: The Scorer computes the score of each Individual in a Population. It applies a list of movers, calculates a variety of score terms and combines them. The scorer also collects statistics and summarizes information. More...

#include <Scorer.hh>

Public Member Functions
	Scorer (FragmentLibrary &library, core::Size n_runs, char ligand_chain)

void	initialize_from_options (EvolutionOptionsCOP options, protocols::rosetta_scripts::XmlObjectsCOP rosetta_script, core::Size rank)

void	score_population (Population &pop)
	Sets the score for all individuals in the population, calculates it where needed. More...

void	score_individual (Individual &individual)
	Checks if this individuals ligand was already scores, scores it if not, and sets the score for the individual. More...

void	score_ligand (LigandIdentifier const &ligand, std::string const &smiles="", core::Size save_n_scores=0)
	Sets the current ligand and calls all steps to score it completely. More...

void	add_mover (moves::MoverOP const &mover)
	Adds a mover. More...

void	set_ligand (LigandIdentifier const &ligand, std::string const &smiles="")
	Sets the current ligand on which should be worked. More...

bool	has_ligand () const
	Checks if a ligand is currently set. More...

bool	next_step (core::Size save_n_scores=0)
	Performs the next scoring step on the current individual. Returns true, if this was the last step. More...

bool	is_scored (LigandIdentifier const &ligand) const
	Returns true if the ligand was already scored. More...

std::map< std::string, core::Real > const &	get_scores (LigandIdentifier const &ligand) const
	Returns all scores in a map with a string identifier. More...

void	set_main_term (std::string const &score_term)
	Sets which term should be used for optimization. More...

void	set_base_similarity_penalty (core::Real base_penalty)
	Sets the penalty for ligands which are appear more than once within a population. More...

void	set_pose_path (std::string const &path)
	Sets the path where poses should be saved. Leave it empty to save in the current working directory. More...

void	set_score_function (core::scoring::ScoreFunctionOP score_function)
	Sets the desired score function. More...

void	set_scores (LigandIdentifier const &identifier, std::map< std::string, core::Real > const &scores)
	Sets all score terms for an identifier if not set yet. More...

core::Size	n_score_terms () const
	Return how many score terms are calculated. More...

utility::vector1< core::Real >	get_raw_scores (LigandIdentifier const &identifier) const
	Returns the raw scores of an identifier for mpi communication. More...

void	load_scores (std::string const &path)
	Loads scores for combinations of reagents and reactions from file. These are used during the run instead of rescoring. Format is the output format of RLE. More...

void	set_raw_scores (LigandIdentifier const &identifier, double const *raw_scores)
	Transforms raw double scores into a proper map and calls set_scores @detail Expects scores in the same order as score_terms. More...

void	save_results () const
	Writes all results to disk. More...

void	save_external_scoring_results (core::Size rank)
	Writes multiple scores per ligand to disk. More...

std::map< LigandIdentifier, std::set< core::Size > > const &	expose_id_memory () const
	For debugging and benchmarking purposes. More...

bool	check_memory (LigandIdentifier const &ligand)
	Checks if score for this ligand is available in memory and loads it if possible. More...

utility::vector1< LigandIdentifier >	get_best_loaded (core::Size size) const
	Returns a list of LigandIdentifiers for loaded scores sorted by their main term score. More...

void	set_similarity_penalty_threshold (core::Real threshold)

Private Member Functions
void	create_pose ()
	Creates a pose and rotamers for the current ligand. More...

void	apply_movers ()
	Applies all movers in order to the current ligands pose. More...

void	calculate_scores (core::Size save_n_scores=0)
	Calculates all scores for the current ligand and saves them if lower than the old ones. More...

void	dump_pose ()
	Dumps the current best pose to disk with the ligand identifier as name. More...

utility::vector1< std::string >	ligand_line (LigandIdentifier const &identifier) const

Private Attributes
char	ligand_chain_ = 'X'

std::string	pose_path_

std::string	main_score_term_

core::Size	n_runs_ = 0

core::Size	current_runs_ = 0

LigandIdentifier	current_ligand_

std::string	current_ligand_smiles_

FragmentLibrary &	library_

core::pose::PoseOP	basic_pose_ = nullptr

core::pose::PoseOP	best_pose_ = nullptr

core::pose::PoseOP	working_pose_

utility::vector1< moves::MoverOP >	mover_

std::map< LigandIdentifier, std::map< std::string, core::Real > >	score_memory_

std::map< std::string, std::map< utility::vector1< std::string >, std::map< std::string, core::Real > > >	loaded_score_memory_
	Important! LigendIdentifier here is NOT the same as in the rest of the program. This uses the real names from reactions and reagents. More...

std::map< LigandIdentifier, std::set< core::Size > >	id_memory_

bool	score_next_ = false

core::scoring::ScoreFunctionOP	score_function_ = nullptr

core::Real	base_similarity_penalty_ = 0.2

core::Real	similarity_penalty_threshold_ = 0.95

Detailed Description

: The Scorer computes the score of each Individual in a Population. It applies a list of movers, calculates a variety of score terms and combines them. The scorer also collects statistics and summarizes information.

Constructor & Destructor Documentation

◆ Scorer()

protocols::ligand_evolution::Scorer::Scorer	(	FragmentLibrary &	library,
		core::Size	n_runs,
		char	ligand_chain
	)

Member Function Documentation

◆ add_mover()

void protocols::ligand_evolution::Scorer::add_mover ( moves::MoverOP const & mover )

Adds a mover.

References mover_, and protocols::TR().

Referenced by initialize_from_options().

◆ apply_movers()

void protocols::ligand_evolution::Scorer::apply_movers ( )

private

Applies all movers in order to the current ligands pose.

References basic_pose_, mover_, and working_pose_.

Referenced by next_step().

◆ calculate_scores()

void protocols::ligand_evolution::Scorer::calculate_scores ( core::Size save_n_scores = 0 )

private

Calculates all scores for the current ligand and saves them if lower than the old ones.

If save_all_scores is set, all scores are save in memory. This should only be used for external smiles scoring since it overrides a lot of otherwise needed and/or desired features.

References basic_pose_, best_pose_, current_ligand_, current_runs_, protocols::ligand_docking::get_interface_deltas(), is_scored(), ligand_chain_, main_score_term_, protocols::hybridization::score, score_function_, score_memory_, protocols::ligand_evolution::score_terms_, protocols::TR(), and working_pose_.

Referenced by next_step().

◆ check_memory()

bool protocols::ligand_evolution::Scorer::check_memory ( LigandIdentifier const & ligand )

Checks if score for this ligand is available in memory and loads it if possible.

References library_, loaded_score_memory_, protocols::ligand_evolution::FragmentLibrary::reaction_id(), protocols::ligand_evolution::FragmentLibrary::reagent_id(), score_memory_, and protocols::TR().

Referenced by score_ligand().

◆ create_pose()

void protocols::ligand_evolution::Scorer::create_pose ( )

private

Creates a pose and rotamers for the current ligand.

References basic_pose_, protocols::ligand_evolution::FragmentLibrary::create_ligand_pose(), current_ligand_, current_ligand_smiles_, library_, ligand_chain_, and protocols::TR().

Referenced by next_step().

◆ dump_pose()

void protocols::ligand_evolution::Scorer::dump_pose ( )

private

Dumps the current best pose to disk with the ligand identifier as name.

References best_pose_, current_ligand_, pose_path_, and protocols::TR().

Referenced by next_step().

◆ expose_id_memory()

std::map< LigandIdentifier, std::set< core::Size > > const & protocols::ligand_evolution::Scorer::expose_id_memory ( ) const

For debugging and benchmarking purposes.

References id_memory_.

◆ get_best_loaded()

utility::vector1< LigandIdentifier > protocols::ligand_evolution::Scorer::get_best_loaded ( core::Size size ) const

Returns a list of LigandIdentifiers for loaded scores sorted by their main term score.

Parameters

size	Sets how many identifiers should be returned. If <= 0, all will be returned

References library_, loaded_score_memory_, main_score_term_, protocols::mean_field::min(), core::scoring::pair, protocols::ligand_evolution::FragmentLibrary::reaction_name_to_index(), protocols::ligand_evolution::FragmentLibrary::reagent_name_to_index(), protocols::hybridization::score, and protocols::TR().

Referenced by protocols::ligand_evolution::Population::initialize_from_evotoptions().

◆ get_raw_scores()

utility::vector1< core::Real > protocols::ligand_evolution::Scorer::get_raw_scores ( LigandIdentifier const & identifier ) const

Returns the raw scores of an identifier for mpi communication.

References score_memory_, and protocols::ligand_evolution::score_terms_.

◆ get_scores()

std::map< std::string, core::Real > const & protocols::ligand_evolution::Scorer::get_scores ( LigandIdentifier const & ligand ) const

Returns all scores in a map with a string identifier.

References protocols::sewing::data_storage::ligand, and score_memory_.

◆ has_ligand()

bool protocols::ligand_evolution::Scorer::has_ligand ( ) const

Checks if a ligand is currently set.

References current_ligand_.

◆ initialize_from_options()

void protocols::ligand_evolution::Scorer::initialize_from_options	(	EvolutionOptionsCOP	options,
		protocols::rosetta_scripts::XmlObjectsCOP	rosetta_script,
		core::Size	rank
	)

References add_mover(), load_scores(), set_base_similarity_penalty(), set_main_term(), set_pose_path(), set_score_function(), and set_similarity_penalty_threshold().

◆ is_scored()

bool protocols::ligand_evolution::Scorer::is_scored ( LigandIdentifier const & ligand ) const

Returns true if the ligand was already scored.

References protocols::sewing::data_storage::ligand, and score_memory_.

Referenced by calculate_scores(), score_ligand(), set_ligand(), and set_scores().

◆ ligand_line()

utility::vector1< std::string > protocols::ligand_evolution::Scorer::ligand_line ( LigandIdentifier const & identifier ) const

private

References protocols::ligand_evolution::FragmentLibrary::identifier_to_smiles(), library_, protocols::ligand_evolution::FragmentLibrary::max_positions(), protocols::ligand_evolution::FragmentLibrary::reaction_id(), protocols::ligand_evolution::FragmentLibrary::reaction_positions(), protocols::ligand_evolution::FragmentLibrary::reagent_id(), protocols::hybridization::score, score_memory_, protocols::ligand_evolution::score_terms_, and core::id::to_string().

Referenced by save_results().

◆ load_scores()

void protocols::ligand_evolution::Scorer::load_scores ( std::string const & path )

Loads scores for combinations of reagents and reactions from file. These are used during the run instead of rescoring. Format is the output format of RLE.

References library_, loaded_score_memory_, main_score_term_, protocols::ligand_evolution::FragmentLibrary::max_positions(), protocols::hybridization::path, protocols::ligand_evolution::score_terms_, core::id::to_string(), and protocols::TR().

Referenced by initialize_from_options().

◆ n_score_terms()

core::Size protocols::ligand_evolution::Scorer::n_score_terms ( ) const

Return how many score terms are calculated.

References protocols::ligand_evolution::score_terms_.

◆ next_step()

bool protocols::ligand_evolution::Scorer::next_step ( core::Size save_n_scores = 0 )

Performs the next scoring step on the current individual. Returns true, if this was the last step.

References apply_movers(), basic_pose_, best_pose_, calculate_scores(), create_pose(), current_ligand_, current_ligand_smiles_, current_runs_, dump_pose(), n_runs_, score_next_, protocols::ligand_evolution::score_terms_, set_scores(), and protocols::TR().

Referenced by score_ligand().

◆ save_external_scoring_results()

void protocols::ligand_evolution::Scorer::save_external_scoring_results ( core::Size rank )

Writes multiple scores per ligand to disk.

References protocols::ligand_evolution::FragmentLibrary::identifier_to_smiles(), library_, core::conformation::membrane::out, core::scoring::pair, score_memory_, protocols::ligand_evolution::score_terms_, core::id::to_string(), and protocols::TR().

◆ save_results()

void protocols::ligand_evolution::Scorer::save_results ( ) const

Writes all results to disk.

References library_, ligand_line(), main_score_term_, protocols::mean_field::max(), protocols::ligand_evolution::FragmentLibrary::max_positions(), core::conformation::membrane::out, core::scoring::pair, score_memory_, protocols::ligand_evolution::score_terms_, core::id::to_string(), and protocols::TR().

◆ score_individual()

void protocols::ligand_evolution::Scorer::score_individual ( Individual & individual )

Checks if this individuals ligand was already scores, scores it if not, and sets the score for the individual.

References protocols::ligand_evolution::Individual::id(), id_memory_, protocols::ligand_evolution::Individual::identifier(), main_score_term_, protocols::ligand_evolution::Individual::score(), score_ligand(), score_memory_, and protocols::ligand_evolution::score_terms_.

Referenced by score_population().

◆ score_ligand()

void protocols::ligand_evolution::Scorer::score_ligand	(	LigandIdentifier const &	ligand,
		std::string const &	smiles = `""`,
		core::Size	save_n_scores = `0`
	)

Sets the current ligand and calls all steps to score it completely.

References check_memory(), is_scored(), protocols::sewing::data_storage::ligand, next_step(), set_ligand(), and protocols::TR().

Referenced by score_individual().

◆ score_population()

void protocols::ligand_evolution::Scorer::score_population ( Population & pop )

Sets the score for all individuals in the population, calculates it where needed.

If the same ligand is multiple times present within the population, each occures after the first gets an increasing penalty.

References base_similarity_penalty_, protocols::ligand_evolution::Individual::id(), protocols::ligand_evolution::Individual::identifier(), protocols::ligand_evolution::Population::individual(), protocols::ligand_evolution::Population::individuals(), library_, protocols::ligand_evolution::Individual::score(), score_individual(), protocols::ligand_evolution::FragmentLibrary::similarity(), similarity_penalty_threshold_, protocols::ligand_evolution::Population::size(), protocols::ligand_evolution::Population::sort(), and protocols::TR().

◆ set_base_similarity_penalty()

void protocols::ligand_evolution::Scorer::set_base_similarity_penalty ( core::Real base_penalty )

Sets the penalty for ligands which are appear more than once within a population.

The penalty is a relative fraction of the current main score for each ligand. It starts at 0 and increases with each additional ligand by the base penalty

References base_similarity_penalty_.

Referenced by initialize_from_options().

◆ set_ligand()

void protocols::ligand_evolution::Scorer::set_ligand	(	LigandIdentifier const &	ligand,
		std::string const &	smiles = `""`
	)

Sets the current ligand on which should be worked.

References current_ligand_, current_ligand_smiles_, current_runs_, is_scored(), protocols::sewing::data_storage::ligand, and protocols::TR().

Referenced by score_ligand().

◆ set_main_term()

void protocols::ligand_evolution::Scorer::set_main_term ( std::string const & score_term )

Sets which term should be used for optimization.

References main_score_term_, protocols::ligand_evolution::score_terms_, and protocols::TR().

Referenced by initialize_from_options().

◆ set_pose_path()

void protocols::ligand_evolution::Scorer::set_pose_path ( std::string const & path )

Sets the path where poses should be saved. Leave it empty to save in the current working directory.

References protocols::hybridization::path, and pose_path_.

Referenced by initialize_from_options().

◆ set_raw_scores()

void protocols::ligand_evolution::Scorer::set_raw_scores	(	LigandIdentifier const &	identifier,
		double const *	raw_scores
	)

Transforms raw double scores into a proper map and calls set_scores @detail Expects scores in the same order as score_terms.

References protocols::ligand_evolution::score_terms_, and set_scores().

◆ set_score_function()

void protocols::ligand_evolution::Scorer::set_score_function ( core::scoring::ScoreFunctionOP score_function )

Sets the desired score function.

References score_function_.

Referenced by initialize_from_options().

◆ set_scores()

void protocols::ligand_evolution::Scorer::set_scores	(	LigandIdentifier const &	identifier,
		std::map< std::string, core::Real > const &	scores
	)

Sets all score terms for an identifier if not set yet.

This functions expects that the scores were calculated by another instance of a Scorer which took care of all runs and wrote the best pose to disk

References is_scored(), score_memory_, and protocols::TR().

Referenced by next_step(), and set_raw_scores().

◆ set_similarity_penalty_threshold()

void protocols::ligand_evolution::Scorer::set_similarity_penalty_threshold ( core::Real threshold )

Referenced by initialize_from_options().

Member Data Documentation

◆ base_similarity_penalty_

core::Real protocols::ligand_evolution::Scorer::base_similarity_penalty_ = 0.2

private

Referenced by score_population(), and set_base_similarity_penalty().

◆ basic_pose_

core::pose::PoseOP protocols::ligand_evolution::Scorer::basic_pose_ = nullptr

private

Referenced by apply_movers(), calculate_scores(), create_pose(), and next_step().

◆ best_pose_

core::pose::PoseOP protocols::ligand_evolution::Scorer::best_pose_ = nullptr

private

Referenced by calculate_scores(), dump_pose(), and next_step().

◆ current_ligand_

LigandIdentifier protocols::ligand_evolution::Scorer::current_ligand_

private

Referenced by calculate_scores(), create_pose(), dump_pose(), has_ligand(), next_step(), and set_ligand().

◆ current_ligand_smiles_

std::string protocols::ligand_evolution::Scorer::current_ligand_smiles_

private

Referenced by create_pose(), next_step(), and set_ligand().

◆ current_runs_

core::Size protocols::ligand_evolution::Scorer::current_runs_ = 0

private

Referenced by calculate_scores(), next_step(), and set_ligand().

◆ id_memory_

std::map< LigandIdentifier, std::set< core::Size > > protocols::ligand_evolution::Scorer::id_memory_

private

Referenced by expose_id_memory(), and score_individual().

◆ library_

FragmentLibrary& protocols::ligand_evolution::Scorer::library_

private

Referenced by check_memory(), create_pose(), get_best_loaded(), ligand_line(), load_scores(), save_external_scoring_results(), save_results(), and score_population().

◆ ligand_chain_

char protocols::ligand_evolution::Scorer::ligand_chain_ = 'X'

private

Referenced by calculate_scores(), and create_pose().

◆ loaded_score_memory_

std::map< std::string, std::map< utility::vector1< std::string >, std::map< std::string, core::Real > > > protocols::ligand_evolution::Scorer::loaded_score_memory_

private

Important! LigendIdentifier here is NOT the same as in the rest of the program. This uses the real names from reactions and reagents.

Referenced by check_memory(), get_best_loaded(), and load_scores().

◆ main_score_term_

std::string protocols::ligand_evolution::Scorer::main_score_term_

private

Referenced by calculate_scores(), get_best_loaded(), load_scores(), save_results(), score_individual(), and set_main_term().

◆ mover_

utility::vector1< moves::MoverOP > protocols::ligand_evolution::Scorer::mover_

private

Referenced by add_mover(), and apply_movers().

◆ n_runs_

core::Size protocols::ligand_evolution::Scorer::n_runs_ = 0

private

Referenced by next_step().

◆ pose_path_

std::string protocols::ligand_evolution::Scorer::pose_path_

private

Referenced by dump_pose(), and set_pose_path().

◆ score_function_

core::scoring::ScoreFunctionOP protocols::ligand_evolution::Scorer::score_function_ = nullptr

private

Referenced by calculate_scores(), and set_score_function().

◆ score_memory_

std::map< LigandIdentifier, std::map< std::string, core::Real > > protocols::ligand_evolution::Scorer::score_memory_

private

Referenced by calculate_scores(), check_memory(), get_raw_scores(), get_scores(), is_scored(), ligand_line(), save_external_scoring_results(), save_results(), score_individual(), and set_scores().

◆ score_next_

bool protocols::ligand_evolution::Scorer::score_next_ = false

private

Referenced by next_step().

◆ similarity_penalty_threshold_

core::Real protocols::ligand_evolution::Scorer::similarity_penalty_threshold_ = 0.95

private

Referenced by score_population(), and set_similarity_penalty_threshold().

◆ working_pose_

core::pose::PoseOP protocols::ligand_evolution::Scorer::working_pose_

private

Referenced by apply_movers(), and calculate_scores().

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

src/protocols/ligand_evolution/Scorer.hh
src/protocols/ligand_evolution/Scorer.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Scorer()

Member Function Documentation

◆ add_mover()

◆ apply_movers()

◆ calculate_scores()

◆ check_memory()

◆ create_pose()

◆ dump_pose()

◆ expose_id_memory()

◆ get_best_loaded()

◆ get_raw_scores()

◆ get_scores()

◆ has_ligand()

◆ initialize_from_options()

◆ is_scored()

◆ ligand_line()

◆ load_scores()

◆ n_score_terms()

◆ next_step()

◆ save_external_scoring_results()

◆ save_results()

◆ score_individual()

◆ score_ligand()

◆ score_population()

◆ set_base_similarity_penalty()

◆ set_ligand()

◆ set_main_term()

◆ set_pose_path()

◆ set_raw_scores()

◆ set_score_function()

◆ set_scores()

◆ set_similarity_penalty_threshold()

Member Data Documentation

◆ base_similarity_penalty_

◆ basic_pose_

◆ best_pose_

◆ current_ligand_

◆ current_ligand_smiles_

◆ current_runs_

◆ id_memory_

◆ library_

◆ ligand_chain_

◆ loaded_score_memory_

◆ main_score_term_

◆ mover_

◆ n_runs_

◆ pose_path_

◆ score_function_

◆ score_memory_

◆ score_next_

◆ similarity_penalty_threshold_

◆ working_pose_