protocols::ligand_evolution::Mutator Class Reference

Take a single individual, and returns a desired number of point mutated individuals based on the input one. More...

#include <Mutator.hh>

Inheritance diagram for protocols::ligand_evolution::Mutator:

Public Member Functions
	Mutator (FragmentLibrary const &library, utility::vector1< core::Real > const &weights, core::Real min_similarity, core::Real max_similarity)
utility::vector1< Individual >	apply (utility::vector1< Individual > const &parents, core::Size n_offspring) const override
	Accepts a list of parents and creates n_offspring mutants @detail Based on the internal values this mutation process changes either one of the reagents or the reaction and maps offspring to the closest ligand. More...
std::string const &	name () const override
	Returns the name of this mutator. More...
void	set_min_similarity (core::Real min_similarity)
	Sets the minimum similarity for mutations. More...
void	set_max_similarity (core::Real max_similarity)
	Sets the maximum similarity for mutations. More...

Private Member Functions
Individual	mutate (Individual const &individual) const

Private Attributes
core::Real	min_similarity_ = 0.6
	If possible this is the minimum similarity at which a reagent point mutation will be selected. More...
core::Real	max_similarity_ = 0.99
	This is the maximum similarity for reagents to be considered as possible mutants. More...
FragmentLibrary const &	library_
	Since this function regularly produces offspring and consults a FragmentLibrary for this, it keeps a ownership to one. More...
numeric::random::WeightedSampler	reaction_or_reagent_
	Randomly chooses what feature will be mutated based on the given weights. More...
std::string	name_ = "Mutator"
	A name to identify the type of this object. More...

Detailed Description

Take a single individual, and returns a desired number of point mutated individuals based on the input one.

Constructor & Destructor Documentation

Mutator()

protocols::ligand_evolution::Mutator::Mutator	(	FragmentLibrary const &	library,
		utility::vector1< core::Real > const &	weights,
		core::Real	min_similarity,
		core::Real	max_similarity
	)

Member Function Documentation

apply()

utility::vector1< Individual > protocols::ligand_evolution::Mutator::apply ( utility::vector1< Individual > const &  parents, core::Size  n_offspring  ) const

overridevirtual

Accepts a list of parents and creates n_offspring mutants @detail Based on the internal values this mutation process changes either one of the reagents or the reaction and maps offspring to the closest ligand.

Implements protocols::ligand_evolution::OffspringFactory.

References mutate(), and protocols::TR().

mutate()

Individual protocols::ligand_evolution::Mutator::mutate ( Individual const &  individual ) const

private

References protocols::ligand_evolution::FragmentLibrary::get_similar_reagents(), protocols::ligand_evolution::Individual::id(), protocols::ligand_evolution::Individual::identifier(), library_, max_similarity_, min_similarity_, protocols::ligand_evolution::FragmentLibrary::random_reaction(), reaction_or_reagent_, protocols::ligand_evolution::FragmentLibrary::reaction_positions(), protocols::ligand_evolution::FragmentLibrary::reagents_size(), and protocols::TR().

Referenced by apply().

name()

std::string const & protocols::ligand_evolution::Mutator::name ( ) const

overridevirtual

Returns the name of this mutator.

Implements protocols::ligand_evolution::OffspringFactory.

References name_.

set_max_similarity()

void protocols::ligand_evolution::Mutator::set_max_similarity

(

core::Real

max_similarity

)

Sets the maximum similarity for mutations.

References max_similarity_.

set_min_similarity()

void protocols::ligand_evolution::Mutator::set_min_similarity

(

core::Real

min_similarity

)

Sets the minimum similarity for mutations.

References min_similarity_.

Member Data Documentation

library_

FragmentLibrary const& protocols::ligand_evolution::Mutator::library_

private

Since this function regularly produces offspring and consults a FragmentLibrary for this, it keeps a ownership to one.

Referenced by mutate().

max_similarity_

core::Real protocols::ligand_evolution::Mutator::max_similarity_ = 0.99

private

This is the maximum similarity for reagents to be considered as possible mutants.

Referenced by mutate(), and set_max_similarity().

min_similarity_

core::Real protocols::ligand_evolution::Mutator::min_similarity_ = 0.6

private

If possible this is the minimum similarity at which a reagent point mutation will be selected.

Referenced by mutate(), and set_min_similarity().

name_

std::string protocols::ligand_evolution::Mutator::name_ = "Mutator"

private

A name to identify the type of this object.

Referenced by name().

reaction_or_reagent_

numeric::random::WeightedSampler protocols::ligand_evolution::Mutator::reaction_or_reagent_

private

Randomly chooses what feature will be mutated based on the given weights.

Referenced by mutate().

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

• src/protocols/ligand_evolution/offspring_factory/Mutator.hh
• src/protocols/ligand_evolution/offspring_factory/Mutator.cc