protocols::ligand_evolution Namespace Reference

Classes
class	EvolutionManager
	The EvolutionManager combines all required resources for the evolutionary ligand optimization and handles them as needed. More...
class	EvolutionOptions
	Within EvolutionOptions class combines all options and settings are collected, defaults saved and sanity checks performed before running. More...
class	FragmentLibrary
	The FragmentLibrary implements a combinatorial library for reaction and reagent data. Its main task is to hold chemical information and provide new ligands. More...
class	Reagent
	Internal class to handle reagent information more easily. More...
class	Reaction
	Internal class to handle reaction information more easily. More...
class	Individual
	The individual holds all information about a single solution in an evolutionary optimization process. More...
class	Crossover
	Takes two individuals and produces a set amount of offspring using a crossover. More...
class	IdentityFactory
	Take a single individual, and returns a desired number of point mutated individuals based on the input one. More...
class	Mutator
	Take a single individual, and returns a desired number of point mutated individuals based on the input one. More...
class	OffspringFactory
	: An abstract class to give an interface for producing offspring from individuals More...
class	Population
	@ Summarizes and contains all Individuals of one generation More...
class	Scorer
	: 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...
class	ElitistSelector
	Selects only the best scored individuals. More...
class	RouletteSelector
	Selects only the best scored individuals. More...
class	Selector
	: An abstract class to give an interface for subset selection of Population More...
class	TournamentSelector
	Selects only the best scored individuals. More...

Typedefs
typedef utility::pointer::shared_ptr< EvolutionManager >	EvolutionManagerOP
typedef utility::pointer::shared_ptr< EvolutionManager const >	EvolutionManagerCOP
typedef utility::pointer::shared_ptr< EvolutionOptions >	EvolutionOptionsOP
typedef utility::pointer::shared_ptr< EvolutionOptions const >	EvolutionOptionsCOP
typedef utility::pointer::shared_ptr< FragmentLibrary >	FragmentLibraryOP
typedef utility::pointer::shared_ptr< FragmentLibrary const >	FragmentLibraryCOP
typedef utility::pointer::shared_ptr< Reagent >	ReagentOP
typedef utility::pointer::shared_ptr< Reagent const >	ReagentCOP
typedef utility::pointer::shared_ptr< Reaction >	ReactionOP
typedef utility::pointer::shared_ptr< Reaction const >	ReactionCOP
typedef utility::vector1< core::Size >	LigandIdentifier
	LigandIdentifiers are a vector of ints which should encode all information needed by the FragmentLibrary to create a new ligand. More...
typedef utility::vector1< std::pair< core::Size, core::Real > >	ReagentSimilarityList
	ReagentSimilarityList is a list of reagent ids combined with a similarity score, mainly used for fragment searches. More...
typedef utility::pointer::shared_ptr< Individual >	IndividualOP
typedef utility::pointer::shared_ptr< Individual const >	IndividualCOP
typedef utility::pointer::shared_ptr< Crossover >	CrossoverOP
typedef utility::pointer::shared_ptr< Crossover const >	CrossoverCOP
typedef utility::pointer::shared_ptr< IdentityFactory >	IdentityFactoryOP
typedef utility::pointer::shared_ptr< IdentityFactory const >	IdentityFactoryCOP
typedef utility::pointer::shared_ptr< Mutator >	MutatorOP
typedef utility::pointer::shared_ptr< Mutator const >	MutatorCOP
typedef utility::pointer::shared_ptr< OffspringFactory >	OffspringFactoryOP
typedef utility::pointer::shared_ptr< OffspringFactory const >	OffspringFactoryCOP
typedef utility::pointer::shared_ptr< Population >	PopulationOP
typedef utility::pointer::shared_ptr< Population const >	PopulationCOP
typedef utility::pointer::shared_ptr< Scorer >	ScorerOP
typedef utility::pointer::shared_ptr< Scorer const >	ScorerCOP
typedef utility::pointer::shared_ptr< ElitistSelector >	ElitistSelectorOP
typedef utility::pointer::shared_ptr< ElitistSelector const >	ElitistSelectorCOP
typedef utility::pointer::shared_ptr< RouletteSelector >	RouletteSelectorOP
typedef utility::pointer::shared_ptr< RouletteSelector const >	RouletteSelectorCOP
typedef utility::pointer::shared_ptr< Selector >	SelectorOP
typedef utility::pointer::shared_ptr< Selector const >	SelectorCOP
typedef utility::pointer::shared_ptr< TournamentSelector >	TournamentSelectorOP
typedef utility::pointer::shared_ptr< TournamentSelector const >	TournamentSelectorCOP
typedef utility::pointer::shared_ptr< WorkManager >	WorkManagerOP
typedef utility::pointer::shared_ptr< WorkManager const >	WorkManagerCOP
typedef utility::pointer::shared_ptr< Worker >	WorkerOP
typedef utility::pointer::shared_ptr< Worker const >	WorkerCOP

Variables
utility::vector1< std::string > const	score_terms_ { "ligand_interface_delta", "total_REU", "ligand_interface_delta_EFFICIENCY", "lid_root2", "lid_root3" }

Typedef Documentation

CrossoverCOP

typedef utility::pointer::shared_ptr< Crossover const > protocols::ligand_evolution::CrossoverCOP

CrossoverOP

typedef utility::pointer::shared_ptr< Crossover > protocols::ligand_evolution::CrossoverOP

ElitistSelectorCOP

typedef utility::pointer::shared_ptr< ElitistSelector const > protocols::ligand_evolution::ElitistSelectorCOP

ElitistSelectorOP

typedef utility::pointer::shared_ptr< ElitistSelector > protocols::ligand_evolution::ElitistSelectorOP

EvolutionManagerCOP

typedef utility::pointer::shared_ptr< EvolutionManager const > protocols::ligand_evolution::EvolutionManagerCOP

EvolutionManagerOP

typedef utility::pointer::shared_ptr< EvolutionManager > protocols::ligand_evolution::EvolutionManagerOP

EvolutionOptionsCOP

typedef utility::pointer::shared_ptr< EvolutionOptions const > protocols::ligand_evolution::EvolutionOptionsCOP

EvolutionOptionsOP

typedef utility::pointer::shared_ptr< EvolutionOptions > protocols::ligand_evolution::EvolutionOptionsOP

FragmentLibraryCOP

typedef utility::pointer::shared_ptr< FragmentLibrary const > protocols::ligand_evolution::FragmentLibraryCOP

FragmentLibraryOP

typedef utility::pointer::shared_ptr< FragmentLibrary > protocols::ligand_evolution::FragmentLibraryOP

IdentityFactoryCOP

typedef utility::pointer::shared_ptr< IdentityFactory const > protocols::ligand_evolution::IdentityFactoryCOP

IdentityFactoryOP

typedef utility::pointer::shared_ptr< IdentityFactory > protocols::ligand_evolution::IdentityFactoryOP

IndividualCOP

typedef utility::pointer::shared_ptr< Individual const > protocols::ligand_evolution::IndividualCOP

IndividualOP

typedef utility::pointer::shared_ptr< Individual > protocols::ligand_evolution::IndividualOP

LigandIdentifier

typedef utility::vector1< core::Size > protocols::ligand_evolution::LigandIdentifier

LigandIdentifiers are a vector of ints which should encode all information needed by the FragmentLibrary to create a new ligand.

MutatorCOP

typedef utility::pointer::shared_ptr< Mutator const > protocols::ligand_evolution::MutatorCOP

MutatorOP

typedef utility::pointer::shared_ptr< Mutator > protocols::ligand_evolution::MutatorOP

OffspringFactoryCOP

typedef utility::pointer::shared_ptr< OffspringFactory const > protocols::ligand_evolution::OffspringFactoryCOP

OffspringFactoryOP

typedef utility::pointer::shared_ptr< OffspringFactory > protocols::ligand_evolution::OffspringFactoryOP

PopulationCOP

typedef utility::pointer::shared_ptr< Population const > protocols::ligand_evolution::PopulationCOP

PopulationOP

typedef utility::pointer::shared_ptr< Population > protocols::ligand_evolution::PopulationOP

ReactionCOP

typedef utility::pointer::shared_ptr< Reaction const > protocols::ligand_evolution::ReactionCOP

ReactionOP

typedef utility::pointer::shared_ptr< Reaction > protocols::ligand_evolution::ReactionOP

ReagentCOP

typedef utility::pointer::shared_ptr< Reagent const > protocols::ligand_evolution::ReagentCOP

ReagentOP

typedef utility::pointer::shared_ptr< Reagent > protocols::ligand_evolution::ReagentOP

ReagentSimilarityList

typedef utility::vector1< std::pair< core::Size, core::Real > > protocols::ligand_evolution::ReagentSimilarityList

ReagentSimilarityList is a list of reagent ids combined with a similarity score, mainly used for fragment searches.

RouletteSelectorCOP

typedef utility::pointer::shared_ptr< RouletteSelector const > protocols::ligand_evolution::RouletteSelectorCOP

RouletteSelectorOP

typedef utility::pointer::shared_ptr< RouletteSelector > protocols::ligand_evolution::RouletteSelectorOP

ScorerCOP

typedef utility::pointer::shared_ptr< Scorer const > protocols::ligand_evolution::ScorerCOP

ScorerOP

typedef utility::pointer::shared_ptr< Scorer > protocols::ligand_evolution::ScorerOP

SelectorCOP

typedef utility::pointer::shared_ptr< Selector const > protocols::ligand_evolution::SelectorCOP

SelectorOP

typedef utility::pointer::shared_ptr< Selector > protocols::ligand_evolution::SelectorOP

TournamentSelectorCOP

typedef utility::pointer::shared_ptr< TournamentSelector const > protocols::ligand_evolution::TournamentSelectorCOP

TournamentSelectorOP

typedef utility::pointer::shared_ptr< TournamentSelector > protocols::ligand_evolution::TournamentSelectorOP

WorkerCOP

typedef utility::pointer::shared_ptr< Worker const > protocols::ligand_evolution::WorkerCOP

WorkerOP

typedef utility::pointer::shared_ptr< Worker > protocols::ligand_evolution::WorkerOP

WorkManagerCOP

typedef utility::pointer::shared_ptr< WorkManager const > protocols::ligand_evolution::WorkManagerCOP

WorkManagerOP

typedef utility::pointer::shared_ptr< WorkManager > protocols::ligand_evolution::WorkManagerOP

Variable Documentation

score_terms_

utility::vector1< std::string > const protocols::ligand_evolution::score_terms_ { "ligand_interface_delta", "total_REU", "ligand_interface_delta_EFFICIENCY", "lid_root2", "lid_root3" }

Referenced by protocols::ligand_evolution::Scorer::calculate_scores(), protocols::ligand_evolution::EvolutionOptions::check_scorer_setup(), protocols::ligand_evolution::Scorer::get_raw_scores(), protocols::ligand_evolution::Scorer::ligand_line(), protocols::ligand_evolution::Scorer::load_scores(), protocols::ligand_evolution::Scorer::n_score_terms(), protocols::ligand_evolution::Scorer::next_step(), protocols::ligand_evolution::Scorer::save_external_scoring_results(), protocols::ligand_evolution::Scorer::save_results(), protocols::ligand_evolution::Scorer::score_individual(), protocols::ligand_evolution::Scorer::set_main_term(), and protocols::ligand_evolution::Scorer::set_raw_scores().