map_from_dofs (Multivec const &dofs) const
	Expand free variables and combine with fixed to make an Energy Map. More...

utility::vector1< Real >	get_reference_energies_from_dofs (Multivec const &dofs) const

void	set_starting_reference_energies (utility::vector1< Real > const &values)

void	wait_for_remote_vars () const
	Non-driver node wait for MPI vars to evaluate either the func or the dfunc. More...

void	declare_minimization_over () const
	For driver node: inform the non-driver nodes that minimization is over. Must be called before object is destructed (Should not be called in the destructor, as dstors should not throw exceptions, and MPI communication can absolutely result in exceptions). More...

void	fix_reference_energies (bool setting)

bool	fix_reference_energies () const
	Are the reference energies being optimized at all, or are they being held fixed? More...

Public Member Functions inherited from core::optimization::Multifunc
virtual void	dump (Multivec const &, Multivec const &) const

Private Member Functions
void	mpi_broadcast_eval_func (Multivec const &vars) const
	send out messages over MPI for remote nodes to evaluate their func given the input vars. More...

void	mpi_broadcast_eval_dfunc (Multivec const &vars) const
	send out messages over MPI for remote nodes to evaluate their dfunc given the input vars. More...

void	mpi_broadcast_send_vars (Multivec const &vars) const

void	mpi_broadcast_receive_vars (Multivec &vars) const

Real	mpi_receive_func () const
	collect func values from remote nodes and return their sum. More...

void	mpi_receive_dfunc (Multivec &dE_vars) const
	collect dfunc valresultsues from remote nodes and increment the values in the dE_dvars input array. More...

Private Attributes
Size const	num_energy_dofs_

int const	num_ref_dofs_

int const	num_total_dofs_

OptEData const &	opte_data_
	Rotamer energy components for all positions. More...

EnergyMap const &	fixed_terms_

ScoreTypes const &	score_list_

ScoreTypes const &	fixed_score_list_

bool	fix_reference_energies_

utility::vector1< Real >	starting_reference_energies_

Multivec	component_weights_

int	mpi_rank_

int	mpi_nprocs_

bool	distribute_over_mpi_

Detailed Description

OptE mode multifunction class.

Member Typedef Documentation

typedef core::scoring::EnergyMap protocols::optimize_weights::OptEMultifunc::EnergyMap

typedef core::optimization::Multivec protocols::optimize_weights::OptEMultifunc::Multivec

typedef core::Real protocols::optimize_weights::OptEMultifunc::Real

typedef core::scoring::ScoreTypes protocols::optimize_weights::OptEMultifunc::ScoreTypes

typedef core::Size protocols::optimize_weights::OptEMultifunc::Size

Constructor & Destructor Documentation

protocols::optimize_weights::OptEMultifunc::OptEMultifunc	(	OptEData &	opte_data_in,
		EnergyMap const &	fixed_terms_in,
		int	num_free_in,
		ScoreTypes &	score_list_in,
		ScoreTypes &	fixed_score_list_in,
		Multivec const &	component_weights
	)

OptEMultifunc::OptEMultifunc

References chemical, distribute_over_mpi_, mpi_nprocs_, mpi_rank_, basic::options::OptionKeys::optE::mpi_weight_minimization, num_canonical_aas, and basic::options::option.

protocols::optimize_weights::OptEMultifunc::OptEMultifunc	(	OptEData &	opte_data_in,
		EnergyMap const &	fixed_terms_in,
		int	num_free_in,
		ScoreTypes const &	score_list_in,
		ScoreTypes const &	fixed_score_list_in,
		utility::vector1< Real > const &	reference_energies_in,
		Multivec const &	component_weights
	)

OptEMultifunc::OptEMultifunc

References distribute_over_mpi_, mpi_nprocs_, mpi_rank_, basic::options::OptionKeys::optE::mpi_weight_minimization, basic::options::option, and size().

virtual protocols::optimize_weights::OptEMultifunc::~OptEMultifunc ( )

inlinevirtual

Destructor.

Member Function Documentation

void protocols::optimize_weights::OptEMultifunc::declare_minimization_over ( ) const

For driver node: inform the non-driver nodes that minimization is over. Must be called before object is destructed (Should not be called in the destructor, as dstors should not throw exceptions, and MPI communication can absolutely result in exceptions).

References protocols::optimize_weights::END_OF_MINIMIZATION.

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

void protocols::optimize_weights::OptEMultifunc::dfunc	(	Multivec const &	vars,
		Multivec &	dE_dvars
	)		const

virtual

OptE dfunc.

OptE dfunc – gets the partial derivatives of func for each dimension being minimized.

Implements core::optimization::Multifunc.

References component_weights_, distribute_over_mpi_, fix_reference_energies_, fixed_score_list_, fixed_terms_, mpi_broadcast_eval_dfunc(), mpi_rank_, mpi_receive_dfunc(), num_energy_dofs_, num_ref_dofs_, num_total_dofs_, opte_data_, protocols::optimize_weights::OptEPositionDataFactory::optE_type_name(), protocols::optimize_weights::OptEData::position_data_begin(), protocols::optimize_weights::OptEData::position_data_end(), score, score_list_, starting_reference_energies_, and protocols::optimize_weights::TR.

Referenced by wait_for_remote_vars().

void protocols::optimize_weights::OptEMultifunc::fix_reference_energies ( bool setting )

inline

References fix_reference_energies_.

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

bool protocols::optimize_weights::OptEMultifunc::fix_reference_energies ( ) const

inline

Are the reference energies being optimized at all, or are they being held fixed?

References fix_reference_energies_.

Multivec protocols::optimize_weights::OptEMultifunc::get_dofs_from_energy_map ( EnergyMap const & start_vals ) const

Does actual work for OptE minimization.

Extract variable weights from an Energy Map.

Extract variable weights from an Energy Map

OptEMultifunc::get_dofs_from_energy_map()

References fix_reference_energies_, num_energy_dofs_, num_total_dofs_, score_list_, and starting_reference_energies_.

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

EnergyMap protocols::optimize_weights::OptEMultifunc::get_energy_map_from_dofs ( Multivec const & dofs ) const

Expand free variables and combine with fixed to make an Energy Map.

Expand free variables and combine with fixed to make an Energy Map. Used by the IterativeOptEDriver at the end of weight minimization to create an EnergyMap that uses the new weight set. This EnergyMap then gets output into a optE log file.

OptEMultifunc::get_energy_map_from_dofs()

References fixed_score_list_, fixed_terms_, and score_list_.

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

utility::vector1< Real > protocols::optimize_weights::OptEMultifunc::get_reference_energies_from_dofs ( Multivec const & dofs ) const

References fix_reference_energies_, num_energy_dofs_, num_ref_dofs_, and starting_reference_energies_.

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

void protocols::optimize_weights::OptEMultifunc::mpi_broadcast_eval_dfunc ( Multivec const & vars ) const

private

send out messages over MPI for remote nodes to evaluate their dfunc given the input vars.

References protocols::optimize_weights::EVAL_DFUNC, mpi_broadcast_send_vars(), and vars.

Referenced by dfunc().

void protocols::optimize_weights::OptEMultifunc::mpi_broadcast_eval_func ( Multivec const & vars ) const

private

send out messages over MPI for remote nodes to evaluate their func given the input vars.

References protocols::optimize_weights::EVAL_FUNC, mpi_broadcast_send_vars(), and vars.

Referenced by operator()().

void protocols::optimize_weights::OptEMultifunc::mpi_broadcast_receive_vars ( Multivec & vars ) const

private

References vars.

Referenced by wait_for_remote_vars().

void protocols::optimize_weights::OptEMultifunc::mpi_broadcast_send_vars ( Multivec const & vars ) const

private

References vars.

Referenced by mpi_broadcast_eval_dfunc(), and mpi_broadcast_eval_func().

void protocols::optimize_weights::OptEMultifunc::mpi_receive_dfunc ( Multivec & dE_vars ) const

private

collect dfunc valresultsues from remote nodes and increment the values in the dE_dvars input array.

References mpi_nprocs_.

Referenced by dfunc().

Real protocols::optimize_weights::OptEMultifunc::mpi_receive_func ( ) const

private

collect func values from remote nodes and return their sum.

References mpi_nprocs_, and protocols::analysis::total.

Referenced by operator()().

Real protocols::optimize_weights::OptEMultifunc::operator() ( Multivec const & vars ) const

virtual

The objective function for optE. Called in IterativeOptEDriver when optimizing the weights. Sums over all of the PositionData objects in the OptEData object, and calls get_score() on each of them. Each PositionData object implements print_score() and get_score() methods that print/return how good a weight set is for optimizing the metric that PositionData object represents.

OptEMultifunc::operator()

Implements core::optimization::Multifunc.

References component_weights_, distribute_over_mpi_, utility::exit(), fix_reference_energies_, fixed_score_list_, fixed_terms_, basic::options::OptionKeys::optE::limit_bad_scores, mpi_broadcast_eval_func(), mpi_rank_, mpi_receive_func(), num_energy_dofs_, num_ref_dofs_, num_total_dofs_, opte_data_, protocols::optimize_weights::OptEPositionDataFactory::optE_type_name(), basic::options::option, protocols::optimize_weights::OptEData::position_data_begin(), protocols::optimize_weights::OptEData::position_data_end(), s, score, score_list_, starting_reference_energies_, protocols::optimize_weights::TR, and user.