protocols::pack_daemon::EntityFunc Class Reference

#include <DynamicAggregateFunction.hh>

Public Types
typedef utility::pointer::ReferenceCount	parent
typedef protocols::genetic_algorithm::Entity	Entity
typedef numeric::expression_parser::Expression	Expression
typedef numeric::expression_parser::ExpressionOP	ExpressionOP
typedef numeric::expression_parser::ExpressionCOP	ExpressionCOP
typedef numeric::expression_parser::VariableExpression	VariableExpression
typedef numeric::expression_parser::VariableExpressionOP	VariableExpressionOP
typedef numeric::expression_parser::VariableExpressionCOP	VariableExpressionCOP
typedef numeric::expression_parser::ArithmeticASTExpressionOP	ArithmeticASTExpressionOP
typedef core::Size	Size

Public Member Functions
	EntityFunc ()
virtual	~EntityFunc ()
void	set_num_entity_elements (Size num_ee)
void	initialize_from_input_file (std::istream &input)
core::Real	evaluate (Entity const &entity, bool verbose=false)
ExpressionCOP	variable_expression (numeric::expression_parser::ArithmeticASTValue const &) const
ExpressionCOP	function_expression (numeric::expression_parser::FunctionTokenCOP function, utility::vector1< ExpressionCOP > const &args) const

Private Member Functions
void	initialize_scanner_and_function_names ()
void	process_AA_SET_line (std::string const &line, Size line_number, std::istream &input_line)
void	process_SET_CONDITION_line (std::string const &line, Size line_number, std::istream &input_line)
void	process_SUB_EXPRESSION_line (std::string const &line, Size line_number, std::istream &input_line, std::map< std::string, ArithmeticASTExpressionOP > &expression_asts)
void	process_SCORE_line (std::string const &line, Size line_number, std::istream &input_line, ArithmeticASTExpressionOP &score_expression_ast)
void	turn_expression_ASTs_into_expressions (std::map< std::string, ArithmeticASTExpressionOP > const &expression_asts, ArithmeticASTExpressionOP score_expression_ast)
void	assign_entity_sequence_to_variables (Entity const &entity)

Private Attributes
Size	num_entity_elements_
utility::vector1 < VariableExpressionOP >	entity_aas_
std::map< std::string, utility::vector1< core::Real > >	aa_sets_name_map_
std::map< std::string, Size >	aa_sets_dec_line_
std::map< std::string, ExpressionCOP >	subexpression_name_map_
std::map< std::string, Size >	subexpression_name_dec_line_
std::map< std::string, VariableExpressionOP >	variable_expression_map_
utility::vector1< std::pair < ExpressionCOP, SurrogateVariableExpressionOP > >	expression_evaluation_order_
ExpressionCOP	score_expression_
numeric::expression_parser::ArithmeticScannerOP	scanner_
std::set< std::string >	function_names_
	Function names may not be used as variable names. More...
std::set< std::string >	illegal_variable_names_

Member Typedef Documentation

typedef numeric::expression_parser::ArithmeticASTExpressionOP protocols::pack_daemon::EntityFunc::ArithmeticASTExpressionOP

typedef protocols::genetic_algorithm::Entity protocols::pack_daemon::EntityFunc::Entity

typedef numeric::expression_parser::Expression protocols::pack_daemon::EntityFunc::Expression

typedef numeric::expression_parser::ExpressionCOP protocols::pack_daemon::EntityFunc::ExpressionCOP

typedef numeric::expression_parser::ExpressionOP protocols::pack_daemon::EntityFunc::ExpressionOP

typedef utility::pointer::ReferenceCount protocols::pack_daemon::EntityFunc::parent

typedef core::Size protocols::pack_daemon::EntityFunc::Size

typedef numeric::expression_parser::VariableExpression protocols::pack_daemon::EntityFunc::VariableExpression

typedef numeric::expression_parser::VariableExpressionCOP protocols::pack_daemon::EntityFunc::VariableExpressionCOP

typedef numeric::expression_parser::VariableExpressionOP protocols::pack_daemon::EntityFunc::VariableExpressionOP

Constructor & Destructor Documentation

protocols::pack_daemon::EntityFunc::EntityFunc

(

)

protocols::pack_daemon::EntityFunc::~EntityFunc ( )

virtual

Member Function Documentation

void protocols::pack_daemon::EntityFunc::assign_entity_sequence_to_variables ( Entity const &  entity )

private

References entity_aas_, num_entity_elements_, runtime_assert, protocols::genetic_algorithm::Entity::traits(), and protocols::multistate_design::PosType::type().

Referenced by evaluate().

core::Real protocols::pack_daemon::EntityFunc::evaluate	(	Entity const &	entity,
		bool	verbose = false
	)

References assign_entity_sequence_to_variables(), expression_evaluation_order_, and score_expression_.

ExpressionCOP protocols::pack_daemon::EntityFunc::function_expression	(	numeric::expression_parser::FunctionTokenCOP	function,
		utility::vector1< ExpressionCOP > const &	args
	)		const

References utility::to_string().

Referenced by protocols::pack_daemon::EntityFuncExpressionCreator::handle_function_expression().

void protocols::pack_daemon::EntityFunc::initialize_from_input_file

(

std::istream &

input

)

References initialize_scanner_and_function_names(), num_entity_elements_, process_AA_SET_line(), process_SCORE_line(), process_SET_CONDITION_line(), process_SUB_EXPRESSION_line(), and turn_expression_ASTs_into_expressions().

void protocols::pack_daemon::EntityFunc::initialize_scanner_and_function_names ( )

private

References numeric::expression_parser::ArithmeticScanner::add_function(), numeric::expression_parser::ArithmeticScanner::add_variable(), entity_aas_, function_names_, illegal_variable_names_, num_entity_elements_, scanner_, subexpression_name_dec_line_, subexpression_name_map_, utility::to_string(), and variable_expression_map_.

Referenced by initialize_from_input_file().

void protocols::pack_daemon::EntityFunc::process_AA_SET_line ( std::string const &  line, Size  line_number, std::istream &  input_line  )

private

References core::chemical::aa_from_oneletter_code(), aa_sets_dec_line_, aa_sets_name_map_, function_names_, illegal_variable_names_, core::chemical::oneletter_code_specifies_aa(), subexpression_name_dec_line_, subexpression_name_map_, and utility::to_string().

Referenced by initialize_from_input_file().

void protocols::pack_daemon::EntityFunc::process_SCORE_line ( std::string const &  line, Size  line_number, std::istream &  input_line, ArithmeticASTExpressionOP &  score_expression_ast  )

private

References numeric::expression_parser::ArithmeticScanner::scan(), scanner_, and utility::to_string().

Referenced by initialize_from_input_file().

void protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line ( std::string const &  line, Size  line_number, std::istream &  input_line  )

private

References core::chemical::aa_from_oneletter_code(), aa_sets_dec_line_, aa_sets_name_map_, numeric::expression_parser::ArithmeticScanner::add_variable(), expression_evaluation_order_, function_names_, illegal_variable_names_, num_entity_elements_, core::chemical::oneletter_code_specifies_aa(), scanner_, subexpression_name_dec_line_, subexpression_name_map_, utility::to_string(), and variable_expression_map_.

Referenced by initialize_from_input_file().

void protocols::pack_daemon::EntityFunc::process_SUB_EXPRESSION_line ( std::string const &  line, Size  line_number, std::istream &  input_line, std::map< std::string, ArithmeticASTExpressionOP > &  expression_asts  )

private

References aa_sets_dec_line_, aa_sets_name_map_, numeric::expression_parser::ArithmeticScanner::add_variable(), expression_evaluation_order_, function_names_, illegal_variable_names_, numeric::expression_parser::ArithmeticScanner::scan(), scanner_, subexpression_name_dec_line_, subexpression_name_map_, utility::to_string(), and variable_expression_map_.

Referenced by initialize_from_input_file().

void protocols::pack_daemon::EntityFunc::set_num_entity_elements

(

Size

num_ee

)

References num_entity_elements_.

void protocols::pack_daemon::EntityFunc::turn_expression_ASTs_into_expressions ( std::map< std::string, ArithmeticASTExpressionOP > const &  expression_asts, ArithmeticASTExpressionOP  score_expression_ast  )

private

References expression_evaluation_order_, score_expression_, and subexpression_name_map_.

Referenced by initialize_from_input_file().

ExpressionCOP protocols::pack_daemon::EntityFunc::variable_expression

(

numeric::expression_parser::ArithmeticASTValue const &

var_node

)

const

References numeric::expression_parser::ArithmeticASTValue::is_literal(), numeric::expression_parser::ArithmeticASTValue::literal_value(), utility::to_string(), utility_exit_with_message, variable_expression_map_, and numeric::expression_parser::ArithmeticASTValue::variable_name().

Referenced by protocols::pack_daemon::EntityFuncExpressionCreator::handle_variable_expression().

Member Data Documentation

std::map< std::string, Size > protocols::pack_daemon::EntityFunc::aa_sets_dec_line_

private

Referenced by process_AA_SET_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

std::map< std::string, utility::vector1< core::Real > > protocols::pack_daemon::EntityFunc::aa_sets_name_map_

private

Referenced by process_AA_SET_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

utility::vector1< VariableExpressionOP > protocols::pack_daemon::EntityFunc::entity_aas_

private

Referenced by assign_entity_sequence_to_variables(), and initialize_scanner_and_function_names().

utility::vector1< std::pair< ExpressionCOP, SurrogateVariableExpressionOP > > protocols::pack_daemon::EntityFunc::expression_evaluation_order_

private

Evaluate the subexpressions and then store them in the surrogate variable expressions in order.

Referenced by evaluate(), process_SET_CONDITION_line(), process_SUB_EXPRESSION_line(), and turn_expression_ASTs_into_expressions().

std::set< std::string > protocols::pack_daemon::EntityFunc::function_names_

private

Function names may not be used as variable names.

Referenced by initialize_scanner_and_function_names(), process_AA_SET_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

std::set< std::string > protocols::pack_daemon::EntityFunc::illegal_variable_names_

private

This set represents strings that may not be used as variable names but which are not funciton names

Referenced by initialize_scanner_and_function_names(), process_AA_SET_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

Size protocols::pack_daemon::EntityFunc::num_entity_elements_

private

Referenced by assign_entity_sequence_to_variables(), initialize_from_input_file(), initialize_scanner_and_function_names(), process_SET_CONDITION_line(), and set_num_entity_elements().

numeric::expression_parser::ArithmeticScannerOP protocols::pack_daemon::EntityFunc::scanner_

private

Referenced by initialize_scanner_and_function_names(), process_SCORE_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

ExpressionCOP protocols::pack_daemon::EntityFunc::score_expression_

private

Referenced by evaluate(), and turn_expression_ASTs_into_expressions().

std::map< std::string, Size > protocols::pack_daemon::EntityFunc::subexpression_name_dec_line_

private

Referenced by initialize_scanner_and_function_names(), process_AA_SET_line(), process_SET_CONDITION_line(), and process_SUB_EXPRESSION_line().

std::map< std::string, ExpressionCOP > protocols::pack_daemon::EntityFunc::subexpression_name_map_

private

Referenced by initialize_scanner_and_function_names(), process_AA_SET_line(), process_SET_CONDITION_line(), process_SUB_EXPRESSION_line(), and turn_expression_ASTs_into_expressions().

std::map< std::string, VariableExpressionOP > protocols::pack_daemon::EntityFunc::variable_expression_map_

private

Referenced by initialize_scanner_and_function_names(), process_SET_CONDITION_line(), process_SUB_EXPRESSION_line(), and variable_expression().

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

• symlinks/rosetta/src/protocols/pack_daemon/DynamicAggregateFunction.hh
• symlinks/rosetta/src/protocols/pack_daemon/DynamicAggregateFunction.cc