The EvolutionManager combines all required resources for the evolutionary ligand optimization and handles them as needed. More...

#include <EvolutionManager.hh>

Public Member Functions
	EvolutionManager (int rank)
	If rank is different than 0 a mpi system is expected. More...

void	run (int mpi_size=1)
	Main function that handles evolutionary optimization. More...

void	init ()

std::string	scores_to_str () const
	Prints scores of all individuals. More...

Private Member Functions
void	score ()
	Scores the entire population. More...

void	init_workmanager ()

void	calculate_quantiles ()
	Calculates the current quantiles. More...

void	write_population_information () const
	Saves information about the population and its history to disk. For debugging and benchmarking purposes. More...

void	init_evolution_protocol (EvolutionOptionsCOP options)

void	external_scoring (int mpi_size)

Private Attributes
core::Size	max_generations_
	Defines after how many generations optimization will stop. More...

Population	population_
	Contains and manages all evolutionary information for all ligands. More...

ScorerOP	scorer_ = nullptr
	Manages the scoring of ligands as well as keeping track of scores. More...

WorkManagerOP	work_manager_ = nullptr
	Handles mpi communication to distribute the scoring work. More...

FragmentLibrary	library_
	Holds all molecular information about the protein and the ligands. More...

core::Size	main_selector_
	The selector which will be applied to advance the generation. More...

utility::vector1< SelectorOP >	selectors_
	Holds all selectors. More...

std::map< std::string, core::Size >	selector_map_
	Maps selector names to indices in selector list. More...

utility::vector1< OffspringFactoryOP >	factories_
	Holds all offspring factories. More...

std::map< std::string, core::Size >	factory_map_
	Maps factory names to indices in factory list. More...

utility::vector1< utility::vector1< core::Size > >	offspring_options_
	Holds arrays of size 5, defining index of selector, index of factory, selection size, offspring size, if parent will be kept in pool. More...

int	rank_ = 0

utility::vector1< core::Real >	quantiles = { 9999.9, 9999.9, 9999.9, 9999.9 }
	Stores statistical information about score distribution within the population. More...

core::Size	external_scoring_ = 0
	Used to distinguish between scoring of external molecules and internal evolutionary optimization. More...

Detailed Description

The EvolutionManager combines all required resources for the evolutionary ligand optimization and handles them as needed.

Constructor & Destructor Documentation

◆ EvolutionManager()

protocols::ligand_evolution::EvolutionManager::EvolutionManager ( int rank )

explicit

If rank is different than 0 a mpi system is expected.

Member Function Documentation

◆ calculate_quantiles()

void protocols::ligand_evolution::EvolutionManager::calculate_quantiles ( )

private

Calculates the current quantiles.

References protocols::ligand_evolution::Population::individual(), population_, quantiles, protocols::ligand_evolution::Individual::score(), protocols::ligand_evolution::Population::size(), and protocols::ligand_evolution::Population::sort().

Referenced by run().

◆ external_scoring()

void protocols::ligand_evolution::EvolutionManager::external_scoring ( int mpi_size )

private

References external_scoring_, library_, protocols::ligand_evolution::FragmentLibrary::n_unscored_smiles(), rank_, and scorer_.

Referenced by run().

◆ init()

void protocols::ligand_evolution::EvolutionManager::init ( void )

References protocols::rosetta_scripts::XmlObjects::create_from_file(), external_scoring_, init_evolution_protocol(), init_workmanager(), protocols::ligand_evolution::Population::initialize_from_evotoptions(), protocols::ligand_evolution::FragmentLibrary::initialize_from_options(), library_, max_generations_, population_, rank_, scorer_, and protocols::TR().

◆ init_evolution_protocol()

void protocols::ligand_evolution::EvolutionManager::init_evolution_protocol ( EvolutionOptionsCOP options )

private

References factories_, factory_map_, library_, main_selector_, offspring_options_, selector_map_, selectors_, and protocols::TR().

Referenced by init().

◆ init_workmanager()

void protocols::ligand_evolution::EvolutionManager::init_workmanager ( )

private

References library_, protocols::ligand_evolution::FragmentLibrary::max_positions(), scorer_, and work_manager_.

Referenced by init().

◆ run()

void protocols::ligand_evolution::EvolutionManager::run ( int mpi_size = 1 )

◆ score()

void protocols::ligand_evolution::EvolutionManager::score ( )

private

Scores the entire population.

References population_, scorer_, and work_manager_.

Referenced by run().

◆ scores_to_str()

std::string protocols::ligand_evolution::EvolutionManager::scores_to_str ( ) const

Prints scores of all individuals.

References protocols::ligand_evolution::Population::individuals(), population_, protocols::kinmatch::str(), and core::id::to_string().

Referenced by run().

◆ write_population_information()

void protocols::ligand_evolution::EvolutionManager::write_population_information ( ) const

private

Saves information about the population and its history to disk. For debugging and benchmarking purposes.

References protocols::ligand_evolution::Population::expose_generation_log(), protocols::ligand_evolution::Population::expose_inheritance_graph(), core::conformation::membrane::out, population_, and scorer_.

Referenced by run().

Member Data Documentation

◆ external_scoring_

core::Size protocols::ligand_evolution::EvolutionManager::external_scoring_ = 0

private

Used to distinguish between scoring of external molecules and internal evolutionary optimization.

Referenced by external_scoring(), init(), and run().

◆ factories_

utility::vector1< OffspringFactoryOP > protocols::ligand_evolution::EvolutionManager::factories_

private

Holds all offspring factories.

Referenced by init_evolution_protocol(), and run().

◆ factory_map_

std::map< std::string, core::Size > protocols::ligand_evolution::EvolutionManager::factory_map_

private

Maps factory names to indices in factory list.

Referenced by init_evolution_protocol().

◆ library_

FragmentLibrary protocols::ligand_evolution::EvolutionManager::library_

private

Holds all molecular information about the protein and the ligands.

Referenced by external_scoring(), init(), init_evolution_protocol(), and init_workmanager().

◆ main_selector_

core::Size protocols::ligand_evolution::EvolutionManager::main_selector_

private

The selector which will be applied to advance the generation.

Referenced by init_evolution_protocol(), and run().

◆ max_generations_

core::Size protocols::ligand_evolution::EvolutionManager::max_generations_

private

Defines after how many generations optimization will stop.

Referenced by init(), and run().

◆ offspring_options_

utility::vector1< utility::vector1< core::Size > > protocols::ligand_evolution::EvolutionManager::offspring_options_

private

Holds arrays of size 5, defining index of selector, index of factory, selection size, offspring size, if parent will be kept in pool.

Factories will be called in order of this array

Referenced by init_evolution_protocol(), and run().

◆ population_

Population protocols::ligand_evolution::EvolutionManager::population_

private

Contains and manages all evolutionary information for all ligands.

Referenced by calculate_quantiles(), init(), run(), score(), scores_to_str(), and write_population_information().

◆ quantiles

utility::vector1< core::Real > protocols::ligand_evolution::EvolutionManager::quantiles = { 9999.9, 9999.9, 9999.9, 9999.9 }

private

Stores statistical information about score distribution within the population.

Referenced by calculate_quantiles(), and run().

◆ rank_

int protocols::ligand_evolution::EvolutionManager::rank_ = 0

private

Referenced by external_scoring(), init(), and run().

◆ scorer_

ScorerOP protocols::ligand_evolution::EvolutionManager::scorer_ = nullptr

private

Manages the scoring of ligands as well as keeping track of scores.

Referenced by external_scoring(), init(), init_workmanager(), run(), score(), and write_population_information().

◆ selector_map_

std::map< std::string, core::Size > protocols::ligand_evolution::EvolutionManager::selector_map_

private

Maps selector names to indices in selector list.

Referenced by init_evolution_protocol().

◆ selectors_

utility::vector1< SelectorOP > protocols::ligand_evolution::EvolutionManager::selectors_

private

Holds all selectors.

Referenced by init_evolution_protocol(), and run().

◆ work_manager_

WorkManagerOP protocols::ligand_evolution::EvolutionManager::work_manager_ = nullptr

private

Handles mpi communication to distribute the scoring work.

Referenced by init_workmanager(), run(), and score().

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

src/protocols/ligand_evolution/EvolutionManager.hh
src/protocols/ligand_evolution/EvolutionManager.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EvolutionManager()

Member Function Documentation

◆ calculate_quantiles()

◆ external_scoring()

◆ init()

◆ init_evolution_protocol()

◆ init_workmanager()

◆ run()

◆ score()

◆ scores_to_str()

◆ write_population_information()

Member Data Documentation

◆ external_scoring_

◆ factories_

◆ factory_map_

◆ library_

◆ main_selector_

◆ max_generations_

◆ offspring_options_

◆ population_

◆ quantiles

◆ rank_

◆ scorer_

◆ selector_map_

◆ selectors_

◆ work_manager_