protocols::pack_daemon::EntityFunc Class Reference

#include <DynamicAggregateFunction.hh>

Inheritance diagram for protocols::pack_daemon::EntityFunc:

Public Types
typedef utility::VirtualBase	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 ()
	~EntityFunc () override
void	set_num_entity_elements (core::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, core::Size line_number, std::istream &input_line)
void	process_SET_CONDITION_line (std::string const &line, core::Size line_number, std::istream &input_line)
void	process_SUB_EXPRESSION_line (std::string const &line, core::Size line_number, std::istream &input_line, std::map< std::string, ArithmeticASTExpressionOP > &expression_asts)
void	process_SCORE_line (std::string const &line, core::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
core::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, core::Size >	aa_sets_dec_line_
std::map< std::string, ExpressionCOP >	subexpression_name_map_
std::map< std::string, core::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

ArithmeticASTExpressionOP

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

Entity

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

Expression

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

ExpressionCOP

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

ExpressionOP

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

parent

typedef utility::VirtualBase protocols::pack_daemon::EntityFunc::parent

Size

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

VariableExpression

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

VariableExpressionCOP

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

VariableExpressionOP

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

Constructor & Destructor Documentation

EntityFunc()

protocols::pack_daemon::EntityFunc::EntityFunc

(

)

~EntityFunc()

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

overridedefault

Member Function Documentation

assign_entity_sequence_to_variables()

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

private

References entity_aas_, num_entity_elements_, and protocols::genetic_algorithm::Entity::traits().

Referenced by evaluate().

evaluate()

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

References assign_entity_sequence_to_variables(), expression_evaluation_order_, score_expression_, and protocols::pack_daemon::TR().

function_expression()

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

References core::id::to_string().

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

initialize_from_input_file()

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().

initialize_scanner_and_function_names()

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

private

References entity_aas_, function_names_, illegal_variable_names_, num_entity_elements_, scanner_, subexpression_name_dec_line_, subexpression_name_map_, core::id::to_string(), and variable_expression_map_.

Referenced by initialize_from_input_file().

process_AA_SET_line()

void protocols::pack_daemon::EntityFunc::process_AA_SET_line ( std::string const &  line, core::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 core::id::to_string().

Referenced by initialize_from_input_file().

process_SCORE_line()

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

private

References scanner_, core::id::to_string(), and protocols::pack_daemon::TR().

Referenced by initialize_from_input_file().

process_SET_CONDITION_line()

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

private

References core::chemical::aa_from_oneletter_code(), aa_sets_dec_line_, aa_sets_name_map_, 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_, core::id::to_string(), and variable_expression_map_.

Referenced by initialize_from_input_file().

process_SUB_EXPRESSION_line()

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

private

References aa_sets_dec_line_, aa_sets_name_map_, expression_evaluation_order_, function_names_, illegal_variable_names_, scanner_, subexpression_name_dec_line_, subexpression_name_map_, core::id::to_string(), protocols::pack_daemon::TR(), and variable_expression_map_.

Referenced by initialize_from_input_file().

set_num_entity_elements()

void protocols::pack_daemon::EntityFunc::set_num_entity_elements

(

core::Size

num_ee

)

References num_entity_elements_.

turn_expression_ASTs_into_expressions()

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().

variable_expression()

ExpressionCOP protocols::pack_daemon::EntityFunc::variable_expression

(

numeric::expression_parser::ArithmeticASTValue const &

)

const

References core::id::to_string(), and variable_expression_map_.

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

Member Data Documentation

aa_sets_dec_line_

std::map< std::string, core::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().

aa_sets_name_map_

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().

entity_aas_

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

private

Referenced by assign_entity_sequence_to_variables(), and initialize_scanner_and_function_names().

expression_evaluation_order_

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().

function_names_

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().

illegal_variable_names_

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().

num_entity_elements_

core::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().

scanner_

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().

score_expression_

ExpressionCOP protocols::pack_daemon::EntityFunc::score_expression_

private

Referenced by evaluate(), and turn_expression_ASTs_into_expressions().

subexpression_name_dec_line_

std::map< std::string, core::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().

subexpression_name_map_

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().

variable_expression_map_

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:

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