OptE mode multifunction class. More...

#include <OptEMultifunc.hh>

Inheritance diagram for protocols::optimize_weights::WrapperOptEMultifunc:

Collaboration 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::pointer::ReferenceCount	parent

Public Member Functions
	WrapperOptEMultifunc (ScoreTypes const &free_score_list, Size free_count, ScoreTypes const &fixed_score_list, EnergyMap const &fixed_scores, OptEMultifuncOP optEfunc)

	~WrapperOptEMultifunc ()

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

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

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
virtual	~Multifunc ()
	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, 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< 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_

Size	n_new_dofs_

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 const &	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.

Definition at line 288 of file OptEMultifunc.hh.

Member Typedef Documentation

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

Definition at line 292 of file OptEMultifunc.hh.

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

Definition at line 293 of file OptEMultifunc.hh.

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

Definition at line 294 of file OptEMultifunc.hh.

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

Definition at line 291 of file OptEMultifunc.hh.

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

Definition at line 295 of file OptEMultifunc.hh.

Constructor & Destructor Documentation

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

Definition at line 547 of file OptEMultifunc.cc.

References active_variables_, active_variables_this_dependent_dof_, dof_variables_, free_score_list_, free_score_names_, n_real_dofs_, core::scoring::ScoreTypeManager::name_from_score_type(), core::scoring::name_from_score_type(), new_dof_names_, core::chemical::num_canonical_aas, optE_dof_expressions_, optEmultifunc_dof_order_, real_dof_deriviative_expressions_, and valid_variable_names_.

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

Definition at line 718 of file OptEMultifunc.cc.

Member Function Documentation

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

Definition at line 774 of file OptEMultifunc.cc.

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

virtual

OptE dfunc.

Implements core::optimization::Multifunc.

Definition at line 741 of file OptEMultifunc.cc.

References derived_dofs(), multifunc_, real_dof_deriviative_expressions_, and protocols::optimize_weights::TR().

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

Definition at line 768 of file OptEMultifunc.cc.

References n_real_dofs_.

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

virtual

Implements core::optimization::Multifunc.

Definition at line 725 of file OptEMultifunc.cc.

References derived_dofs(), and protocols::optimize_weights::TR().

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

Definition at line 795 of file OptEMultifunc.cc.

References dof_variables_.

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

Definition at line 811 of file OptEMultifunc.cc.

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)

Definition at line 866 of file OptEMultifunc.cc.

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?

Definition at line 372 of file OptEMultifunc.hh.

Referenced by WrapperOptEMultifunc().

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.

Definition at line 356 of file OptEMultifunc.hh.

Referenced by register_variable_expression(), and WrapperOptEMultifunc().

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.

Definition at line 348 of file OptEMultifunc.hh.

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.

Definition at line 362 of file OptEMultifunc.hh.

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

ScoreTypes protocols::optimize_weights::WrapperOptEMultifunc::fixed_score_list_

private

Definition at line 338 of file OptEMultifunc.hh.

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

private

Definition at line 342 of file OptEMultifunc.hh.

Referenced by register_variable_expression().

EnergyMap protocols::optimize_weights::WrapperOptEMultifunc::fixed_scores_

private

Definition at line 339 of file OptEMultifunc.hh.

Referenced by register_variable_expression().

ScoreTypes protocols::optimize_weights::WrapperOptEMultifunc::free_score_list_

private

Definition at line 337 of file OptEMultifunc.hh.

Referenced by WrapperOptEMultifunc().

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

private

Definition at line 341 of file OptEMultifunc.hh.

Referenced by register_variable_expression(), and WrapperOptEMultifunc().

OptEMultifuncOP protocols::optimize_weights::WrapperOptEMultifunc::multifunc_

private

Definition at line 376 of file OptEMultifunc.hh.

Referenced by dfunc(), and set_multifunc().

Size protocols::optimize_weights::WrapperOptEMultifunc::n_new_dofs_

private

Definition at line 377 of file OptEMultifunc.hh.

Size protocols::optimize_weights::WrapperOptEMultifunc::n_real_dofs_

private

Definition at line 378 of file OptEMultifunc.hh.

Referenced by n_real_dofs(), and WrapperOptEMultifunc().

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

private

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

Definition at line 345 of file OptEMultifunc.hh.

Referenced by register_variable_expression(), and WrapperOptEMultifunc().

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.

Definition at line 369 of file OptEMultifunc.hh.

Referenced by derived_dofs(), and WrapperOptEMultifunc().

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

private

Definition at line 365 of file OptEMultifunc.hh.

Referenced by WrapperOptEMultifunc().

utility::vector1< std::list< std::pair< 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.

Definition at line 374 of file OptEMultifunc.hh.

Referenced by dfunc(), and WrapperOptEMultifunc().

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

Definition at line 351 of file OptEMultifunc.hh.

Referenced by register_variable_expression(), and WrapperOptEMultifunc().

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