#include <DynamicAggregateFunction.hh>

Inheritance diagram for protocols::pack_daemon::DynamicAggregateFunction:

Collaboration diagram for protocols::pack_daemon::DynamicAggregateFunction:

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_

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

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

virtual

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.

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

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

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

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

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.

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.

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.

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.

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

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.

References assign_state_energies_to_variables_and_subexpressions().

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

private

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.

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

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

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

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
	)

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

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

References scanner_.

Referenced by read_all_variables_from_input_file().

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

References variable_expressions_for_npd_properties_.

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

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

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.

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

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

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

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>

varname must be an as-of-yet unused varible name.
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.

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:

an as-of-yet unused variable name to identify this state,
a pdb name giving the file containing the state to be redesigned
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.
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.

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:

an as-of-yet unused variable name identifying the vector
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.

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

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

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

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.

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.

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

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

References protocols::pack_daemon::success_message.

Referenced by distribute_jobs_to_remote_daemons().

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

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

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

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

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.

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_.

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

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

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.

Referenced by function_expression().

Member Data Documentation

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

private

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

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

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

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

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

Referenced by select_relevant_states(), and turn_expression_ASTs_into_expressions().

IterativeVectorExpressionOP protocols::pack_daemon::DynamicAggregateFunction::focused_iterative_vector_expression_

private

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.

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

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

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

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

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

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

private

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

private

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

Referenced by process_ENTITY_FUNCTION_line(), and set_num_entity_elements().

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

private

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

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

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

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

Referenced by set_score_function().

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

private

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.

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

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

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

Referenced by process_NPD_PROPERTY_line(), and process_STATE_VECTOR_line().

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

private

Referenced by create_variable_vector_expressions(), and variable_expression().

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

private

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

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

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

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.

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

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

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

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

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation