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protocols::pack_daemon::DynamicAggregateFunction Class Reference

#include <DynamicAggregateFunction.hh>

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Public Types

typedef MultistateAggregateFunction 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 utility::vector1
< core::Real > 		ExpressionValues
 
typedef core::Size Size
 
- Public Types inherited from protocols::pack_daemon::MultistateAggregateFunction
typedef
utility::pointer::ReferenceCount 		parent
 
typedef utility::vector1
< core::Real > 		StateEnergies
 
typedef utility::vector1
< core::Size > 		StateIndices
 
typedef
protocols::genetic_algorithm::Entity 		Entity
 

Public Member Functions

 DynamicAggregateFunction ()
 
virtual ~DynamicAggregateFunction ()
 
void set_num_entity_elements (Size setting)
 
void set_score_function (core::scoring::ScoreFunction const &sfxn)
 
core::Size num_states () const
 
core::Size num_npd_properties () const
 
virtual core::Real evaluate (StateEnergies const &, StateEnergies const &npd_properties, Entity const &)
 
virtual StateIndices select_relevant_states (StateEnergies const &en, StateEnergies const &npd, Entity const &)
 
void initialize_from_input_file (DaemonSetOP daemon_set, std::istream &input)
 
ExpressionCOP variable_expression (numeric::expression_parser::ArithmeticASTValue const &) const
 
ExpressionCOP function_expression (numeric::expression_parser::FunctionTokenCOP function, utility::vector1< ExpressionCOP > const &args) const
 
void add_file_contents (std::string const &fname, std::string const &contents)
 Pair a file name with a string – instead of opening a file when asked to read this file, the DAF will use the contents of the file as provided. More...
 
std::string state_name (Size state_index) const
 
- Public Member Functions inherited from protocols::pack_daemon::MultistateAggregateFunction
 MultistateAggregateFunction ()
 
virtual ~MultistateAggregateFunction ()
 

Private Member Functions

void read_all_variables_from_input_file (std::istream &input)
 
void initialize_scanner ()
 
void process_STATE_line (std::string const &line, Size line_number, std::istream &input_line)
 
void process_STATE_VECTOR_line (std::string const &line, Size line_number, std::istream &input_line, utility::vector1< std::pair< std::string, std::string > > &strucvec_filenames)
 
void process_POSE_ENERGY_line (std::string const &line, Size line_number, std::istream &input_line)
 
void process_POSE_ENERGY_VECTOR_line (std::string const &line, Size line_number, std::istream &input_line)
 
void process_NPD_PROPERTY_line (std::string const &line, Size line_number, std::istream &input_line)
 
void process_VECTOR_VARIABLE_line (std::string const &line, Size line_number, std::istream &input_line, std::map< std::string, std::list< std::string > > &vector_variables)
 
void process_SCALAR_EXPRESSION_line (std::string const &line, Size line_number, std::istream &input_line, std::map< std::string, ArithmeticASTExpressionOP > &scalar_expression_asts)
 
void process_VECTOR_EXPRESSION_line (std::string const &line, Size line_number, std::istream &input_line, std::map< std::string, std::pair< std::map< std::string, std::string >, ArithmeticASTExpressionOP > > &vector_expression_list)
 
void process_ENTITY_FUNCTION_line (std::string const &line, Size line_number, std::istream &input_line)
 
void process_FITNESS_line (std::string const &line, Size line_number, std::istream &input_line, ArithmeticASTExpressionOP &fitness_expression_ast)
 
void read_state_vector_file (std::string const &vec_varname, std::string const &fname, Size &n_vector_states)
 
void create_state_variable_expressions (Size &count_state, Size &count_npd_index, Size &count_variable_index)
 
void create_variable_vector_expressions (Size &count_state, Size &count_npd_index, Size &count_variable_index)
 
void create_scalar_and_vector_expression_variable_expressions (std::map< std::string, ArithmeticASTExpressionOP > const &scalar_expression_asts, std::map< std::string, std::list< std::string > > const &vector_variables, Size &count_state)
 
void turn_expression_ASTs_into_expressions (std::map< std::string, ArithmeticASTExpressionOP > const &scalar_expression_asts, std::map< std::string, std::pair< std::map< std::string, std::string >, ArithmeticASTExpressionOP > > const &vector_expression_asts, ArithmeticASTExpressionOP fitness_expression_ast)
 
utility::vector1
< VectorExpressionCOP > 		verify_vector_arguments (std::string const &fname, utility::vector1< ExpressionCOP > const &args, Size expected_nargs) const
 
void verify_variable_name_or_throw (std::string const &vname, std::string const &command_name, std::string const &line, Size line_number)
 
void initialize_pack_daemons (DaemonSetOP daemon_set)
 
void count_file_reads (std::map< std::string, Size > &total_reads, std::map< std::string, Size > &reads_completed) const
 
void increment_total_read_count_for_file (std::string const &fname, std::map< std::string, Size > &total_reads, std::map< std::string, Size > &reads_completed) const
 
std::string get_file_contents (std::string const &filename, std::map< std::string, Size > const &total_reads, std::map< std::string, Size > &reads_completed, std::map< std::string, std::string > &file_contents_map) const
 
void initialize_daemon_with_all_states (DaemonSetOP daemon_set, std::map< std::string, Size > const &total_reads, std::map< std::string, Size > &reads_completed)
 
void distribute_jobs_to_remote_daemons (DaemonSetOP daemon_set, std::map< std::string, Size > const &total_reads, std::map< std::string, Size > &reads_completed)
 
StructureFileNames const & file_inputs_for_job (int job_index) const
 
void assign_jobs_to_local_daemon_set (std::list< int > const &job_indices, DaemonSetOP daemon_set, std::map< std::string, Size > const &total_reads, std::map< std::string, Size > &reads_completed, std::map< std::string, std::string > &file_contents_map) const
 
void assign_jobs_to_remote_daemon_sets (int proc_id, std::list< int > const &job_indices, std::map< std::string, Size > const &total_reads, std::map< std::string, Size > &reads_completed, std::map< std::string, std::string > &file_contents_map) const
 
bool verify_remote_daemon_set_initialization_successful (int proc_id) const
 
void send_success_message_to_remote_daemon_set (int proc_id) const
 
void send_error_message_to_remote_daemon_sets () const
 
void assign_state_energies_to_variables_and_subexpressions (StateEnergies const &state_energies, StateEnergies const &npd_properties, Entity const &entity, bool verbose=false)
 
Size count_num_npd_properties () const
 used to determine the number of requested NPD properties that will be calculated; used to size the variable_expressions_for_npd_properties_ array. More...
 

Private Attributes

Size num_entity_elements_
 
core::scoring::ScoreFunctionOP sfxn_
 
ExpressionCOP fitness_exp_
 
utility::vector1
< VariableExpressionOP > 		variable_expressions_for_states_
 
utility::vector1< std::list
< std::pair< Size, std::string > > > 		npd_variable_indices_for_states_
 
utility::vector1
< VariableExpressionOP > 		variable_expressions_for_npd_properties_
 
utility::vector1
< VariableExpressionOP > 		variable_expressions_
 
numeric::expression_parser::ArithmeticScannerOP scanner_
 
std::list< VectorFunctionOP > vfuncs_
 
std::list< std::pair< Size,
std::string > > 		expression_evaluation_order_by_name_
 
utility::vector1< std::pair
< Size, ExpressionCOP > > 		scalar_expressions_
 
std::map< Size,
SurrogateVariableExpressionOP > 		surrogate_expression_map_
 
std::map< std::string,
VariableExpressionCOP > 		scalar_expression_map_
 
std::map< std::string,
VectorExpressionCOP > 		vector_expression_map_
 
std::set< std::string > state_variable_names_
 
std::set< std::string > state_vector_variable_names_
 
std::map< std::string,
ExpressionCOP > 		named_state_expression_map_
 
std::map< std::string,
VariableVectorExpressionOP > 		state_vector_variables_
 
std::map< std::string,
std::list< std::pair
< std::string, std::string > > > 		npd_properties_for_state_variables_
 
std::map< std::string,
ExpressionCOP > 		npd_property_expression_map_
 
std::map< std::string,
VariableVectorExpressionOP > 		npd_property_vector_expression_map_
 
std::set< std::string > function_names_
 Function names may not be used as variable names. More...
 
std::set< std::string > illegal_variable_names_
 
std::map< std::string, Size > variable_names_dec_line_
 
std::map< std::string, Size > scalar_variable_names_dec_line_
 
std::map< std::string, Size > vector_variable_names_dec_line_
 
std::map< std::string,
std::pair< EntityFuncOP,
VariableExpressionOP > > 		entity_funcs_
 
std::map< std::string, Size > entity_funcs_dec_line_
 
std::map< std::string, Size > variable_name_2_variable_exp_index_
 Keep track for each varible name (or scalar expression name) its index in the ?? vector. More...
 
std::map< std::string, Size > state_variable_name_2_state_index_
 Keep track for each state-variable name its state's index. More...
 
std::map< std::string,
StructureFileNames > 		named_state_data_file_names_
 
std::map< std::string,
utility::vector1
< StructureFileNames > > 		state_vector_data_file_names_
 
utility::vector1
< StructureFileNames > 		files_for_state_
 
std::map< std::string,
utility::vector1< Size > > 		state_indices_for_state_vector_
 
IterativeVectorExpressionOP focused_iterative_vector_expression_
 
std::map< std::string,
std::string > 		file_contents_
 

Detailed Description

Definition at line 466 of file DynamicAggregateFunction.hh.

Member Typedef Documentation

typedef numeric::expression_parser::ArithmeticASTExpressionOP protocols::pack_daemon::DynamicAggregateFunction::ArithmeticASTExpressionOP

Definition at line 481 of file DynamicAggregateFunction.hh.

typedef protocols::genetic_algorithm::Entity protocols::pack_daemon::DynamicAggregateFunction::Entity

Definition at line 471 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::Expression protocols::pack_daemon::DynamicAggregateFunction::Expression

Definition at line 473 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::ExpressionCOP protocols::pack_daemon::DynamicAggregateFunction::ExpressionCOP

Definition at line 475 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::ExpressionOP protocols::pack_daemon::DynamicAggregateFunction::ExpressionOP

Definition at line 474 of file DynamicAggregateFunction.hh.

typedef utility::vector1< core::Real > protocols::pack_daemon::DynamicAggregateFunction::ExpressionValues

Definition at line 483 of file DynamicAggregateFunction.hh.

typedef MultistateAggregateFunction protocols::pack_daemon::DynamicAggregateFunction::parent

Definition at line 469 of file DynamicAggregateFunction.hh.

typedef core::Size protocols::pack_daemon::DynamicAggregateFunction::Size

Definition at line 484 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::VariableExpression protocols::pack_daemon::DynamicAggregateFunction::VariableExpression

Definition at line 477 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::VariableExpressionCOP protocols::pack_daemon::DynamicAggregateFunction::VariableExpressionCOP

Definition at line 479 of file DynamicAggregateFunction.hh.

typedef numeric::expression_parser::VariableExpressionOP protocols::pack_daemon::DynamicAggregateFunction::VariableExpressionOP

Definition at line 478 of file DynamicAggregateFunction.hh.

Constructor & Destructor Documentation

protocols::pack_daemon::DynamicAggregateFunction::DynamicAggregateFunction ( )

Definition at line 551 of file DynamicAggregateFunction.cc.

protocols::pack_daemon::DynamicAggregateFunction::~DynamicAggregateFunction ( )
virtual

Definition at line 552 of file DynamicAggregateFunction.cc.

Member Function Documentation

void protocols::pack_daemon::DynamicAggregateFunction::add_file_contents ( std::string const &  fname,
std::string const &  contents 
)

Pair a file name with a string – instead of opening a file when asked to read this file, the DAF will use the contents of the file as provided.

Definition at line 817 of file DynamicAggregateFunction.cc.

References file_contents_.

void protocols::pack_daemon::DynamicAggregateFunction::assign_jobs_to_local_daemon_set ( std::list< int > const &  job_indices,
DaemonSetOP  daemon_set,
std::map< std::string, Size > const &  total_reads,
std::map< std::string, Size > &  reads_completed,
std::map< std::string, std::string > &  file_contents_map 
) const
private

Definition at line 2316 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::StructureFileNames::correspondence_file_name_, core::sequence::end, file_inputs_for_job(), get_file_contents(), npd_variable_indices_for_states_, protocols::pack_daemon::StructureFileNames::pdb_name_, core::import_pose::pose_from_pdbstring(), and protocols::pack_daemon::StructureFileNames::resfile_name_.

Referenced by distribute_jobs_to_remote_daemons(), and initialize_daemon_with_all_states().

void protocols::pack_daemon::DynamicAggregateFunction::assign_jobs_to_remote_daemon_sets ( int  proc_id,
std::list< int > const &  job_indices,
std::map< std::string, Size > const &  total_reads,
std::map< std::string, Size > &  reads_completed,
std::map< std::string, std::string > &  file_contents_map 
) const
private

Definition at line 2351 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::add_daemon, protocols::pack_daemon::StructureFileNames::correspondence_file_name_, core::sequence::end, file_inputs_for_job(), get_file_contents(), npd_variable_indices_for_states_, protocols::pack_daemon::StructureFileNames::pdb_name_, and protocols::pack_daemon::StructureFileNames::resfile_name_.

Referenced by distribute_jobs_to_remote_daemons().

void protocols::pack_daemon::DynamicAggregateFunction::assign_state_energies_to_variables_and_subexpressions ( StateEnergies const &  state_energies,
StateEnergies const &  npd_properties,
Entity const &  entity,
bool  verbose = false 
)
private

Definition at line 2416 of file DynamicAggregateFunction.cc.

References entity_funcs_, scalar_expressions_, variable_expressions_, variable_expressions_for_npd_properties_, and variable_expressions_for_states_.

Referenced by evaluate(), and select_relevant_states().

void protocols::pack_daemon::DynamicAggregateFunction::count_file_reads ( std::map< std::string, Size > &  total_reads,
std::map< std::string, Size > &  reads_completed 
) const
private

Definition at line 2110 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::StructureFileNames::correspondence_file_name_, increment_total_read_count_for_file(), named_state_data_file_names_, protocols::pack_daemon::StructureFileNames::pdb_name_, protocols::pack_daemon::StructureFileNames::resfile_name_, and state_vector_data_file_names_.

Referenced by initialize_pack_daemons().

core::Size protocols::pack_daemon::DynamicAggregateFunction::count_num_npd_properties ( ) const
private

used to determine the number of requested NPD properties that will be calculated; used to size the variable_expressions_for_npd_properties_ array.

Definition at line 2458 of file DynamicAggregateFunction.cc.

References named_state_data_file_names_, npd_properties_for_state_variables_, and state_vector_data_file_names_.

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::create_scalar_and_vector_expression_variable_expressions ( std::map< std::string, ArithmeticASTExpressionOP > const &  scalar_expression_asts,
std::map< std::string, std::list< std::string > > const &  vector_variables,
Size &  count_variable_index 
)
private

creates a variable expression for each sub-expression that will hold the intermediate result of a sub-expression. Increments the count_variable_index input parameter and places the VariableExpression into the variable_expressions_ array into position count_variable_index.

Definition at line 1904 of file DynamicAggregateFunction.cc.

References scalar_expression_map_, surrogate_expression_map_, variable_expressions_, variable_name_2_variable_exp_index_, and vector_expression_map_.

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::create_state_variable_expressions ( Size &  count_state,
Size &  count_npd_index,
Size &  count_variable_index 
)
private

For each element of the named_state_data_file_names_ data member, creates a VariableExpression (named with the variable name given in the STATE command from the DynamicAggregateFunction input file). This variable expression is put into three member variables: the variable_expressions_for_states_ vector, the variable_expressions_ vector, and the named_state_expression_map_. This method increments the count_states input parameter for each VariableExpression that it processes, pairing the value of the count_states variable with the index for this VariableExpression in both the variable_expressions_for_states_ vector and in the variable_expressions_ vector.

Definition at line 1783 of file DynamicAggregateFunction.cc.

References files_for_state_, named_state_data_file_names_, named_state_expression_map_, npd_properties_for_state_variables_, npd_variable_indices_for_states_, scalar_expression_map_, state_variable_name_2_state_index_, variable_expressions_, variable_expressions_for_npd_properties_, variable_expressions_for_states_, and variable_name_2_variable_exp_index_.

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::create_variable_vector_expressions ( Size &  count_state,
Size &  count_npd_index,
Size &  count_variable_index 
)
private

This method iterates across state_vector_data_file_names_ map, and creates a VariableVectorExpression for each entry. It adds this VariableVectorExpression to the state_vector_variables_ map. For each element in the state_vector_data_file_names_ map, and for each state-file-triple held in each particular element, it creates a VariableExpression and pairs the index in the input count_state vector. This VariableExpression is added to three member variables: the variable_expressions_for_states_ vector, the variable_expressions_ vector. Each VariableVectorExpression is given a vector of its set of VariableExpressions in its constructor. It will access these variables directly when it is queried for its vector_values. The indices of the state varaibles are inserted into the state_indices_for_state_vector_ map.

Definition at line 1835 of file DynamicAggregateFunction.cc.

References files_for_state_, npd_properties_for_state_variables_, npd_variable_indices_for_states_, state_indices_for_state_vector_, state_variable_name_2_state_index_, state_vector_data_file_names_, state_vector_variables_, variable_expressions_, variable_expressions_for_npd_properties_, variable_expressions_for_states_, variable_name_2_variable_exp_index_, and vector_expression_map_.

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::distribute_jobs_to_remote_daemons ( DaemonSetOP  daemon_set,
std::map< std::string, Size > const &  total_reads,
std::map< std::string, Size > &  reads_completed 
)
private

Definition at line 2225 of file DynamicAggregateFunction.cc.

References assign_jobs_to_local_daemon_set(), assign_jobs_to_remote_daemon_sets(), protocols::pack_daemon::error_message, send_error_message_to_remote_daemon_sets(), send_success_message_to_remote_daemon_set(), variable_expressions_for_states_, and verify_remote_daemon_set_initialization_successful().

Referenced by initialize_pack_daemons().

core::Real protocols::pack_daemon::DynamicAggregateFunction::evaluate ( StateEnergies const &  state_energies,
StateEnergies const &  npd_properties,
Entity const &  entity 
)
virtual

Implements protocols::pack_daemon::MultistateAggregateFunction.

Definition at line 590 of file DynamicAggregateFunction.cc.

References assign_state_energies_to_variables_and_subexpressions().

StructureFileNames const & protocols::pack_daemon::DynamicAggregateFunction::file_inputs_for_job ( int  job_index) const
private

Definition at line 2309 of file DynamicAggregateFunction.cc.

References files_for_state_.

Referenced by assign_jobs_to_local_daemon_set(), and assign_jobs_to_remote_daemon_sets().

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

Handles the functions that the ExpressionCreator base class does not. Ensures that the functions that are expecting vector arguments are actually given vector arguments. This is not guaranteed by the scanning or parsing of the input file.

Definition at line 733 of file DynamicAggregateFunction.cc.

References verify_vector_arguments().

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

std::string protocols::pack_daemon::DynamicAggregateFunction::get_file_contents ( std::string const &  filename,
std::map< std::string, Size > const &  total_reads,
std::map< std::string, Size > &  reads_completed,
std::map< std::string, std::string > &  file_contents_map 
) const
private

Definition at line 2153 of file DynamicAggregateFunction.cc.

References file_contents_, and protocols::abinitio::filename().

Referenced by assign_jobs_to_local_daemon_set(), and assign_jobs_to_remote_daemon_sets().

void protocols::pack_daemon::DynamicAggregateFunction::increment_total_read_count_for_file ( std::string const &  fname,
std::map< std::string, Size > &  total_reads,
std::map< std::string, Size > &  reads_completed 
) const
private

Definition at line 2137 of file DynamicAggregateFunction.cc.

Referenced by count_file_reads().

void protocols::pack_daemon::DynamicAggregateFunction::initialize_daemon_with_all_states ( DaemonSetOP  daemon_set,
std::map< std::string, Size > const &  total_reads,
std::map< std::string, Size > &  reads_completed 
)
private

Definition at line 2198 of file DynamicAggregateFunction.cc.

References assign_jobs_to_local_daemon_set(), and variable_expressions_for_states_.

Referenced by initialize_pack_daemons().

void protocols::pack_daemon::DynamicAggregateFunction::initialize_from_input_file ( DaemonSetOP  daemon_set,
std::istream &  input 
)

Definition at line 658 of file DynamicAggregateFunction.cc.

References initialize_pack_daemons(), read_all_variables_from_input_file(), and send_error_message_to_remote_daemon_sets().

void protocols::pack_daemon::DynamicAggregateFunction::initialize_pack_daemons ( DaemonSetOP  daemon_set)
private

Definition at line 2087 of file DynamicAggregateFunction.cc.

References count_file_reads(), distribute_jobs_to_remote_daemons(), and initialize_daemon_with_all_states().

Referenced by initialize_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::initialize_scanner ( )
private

Definition at line 951 of file DynamicAggregateFunction.cc.

References scanner_.

Referenced by read_all_variables_from_input_file().

core::Size protocols::pack_daemon::DynamicAggregateFunction::num_npd_properties ( ) const

Definition at line 584 of file DynamicAggregateFunction.cc.

References variable_expressions_for_npd_properties_.

core::Size protocols::pack_daemon::DynamicAggregateFunction::num_states ( ) const

Definition at line 578 of file DynamicAggregateFunction.cc.

References variable_expressions_for_states_.

void protocols::pack_daemon::DynamicAggregateFunction::process_ENTITY_FUNCTION_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line 
)
private

Definition at line 1604 of file DynamicAggregateFunction.cc.

References entity_funcs_, entity_funcs_dec_line_, file_contents_, num_entity_elements_, scanner_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_FITNESS_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line,
ArithmeticASTExpressionOP &  fitness_expression_ast 
)
private

This method reads the line of the input file beginning with the command FITNESS. Each DynamicAggregateFunction input file should contain exactly one FITNESS command. The fitness line should be of the form: FITNESS <expression> where the expression must return a value (it should not be a vector expression) and may refer to functions and variables so long as those variables have been declared earlier in the file. The abstract syntax tree (ast) for the fitness expression is returned in the input parameter, fitness_expression_ast.

Definition at line 1673 of file DynamicAggregateFunction.cc.

References scanner_.

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_NPD_PROPERTY_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line 
)
private

Definition at line 1262 of file DynamicAggregateFunction.cc.

References npd_properties_for_state_variables_, scalar_variable_names_dec_line_, scanner_, state_variable_names_, state_vector_variable_names_, variable_names_dec_line_, vector_variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line 
)
private

Definition at line 1104 of file DynamicAggregateFunction.cc.

References file_contents_, core::import_pose::pose_from_pdbstring(), scalar_expression_map_, scanner_, core::pose::Pose::total_residue(), and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line 
)
private

Definition at line 1163 of file DynamicAggregateFunction.cc.

References file_contents_, core::import_pose::pose_from_pdbstring(), scanner_, core::pose::Pose::total_residue(), vector_expression_map_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_SCALAR_EXPRESSION_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line,
std::map< std::string, ArithmeticASTExpressionOP > &  scalar_expression_asts 
)
private

This methods reads the line beginning with the command SCALAR_EXPRESSION which should be in the following format ( items in <> are explained below) SCALAR_EXPRESSION <varname> = <expression>

  1. varname must be an as-of-yet unused varible name.
  2. The form of expression must return a value (it should not be a vector expression). It may contain functions and variables so long as those variables have been declared earlier in the file. After the expression has been tokenized, it's abstract syntax tree (ast) is created and appended to the input parameter scalar_expression_asts in tandem with the variable name. The variable name is appended to the variables_ and scanner_ member variables. No other member variables are modified in this function.

Definition at line 1418 of file DynamicAggregateFunction.cc.

References expression_evaluation_order_by_name_, scalar_variable_names_dec_line_, scanner_, variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_STATE_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line 
)
private

Reads the contents of the line which should include four things:

  1. an as-of-yet unused variable name to identify this state,
  2. a pdb name giving the file containing the state to be redesigned
  3. a correspondence file name which describes the connection between residues in the state from 2. which should correspond to particular residues that are being designed.
  4. a secondary resfile that describes how other residues in 2. should be repacked or redesigned. The variable name in 1. is checked against the variable_names_dec_line_ member variable, and, if it is absent, be added to both variable_names_dec_line_ and scanner_. This method then adds the file names from 2, 3, and 4 to the named_state_data_file_names_ map.

Definition at line 986 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::StructureFileNames::correspondence_file_name_, named_state_data_file_names_, protocols::pack_daemon::StructureFileNames::pdb_name_, protocols::pack_daemon::StructureFileNames::resfile_name_, scalar_variable_names_dec_line_, scanner_, state_name(), state_variable_names_, variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_STATE_VECTOR_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line,
utility::vector1< std::pair< std::string, std::string > > &  strucvec_filenames 
)
private

This method reads a line beginning with the command STATE_VECTOR looking for two things on this line:

  1. an as-of-yet unused variable name identifying the vector
  2. a file name which contains a list of states. If the variable name is absent from the variables_ set, then this method appends the name to the variables_ set and to the scanner_, and appends the pair (1,2) to the input strucvec_filenames parameter. No other member variables are modified.

Definition at line 1061 of file DynamicAggregateFunction.cc.

References scanner_, state_vector_variable_names_, variable_names_dec_line_, vector_variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_EXPRESSION_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line,
std::map< std::string, std::pair< std::map< std::string, std::string >, ArithmeticASTExpressionOP > > &  vector_expression_list 
)
private

Definition at line 1468 of file DynamicAggregateFunction.cc.

References expression_evaluation_order_by_name_, scanner_, variable_names_dec_line_, vector_variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_VARIABLE_line ( std::string const &  line,
Size  line_number,
std::istream &  input_line,
std::map< std::string, std::list< std::string > > &  vector_variables 
)
private

Definition at line 1349 of file DynamicAggregateFunction.cc.

References scalar_variable_names_dec_line_, scanner_, variable_names_dec_line_, vector_variable_names_dec_line_, and verify_variable_name_or_throw().

Referenced by read_all_variables_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::read_all_variables_from_input_file ( std::istream &  input)
private

Definition at line 832 of file DynamicAggregateFunction.cc.

References count_num_npd_properties(), create_scalar_and_vector_expression_variable_expressions(), create_state_variable_expressions(), create_variable_vector_expressions(), files_for_state_, function_names_, illegal_variable_names_, initialize_scanner(), named_state_data_file_names_, npd_variable_indices_for_states_, process_ENTITY_FUNCTION_line(), process_FITNESS_line(), process_NPD_PROPERTY_line(), process_POSE_ENERGY_line(), process_POSE_ENERGY_VECTOR_line(), process_SCALAR_EXPRESSION_line(), process_STATE_line(), process_STATE_VECTOR_line(), process_VECTOR_EXPRESSION_line(), process_VECTOR_VARIABLE_line(), read_state_vector_file(), state_vector_data_file_names_, turn_expression_ASTs_into_expressions(), variable_expressions_, variable_expressions_for_npd_properties_, and variable_expressions_for_states_.

Referenced by initialize_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::read_state_vector_file ( std::string const &  vec_varname,
std::string const &  fname,
Size &  n_vector_states 
)
private

This function reads the contents of a state-vector file. The input parameter vec_varname refers to the variable name associated with the file named by the second input parameter – this pairing occurred somewhere in the DynamicAggregateFunction input file in a STATE_VECTOR command. The format of the state vector should be a series of lines each with three strings. String 1: the name of the pdb file containing a state that should be repacked. String 2: the name of the correspondence file mapping residues in the input pdb to the shared residues. String 3: the name of the secondary resfile describing how the packer should treat residues other than the correspondence residues in the protein. Lines beginning with "#" are ignored. The triples read from this file are appended to the state_vector_data_file_names_ member variable. The method increments the input variable n_vector_states for each triple that it reads from the state-vector file.

Definition at line 1710 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::StructureFileNames::correspondence_file_name_, file_contents_, protocols::pack_daemon::StructureFileNames::pdb_name_, protocols::pack_daemon::StructureFileNames::resfile_name_, state_vector_data_file_names_, and variable_names_dec_line_.

Referenced by read_all_variables_from_input_file().

DynamicAggregateFunction::StateIndices protocols::pack_daemon::DynamicAggregateFunction::select_relevant_states ( StateEnergies const &  state_energies,
StateEnergies const &  npd_properties,
Entity const &  entity 
)
virtual

Relies on the Expression "active_variables" method to determine which variables are selected and contribute to the fitness function

Implements protocols::pack_daemon::MultistateAggregateFunction.

Definition at line 615 of file DynamicAggregateFunction.cc.

References assign_state_energies_to_variables_and_subexpressions(), fitness_exp_, and state_variable_name_2_state_index_.

void protocols::pack_daemon::DynamicAggregateFunction::send_error_message_to_remote_daemon_sets ( ) const
private

Definition at line 2407 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::error_message.

Referenced by distribute_jobs_to_remote_daemons(), and initialize_from_input_file().

void protocols::pack_daemon::DynamicAggregateFunction::send_success_message_to_remote_daemon_set ( int  proc_id) const
private

Definition at line 2402 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::success_message.

Referenced by distribute_jobs_to_remote_daemons().

void protocols::pack_daemon::DynamicAggregateFunction::set_num_entity_elements ( Size  setting)

Definition at line 555 of file DynamicAggregateFunction.cc.

References num_entity_elements_.

void protocols::pack_daemon::DynamicAggregateFunction::set_score_function ( core::scoring::ScoreFunction const &  sfxn)

Required for processing the POSE_ENERGY and POSE_ENERGY_VECTOR commands

Definition at line 571 of file DynamicAggregateFunction.cc.

References core::scoring::ScoreFunction::clone(), and sfxn_.

std::string protocols::pack_daemon::DynamicAggregateFunction::state_name ( Size  state_index) const

Definition at line 825 of file DynamicAggregateFunction.cc.

References variable_expressions_for_states_.

Referenced by process_STATE_line().

void protocols::pack_daemon::DynamicAggregateFunction::turn_expression_ASTs_into_expressions ( std::map< std::string, ArithmeticASTExpressionOP > const &  scalar_expression_asts,
std::map< std::string, std::pair< std::map< std::string, std::string >, ArithmeticASTExpressionOP > > const &  vector_expression_asts,
ArithmeticASTExpressionOP  fitness_expression_ast 
)
private

Turns expression abstract-syntax trees into Expression objects. The VectorExpressionCreator keeps a reference to me so that it can pass control of flow to me when processing variable- and function-construction events. The scalar_expressions_ array is updated to hold the ExpressionOPs for these sub-expressions as pairs each Expression with the corresponding index of its VariableExpression so that I can later update that VariableExpression (held in the variable_expressions_ array) when evaluating that sub-expression. The fitness_exp_ is assigned to the Expression coming from the fitness_expression_ast.

Definition at line 1949 of file DynamicAggregateFunction.cc.

References expression_evaluation_order_by_name_, fitness_exp_, focused_iterative_vector_expression_, scalar_expressions_, surrogate_expression_map_, variable_name_2_variable_exp_index_, and vector_expression_map_.

Referenced by read_all_variables_from_input_file().

ExpressionCOP protocols::pack_daemon::DynamicAggregateFunction::variable_expression ( numeric::expression_parser::ArithmeticASTValue const &  ) const

returns a VariableExpressionOP or VectorVariableExpressionOP given a particular variable. Throws an exception if a variable is requested that is not a member of any of the following maps: named_state_expression_map_, state_vector_variables_, or sub_expression_map_.

Definition at line 679 of file DynamicAggregateFunction.cc.

References entity_funcs_, focused_iterative_vector_expression_, named_state_expression_map_, scalar_expression_map_, state_vector_variables_, and vector_expression_map_.

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

bool protocols::pack_daemon::DynamicAggregateFunction::verify_remote_daemon_set_initialization_successful ( int  proc_id) const
private

Definition at line 2389 of file DynamicAggregateFunction.cc.

References protocols::pack_daemon::error_message, and protocols::pack_daemon::success_message.

Referenced by distribute_jobs_to_remote_daemons().

void protocols::pack_daemon::DynamicAggregateFunction::verify_variable_name_or_throw ( std::string const &  vname,
std::string const &  command_name,
std::string const &  line,
Size  line_number 
)
private

Definition at line 2055 of file DynamicAggregateFunction.cc.

References entity_funcs_, entity_funcs_dec_line_, function_names_, illegal_variable_names_, and variable_names_dec_line_.

Referenced by process_ENTITY_FUNCTION_line(), process_NPD_PROPERTY_line(), process_POSE_ENERGY_line(), process_POSE_ENERGY_VECTOR_line(), process_SCALAR_EXPRESSION_line(), process_STATE_line(), process_STATE_VECTOR_line(), process_VECTOR_EXPRESSION_line(), and process_VECTOR_VARIABLE_line().

utility::vector1< VectorExpressionCOP > protocols::pack_daemon::DynamicAggregateFunction::verify_vector_arguments ( std::string const &  fname,
utility::vector1< ExpressionCOP > const &  args,
Size  expected_nargs 
) const
private

Verifies that the args array for a vector function has size 1, and that the sole element is a VectorExpression. Returns an owning-pointer to the downcasted VectorExpression, or throws an exception if the downcast fails.

Definition at line 2028 of file DynamicAggregateFunction.cc.

Referenced by function_expression().

Member Data Documentation

std::map< std::string, std::pair< EntityFuncOP, VariableExpressionOP > > protocols::pack_daemon::DynamicAggregateFunction::entity_funcs_
private

Definition at line 772 of file DynamicAggregateFunction.hh.

Referenced by assign_state_energies_to_variables_and_subexpressions(), process_ENTITY_FUNCTION_line(), variable_expression(), and verify_variable_name_or_throw().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::entity_funcs_dec_line_
private

Definition at line 773 of file DynamicAggregateFunction.hh.

Referenced by process_ENTITY_FUNCTION_line(), and verify_variable_name_or_throw().

std::list< std::pair< Size, std::string > > protocols::pack_daemon::DynamicAggregateFunction::expression_evaluation_order_by_name_
private

Definition at line 742 of file DynamicAggregateFunction.hh.

Referenced by process_SCALAR_EXPRESSION_line(), process_VECTOR_EXPRESSION_line(), and turn_expression_ASTs_into_expressions().

std::map< std::string, std::string > protocols::pack_daemon::DynamicAggregateFunction::file_contents_
private

Definition at line 788 of file DynamicAggregateFunction.hh.

Referenced by add_file_contents(), get_file_contents(), process_ENTITY_FUNCTION_line(), process_POSE_ENERGY_line(), process_POSE_ENERGY_VECTOR_line(), and read_state_vector_file().

utility::vector1< StructureFileNames > protocols::pack_daemon::DynamicAggregateFunction::files_for_state_
private

Definition at line 783 of file DynamicAggregateFunction.hh.

Referenced by create_state_variable_expressions(), create_variable_vector_expressions(), file_inputs_for_job(), and read_all_variables_from_input_file().

ExpressionCOP protocols::pack_daemon::DynamicAggregateFunction::fitness_exp_
private

Definition at line 732 of file DynamicAggregateFunction.hh.

Referenced by select_relevant_states(), and turn_expression_ASTs_into_expressions().

IterativeVectorExpressionOP protocols::pack_daemon::DynamicAggregateFunction::focused_iterative_vector_expression_
private

Definition at line 786 of file DynamicAggregateFunction.hh.

Referenced by turn_expression_ASTs_into_expressions(), and variable_expression().

std::set< std::string > protocols::pack_daemon::DynamicAggregateFunction::function_names_
private

Function names may not be used as variable names.

Definition at line 761 of file DynamicAggregateFunction.hh.

Referenced by read_all_variables_from_input_file(), and verify_variable_name_or_throw().

std::set< std::string > protocols::pack_daemon::DynamicAggregateFunction::illegal_variable_names_
private

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

Definition at line 765 of file DynamicAggregateFunction.hh.

Referenced by read_all_variables_from_input_file(), and verify_variable_name_or_throw().

std::map< std::string, StructureFileNames > protocols::pack_daemon::DynamicAggregateFunction::named_state_data_file_names_
private

Definition at line 780 of file DynamicAggregateFunction.hh.

Referenced by count_file_reads(), count_num_npd_properties(), create_state_variable_expressions(), process_STATE_line(), and read_all_variables_from_input_file().

std::map< std::string, ExpressionCOP > protocols::pack_daemon::DynamicAggregateFunction::named_state_expression_map_
private

Definition at line 751 of file DynamicAggregateFunction.hh.

Referenced by create_state_variable_expressions(), and variable_expression().

std::map< std::string, std::list< std::pair< std::string, std::string > > > protocols::pack_daemon::DynamicAggregateFunction::npd_properties_for_state_variables_
private

Definition at line 755 of file DynamicAggregateFunction.hh.

Referenced by count_num_npd_properties(), create_state_variable_expressions(), create_variable_vector_expressions(), and process_NPD_PROPERTY_line().

std::map< std::string, ExpressionCOP > protocols::pack_daemon::DynamicAggregateFunction::npd_property_expression_map_
private

Definition at line 757 of file DynamicAggregateFunction.hh.

std::map< std::string, VariableVectorExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::npd_property_vector_expression_map_
private

Definition at line 758 of file DynamicAggregateFunction.hh.

utility::vector1< std::list< std::pair< Size, std::string > > > protocols::pack_daemon::DynamicAggregateFunction::npd_variable_indices_for_states_
private

Definition at line 734 of file DynamicAggregateFunction.hh.

Referenced by assign_jobs_to_local_daemon_set(), assign_jobs_to_remote_daemon_sets(), create_state_variable_expressions(), create_variable_vector_expressions(), and read_all_variables_from_input_file().

Size protocols::pack_daemon::DynamicAggregateFunction::num_entity_elements_
private

Definition at line 729 of file DynamicAggregateFunction.hh.

Referenced by process_ENTITY_FUNCTION_line(), and set_num_entity_elements().

std::map< std::string, VariableExpressionCOP > protocols::pack_daemon::DynamicAggregateFunction::scalar_expression_map_
private

Definition at line 745 of file DynamicAggregateFunction.hh.

Referenced by create_scalar_and_vector_expression_variable_expressions(), create_state_variable_expressions(), process_POSE_ENERGY_line(), and variable_expression().

utility::vector1< std::pair< Size, ExpressionCOP > > protocols::pack_daemon::DynamicAggregateFunction::scalar_expressions_
private

Definition at line 743 of file DynamicAggregateFunction.hh.

Referenced by assign_state_energies_to_variables_and_subexpressions(), and turn_expression_ASTs_into_expressions().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::scalar_variable_names_dec_line_
private

Definition at line 769 of file DynamicAggregateFunction.hh.

Referenced by process_NPD_PROPERTY_line(), process_SCALAR_EXPRESSION_line(), process_STATE_line(), and process_VECTOR_VARIABLE_line().

numeric::expression_parser::ArithmeticScannerOP protocols::pack_daemon::DynamicAggregateFunction::scanner_
private

Definition at line 739 of file DynamicAggregateFunction.hh.

Referenced by initialize_scanner(), process_ENTITY_FUNCTION_line(), process_FITNESS_line(), process_NPD_PROPERTY_line(), process_POSE_ENERGY_line(), process_POSE_ENERGY_VECTOR_line(), process_SCALAR_EXPRESSION_line(), process_STATE_line(), process_STATE_VECTOR_line(), process_VECTOR_EXPRESSION_line(), and process_VECTOR_VARIABLE_line().

core::scoring::ScoreFunctionOP protocols::pack_daemon::DynamicAggregateFunction::sfxn_
private

Definition at line 730 of file DynamicAggregateFunction.hh.

Referenced by set_score_function().

std::map< std::string, utility::vector1< Size > > protocols::pack_daemon::DynamicAggregateFunction::state_indices_for_state_vector_
private

Definition at line 784 of file DynamicAggregateFunction.hh.

Referenced by create_variable_vector_expressions().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::state_variable_name_2_state_index_
private

Keep track for each state-variable name its state's index.

Definition at line 778 of file DynamicAggregateFunction.hh.

Referenced by create_state_variable_expressions(), create_variable_vector_expressions(), and select_relevant_states().

std::set< std::string > protocols::pack_daemon::DynamicAggregateFunction::state_variable_names_
private

Definition at line 749 of file DynamicAggregateFunction.hh.

Referenced by process_NPD_PROPERTY_line(), and process_STATE_line().

std::map< std::string, utility::vector1< StructureFileNames > > protocols::pack_daemon::DynamicAggregateFunction::state_vector_data_file_names_
private

Definition at line 781 of file DynamicAggregateFunction.hh.

Referenced by count_file_reads(), count_num_npd_properties(), create_variable_vector_expressions(), read_all_variables_from_input_file(), and read_state_vector_file().

std::set< std::string > protocols::pack_daemon::DynamicAggregateFunction::state_vector_variable_names_
private

Definition at line 750 of file DynamicAggregateFunction.hh.

Referenced by process_NPD_PROPERTY_line(), and process_STATE_VECTOR_line().

std::map< std::string, VariableVectorExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::state_vector_variables_
private

Definition at line 752 of file DynamicAggregateFunction.hh.

Referenced by create_variable_vector_expressions(), and variable_expression().

std::map< Size, SurrogateVariableExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::surrogate_expression_map_
private

Definition at line 744 of file DynamicAggregateFunction.hh.

Referenced by create_scalar_and_vector_expression_variable_expressions(), and turn_expression_ASTs_into_expressions().

utility::vector1< VariableExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::variable_expressions_
private

Definition at line 737 of file DynamicAggregateFunction.hh.

Referenced by assign_state_energies_to_variables_and_subexpressions(), create_scalar_and_vector_expression_variable_expressions(), create_state_variable_expressions(), create_variable_vector_expressions(), and read_all_variables_from_input_file().

utility::vector1< VariableExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::variable_expressions_for_npd_properties_
private

Definition at line 735 of file DynamicAggregateFunction.hh.

Referenced by assign_state_energies_to_variables_and_subexpressions(), create_state_variable_expressions(), create_variable_vector_expressions(), num_npd_properties(), and read_all_variables_from_input_file().

utility::vector1< VariableExpressionOP > protocols::pack_daemon::DynamicAggregateFunction::variable_expressions_for_states_
private

Definition at line 733 of file DynamicAggregateFunction.hh.

Referenced by assign_state_energies_to_variables_and_subexpressions(), create_state_variable_expressions(), create_variable_vector_expressions(), distribute_jobs_to_remote_daemons(), initialize_daemon_with_all_states(), num_states(), read_all_variables_from_input_file(), and state_name().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::variable_name_2_variable_exp_index_
private

Keep track for each varible name (or scalar expression name) its index in the ?? vector.

Definition at line 776 of file DynamicAggregateFunction.hh.

Referenced by create_scalar_and_vector_expression_variable_expressions(), create_state_variable_expressions(), create_variable_vector_expressions(), and turn_expression_ASTs_into_expressions().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::variable_names_dec_line_
private

Definition at line 768 of file DynamicAggregateFunction.hh.

Referenced by process_NPD_PROPERTY_line(), process_SCALAR_EXPRESSION_line(), process_STATE_line(), process_STATE_VECTOR_line(), process_VECTOR_EXPRESSION_line(), process_VECTOR_VARIABLE_line(), read_state_vector_file(), and verify_variable_name_or_throw().

std::map< std::string, VectorExpressionCOP > protocols::pack_daemon::DynamicAggregateFunction::vector_expression_map_
private

Definition at line 746 of file DynamicAggregateFunction.hh.

Referenced by create_scalar_and_vector_expression_variable_expressions(), create_variable_vector_expressions(), process_POSE_ENERGY_VECTOR_line(), turn_expression_ASTs_into_expressions(), and variable_expression().

std::map< std::string, Size > protocols::pack_daemon::DynamicAggregateFunction::vector_variable_names_dec_line_
private

Definition at line 770 of file DynamicAggregateFunction.hh.

Referenced by process_NPD_PROPERTY_line(), process_STATE_VECTOR_line(), process_VECTOR_EXPRESSION_line(), and process_VECTOR_VARIABLE_line().

std::list< VectorFunctionOP > protocols::pack_daemon::DynamicAggregateFunction::vfuncs_
private

Definition at line 741 of file DynamicAggregateFunction.hh.

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