OptE mode multifunction class. More...

#include <OptEMultifunc.hh>

Inheritance diagram for protocols::optimize_weights::WrapperOptEMultifunc:

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 Types inherited from core::optimization::Multifunc
typedef utility::VirtualBase	parent

Public Member Functions
	WrapperOptEMultifunc ()

void	init (ScoreTypes const &free_score_list, core::Size free_count, ScoreTypes const &fixed_score_list, EnergyMap const &fixed_scores, OptEMultifuncOP optEfunc)

	~WrapperOptEMultifunc () override

WrapperOptEMultifuncCOP	get_self_ptr () const
	self pointers More...

WrapperOptEMultifuncOP	get_self_ptr ()

WrapperOptEMultifuncCAP	get_self_weak_ptr () const

WrapperOptEMultifuncAP	get_self_weak_ptr ()

Real	operator() (Multivec const &vars) const override

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

core::Size	n_real_dofs () const

utility::vector1< Real >	derived_dofs (Multivec const &vars) const

void	print_dofs (Multivec const &vars, std::ostream &ostr) const

numeric::expression_parser::VariableExpressionOP	register_variable_expression (std::string varname)

void	set_multifunc (OptEMultifuncOP multifunc)

Public Member Functions inherited from core::optimization::Multifunc
	~Multifunc () override=default
	Destructor. More...

virtual bool	abort_min (Multivec const &) const
	Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN! More...

virtual void	dump (Multivec const &, Multivec const &) const
	Error state reached – derivative does not match gradient Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect. More...

Private Attributes
ScoreTypes	free_score_list_

ScoreTypes	fixed_score_list_

EnergyMap	fixed_scores_

std::set< std::string >	free_score_names_

std::set< std::string >	fixed_score_names_

std::set< std::string >	new_dof_names_
	Dofs added by "NEW_DOF" lines in the wrapper input file. More...

std::set< std::string >	dependent_dof_names_
	Dofs marked as dependent by "DEPENDENT_DOF" lines in the wrapper input file. More...

std::set< std::string >	valid_variable_names_
	union of ( free_score_names_ - dependent_dof_names_ ) + fixed_score_names_ + new_dof_names More...

std::set< std::string >	active_variables_this_dependent_dof_

std::map< std::string, OptEVariableExpressionOP >	dof_variables_

std::map< std::string, core::Size >	optEmultifunc_dof_order_

utility::vector1 < numeric::expression_parser::ExpressionCOP >	optE_dof_expressions_

utility::vector1< std::set < std::string > >	active_variables_
	Which variables influence each optE-percieved-dofs? More...

utility::vector1< std::list < std::pair< core::Size, numeric::expression_parser::ExpressionCOP > > >	real_dof_deriviative_expressions_
	For each real dof, a list of each derivative expression and associated optE-percieved-dof id. More...

OptEMultifuncOP	multifunc_

core::Size	n_real_dofs_

Additional Inherited Members
Protected Member Functions inherited from core::optimization::Multifunc
	Multifunc ()
	Default constructor. More...

	Multifunc (Multifunc const &)
	Copy constructor. More...

Multifunc &	operator= (Multifunc const &)
	Copy assignment. More...

Detailed Description

OptE mode multifunction class.

DANGER DANGER DANGER This class must never be allocated on the stack. Instead, it should be allocated (with "new") on the heap. This class hands an owning-pointer to itself to another class to create a call-back mechanism; this owning pointer will be invalid and result in stack corruption if this class is allocated on the stack.

Member Typedef Documentation

typedef core::scoring::EnergyMap protocols::optimize_weights::WrapperOptEMultifunc::EnergyMap

typedef core::optimization::Multivec protocols::optimize_weights::WrapperOptEMultifunc::Multivec

typedef core::Real protocols::optimize_weights::WrapperOptEMultifunc::Real

typedef core::scoring::ScoreTypes protocols::optimize_weights::WrapperOptEMultifunc::ScoreTypes

typedef core::Size protocols::optimize_weights::WrapperOptEMultifunc::Size

Constructor & Destructor Documentation

protocols::optimize_weights::WrapperOptEMultifunc::WrapperOptEMultifunc ( )

default

protocols::optimize_weights::WrapperOptEMultifunc::~WrapperOptEMultifunc ( )

override

Member Function Documentation

utility::vector1< Real > protocols::optimize_weights::WrapperOptEMultifunc::derived_dofs ( Multivec const & vars ) const

References dof_variables_, and optE_dof_expressions_.

Referenced by dfunc(), and operator()().

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

overridevirtual

OptE dfunc.

Implements core::optimization::Multifunc.

References derived_dofs(), core::chemical::element::F, multifunc_, real_dof_deriviative_expressions_, and protocols::optimize_weights::TR().

WrapperOptEMultifuncCOP protocols::optimize_weights::WrapperOptEMultifunc::get_self_ptr ( ) const

inline

self pointers

WrapperOptEMultifuncOP protocols::optimize_weights::WrapperOptEMultifunc::get_self_ptr ( )

inline

WrapperOptEMultifuncCAP protocols::optimize_weights::WrapperOptEMultifunc::get_self_weak_ptr ( ) const

inline

Referenced by init().

WrapperOptEMultifuncAP protocols::optimize_weights::WrapperOptEMultifunc::get_self_weak_ptr ( )

inline

void protocols::optimize_weights::WrapperOptEMultifunc::init	(	ScoreTypes const &	free_score_list,
		core::Size	free_count,
		ScoreTypes const &	fixed_score_list,
		EnergyMap const &	fixed_scores,
		OptEMultifuncOP	optEfunc
	)

References active_variables_, active_variables_this_dependent_dof_, dof_variables_, fixed_score_list_, fixed_scores_, free_score_list_, free_score_names_, get_self_weak_ptr(), multifunc_, n_real_dofs_, core::scoring::name_from_score_type(), new_dof_names_, core::chemical::num_canonical_aas, optE_dof_expressions_, optEmultifunc_dof_order_, real_dof_deriviative_expressions_, core::id::to_string(), and valid_variable_names_.

Size protocols::optimize_weights::WrapperOptEMultifunc::n_real_dofs ( ) const

References n_real_dofs_.

core::Real protocols::optimize_weights::WrapperOptEMultifunc::operator() ( Multivec const & vars ) const

overridevirtual

Implements core::optimization::Multifunc.

References derived_dofs(), core::chemical::element::F, protocols::hybridization::score, and protocols::optimize_weights::TR().

void protocols::optimize_weights::WrapperOptEMultifunc::print_dofs	(	Multivec const &	vars,
		std::ostream &	ostr
	)		const

References dof_variables_.

numeric::expression_parser::VariableExpressionOP protocols::optimize_weights::WrapperOptEMultifunc::register_variable_expression ( std::string varname )

References active_variables_this_dependent_dof_, dependent_dof_names_, dof_variables_, fixed_score_names_, fixed_scores_, free_score_names_, new_dof_names_, core::scoring::ScoreTypeManager::score_type_from_name(), and valid_variable_names_.

void protocols::optimize_weights::WrapperOptEMultifunc::set_multifunc ( OptEMultifuncOP multifunc )

References multifunc_.

Member Data Documentation

utility::vector1< std::set< std::string > > protocols::optimize_weights::WrapperOptEMultifunc::active_variables_

private

Which variables influence each optE-percieved-dofs?

Referenced by init().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::active_variables_this_dependent_dof_

private

During expression creation; keep track of which variables are active. This set Eventually ends up in the active_varibles_ array, and will be used to create derivative expressions.

Referenced by init(), and register_variable_expression().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::dependent_dof_names_

private

Dofs marked as dependent by "DEPENDENT_DOF" lines in the wrapper input file.

Referenced by register_variable_expression().

std::map< std::string, OptEVariableExpressionOP > protocols::optimize_weights::WrapperOptEMultifunc::dof_variables_

private

Not every VariableExpression object registered by the ExpressionVisitor will end up in this map – variables for fixed_score terms are not kept here, they are simply given a fixed value and never asked to update that value. Every vaiable in this list has its value updated at the beginning of scoring.

Referenced by derived_dofs(), init(), print_dofs(), and register_variable_expression().

ScoreTypes protocols::optimize_weights::WrapperOptEMultifunc::fixed_score_list_

private

Referenced by init().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::fixed_score_names_

private

Referenced by register_variable_expression().

EnergyMap protocols::optimize_weights::WrapperOptEMultifunc::fixed_scores_

private

Referenced by init(), and register_variable_expression().

ScoreTypes protocols::optimize_weights::WrapperOptEMultifunc::free_score_list_

private

Referenced by init().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::free_score_names_

private

Referenced by init(), and register_variable_expression().

OptEMultifuncOP protocols::optimize_weights::WrapperOptEMultifunc::multifunc_

private

Referenced by dfunc(), init(), and set_multifunc().

core::Size protocols::optimize_weights::WrapperOptEMultifunc::n_real_dofs_

private

Referenced by init(), and n_real_dofs().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::new_dof_names_

private

Dofs added by "NEW_DOF" lines in the wrapper input file.

Referenced by init(), and register_variable_expression().

utility::vector1< numeric::expression_parser::ExpressionCOP > protocols::optimize_weights::WrapperOptEMultifunc::optE_dof_expressions_

private

non-depdendent dofs are handled by VariableExpressions that map from the real_dof id to the optE-percieved-dof id.

Referenced by derived_dofs(), and init().

std::map< std::string, core::Size > protocols::optimize_weights::WrapperOptEMultifunc::optEmultifunc_dof_order_

private

Referenced by init().

utility::vector1< std::list< std::pair< core::Size, numeric::expression_parser::ExpressionCOP > > > protocols::optimize_weights::WrapperOptEMultifunc::real_dof_deriviative_expressions_

private

For each real dof, a list of each derivative expression and associated optE-percieved-dof id.

Referenced by dfunc(), and init().

std::set< std::string > protocols::optimize_weights::WrapperOptEMultifunc::valid_variable_names_

private

union of ( free_score_names_ - dependent_dof_names_ ) + fixed_score_names_ + new_dof_names

Referenced by init(), and register_variable_expression().

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

src/protocols/optimize_weights/OptEMultifunc.hh
src/protocols/optimize_weights/OptEMultifunc.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation