genetic_algorithm

Bindings for protocols::genetic_algorithm namespace

class pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer

Bases: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer

add_choice(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer, choice: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) None

C++: protocols::genetic_algorithm::DiscreteRandomizer::add_choice(const class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> &) –> void

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer, : pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer

C++: protocols::genetic_algorithm::DiscreteRandomizer::operator=(const class protocols::genetic_algorithm::DiscreteRandomizer &) –> class protocols::genetic_algorithm::DiscreteRandomizer &

choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t

C++: protocols::genetic_algorithm::DiscreteRandomizer::choices() const –> const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &

crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, entity2: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::crossover(class protocols::genetic_algorithm::Entity &, class protocols::genetic_algorithm::Entity &) –> void

entity_length(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) int

C++: protocols::genetic_algorithm::EntityRandomizer::entity_length() const –> unsigned long

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

library_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer) int

C++: protocols::genetic_algorithm::DiscreteRandomizer::library_size() const –> unsigned long

mutate(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::DiscreteRandomizer::mutate(class protocols::genetic_algorithm::Entity &) –> void

mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) float

C++: protocols::genetic_algorithm::EntityRandomizer::mutation_rate() const –> double

random_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::random_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

set_choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer, choices: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) None

C++: protocols::genetic_algorithm::DiscreteRandomizer::set_choices(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> void

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, rate: float) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_mutation_rate(double) –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.Entity

Bases: pybind11_builtins.pybind11_object

Entity: a vector of EntityElements used to describe the state for a system under optimization.

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::Entity::operator=(const class protocols::genetic_algorithm::Entity &) –> class protocols::genetic_algorithm::Entity &

clone(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::Entity::clone() const –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

fitness(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) float

C++: protocols::genetic_algorithm::Entity::fitness() const –> double

fitness_valid(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) bool

C++: protocols::genetic_algorithm::Entity::fitness_valid() const –> bool

read_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, is: pyrosetta.rosetta.std.istream) bool

C++: protocols::genetic_algorithm::Entity::read_checkpoint(std::istream &) –> bool

set_entity_element(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, index: int, element: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) None

C++: protocols::genetic_algorithm::Entity::set_entity_element(unsigned long, class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>) –> void

set_fitness(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, val: float) None

C++: protocols::genetic_algorithm::Entity::set_fitness(double) –> void

set_traits(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, traits: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) None

C++: protocols::genetic_algorithm::Entity::set_traits(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> void

set_traits_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, size: int) None

C++: protocols::genetic_algorithm::Entity::set_traits_size(unsigned long) –> void

show(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, os: pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::Entity::show(std::ostream &) const –> void

to_string(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) str

C++: protocols::genetic_algorithm::Entity::to_string() const –> std::string

traits(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t

C++: protocols::genetic_algorithm::Entity::traits() const –> const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &

traits_string(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) str

C++: protocols::genetic_algorithm::Entity::traits_string() const –> std::string

write_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, os: pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::Entity::write_checkpoint(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

Bases: pybind11_builtins.pybind11_object

Entity element

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement, : pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

C++: protocols::genetic_algorithm::EntityElement::operator=(const class protocols::genetic_algorithm::EntityElement &) –> class protocols::genetic_algorithm::EntityElement &

clone(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

C++: protocols::genetic_algorithm::EntityElement::clone() –> class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>

fresh_instance(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

C++: protocols::genetic_algorithm::EntityElement::fresh_instance() –> class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>

hash(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) int

C++: protocols::genetic_algorithm::EntityElement::hash() const –> unsigned long

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) -> int

C++: protocols::genetic_algorithm::EntityElement::index() const –> unsigned long

  1. index(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement, index: int) -> None

C++: protocols::genetic_algorithm::EntityElement::index(unsigned long) –> void

name(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) str

C++: protocols::genetic_algorithm::EntityElement::name() const –> std::string

to_string(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement) str

C++: protocols::genetic_algorithm::EntityElement::to_string() const –> std::string

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator

Bases: pybind11_builtins.pybind11_object

Entity element creator

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator, : pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator

C++: protocols::genetic_algorithm::EntityElementCreator::operator=(const class protocols::genetic_algorithm::EntityElementCreator &) –> class protocols::genetic_algorithm::EntityElementCreator &

new_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator, word: str) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

C++: protocols::genetic_algorithm::EntityElementCreator::new_entity(const std::string &) –> class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>

widget_name(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator) str

C++: protocols::genetic_algorithm::EntityElementCreator::widget_name() const –> std::string

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory

Bases: pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t, pyrosetta.rosetta.utility.SingletonBase_protocols_genetic_algorithm_EntityElementFactory_t

The %EntityElementFactory is responsible for instantiating entity elements from strings.

assign(self: pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t, : pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t) pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t

C++: utility::factory::WidgetFactory<protocols::genetic_algorithm::EntityElementCreator>::operator=(const class utility::factory::WidgetFactory<class protocols::genetic_algorithm::EntityElementCreator> &) –> class utility::factory::WidgetFactory<class protocols::genetic_algorithm::EntityElementCreator> &

element_from_string(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory, : str) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement

C++: protocols::genetic_algorithm::EntityElementFactory::element_from_string(const std::string &) –> class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>

factory_name(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory) str

C++: protocols::genetic_algorithm::EntityElementFactory::factory_name() const –> std::string

factory_register(self: pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t, creator: protocols::genetic_algorithm::EntityElementCreator) None

C++: utility::factory::WidgetFactory<protocols::genetic_algorithm::EntityElementCreator>::factory_register(class std::shared_ptr<class protocols::genetic_algorithm::EntityElementCreator>) –> void

static get_instance() protocols::genetic_algorithm::EntityElementFactory

C++: utility::SingletonBase<protocols::genetic_algorithm::EntityElementFactory>::get_instance() –> class protocols::genetic_algorithm::EntityElementFactory *

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual, : pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual) pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual

C++: protocols::genetic_algorithm::EntityElementsEqual::operator=(const struct protocols::genetic_algorithm::EntityElementsEqual &) –> struct protocols::genetic_algorithm::EntityElementsEqual &

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, : pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer

C++: protocols::genetic_algorithm::EntityRandomizer::operator=(const class protocols::genetic_algorithm::EntityRandomizer &) –> class protocols::genetic_algorithm::EntityRandomizer &

crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, entity2: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::crossover(class protocols::genetic_algorithm::Entity &, class protocols::genetic_algorithm::Entity &) –> void

entity_length(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) int

C++: protocols::genetic_algorithm::EntityRandomizer::entity_length() const –> unsigned long

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

library_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) int

C++: protocols::genetic_algorithm::EntityRandomizer::library_size() const –> unsigned long

mutate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::mutate(class protocols::genetic_algorithm::Entity &) –> void

mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) float

C++: protocols::genetic_algorithm::EntityRandomizer::mutation_rate() const –> double

random_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::random_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, rate: float) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_mutation_rate(double) –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction, : pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction) pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction

C++: protocols::genetic_algorithm::FitnessFunction::operator=(const class protocols::genetic_algorithm::FitnessFunction &) –> class protocols::genetic_algorithm::FitnessFunction &

evaluate(self: pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) float

C++: protocols::genetic_algorithm::FitnessFunction::evaluate(class protocols::genetic_algorithm::Entity &) –> double

class pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm

Bases: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase

add_entity(*args, **kwargs)

Overloaded function.

  1. add_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

  1. add_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity(class std::shared_ptr<class protocols::genetic_algorithm::Entity>) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

add_parent_entity(*args, **kwargs)

Overloaded function.

  1. add_parent_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

  1. add_parent_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity(class std::shared_ptr<class protocols::genetic_algorithm::Entity>) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

add_parents_from_current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parents_from_current_generation() –> void

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm, : pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm) pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm

C++: protocols::genetic_algorithm::GeneticAlgorithm::operator=(const class protocols::genetic_algorithm::GeneticAlgorithm &) –> class protocols::genetic_algorithm::GeneticAlgorithm &

best_fitness_from_current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) float

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::best_fitness_from_current_generation() const –> double

clear_parents(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::clear_parents() –> void

complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::complete() –> bool

curr_gen_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, index: int) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

retreive a particular entity for the current generation

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::curr_gen_entity(unsigned long) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation() const –> unsigned long

current_generation_begin(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity>*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > >

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> *, class std::vector<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > >

current_generation_complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_complete() –> bool

current_generation_end(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity>*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > >

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> *, class std::vector<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > >

entities_checkpoint_filename(*args, **kwargs)

Overloaded function.

  1. entities_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str

  2. entities_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix: str) -> str

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::entities_checkpoint_filename(std::string) const –> std::string

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

evaluate_fitnesses(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm) None

C++: protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses() –> void

evolve_next_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::evolve_next_generation() –> void

fill_by_crossover(*args, **kwargs)

Overloaded function.

  1. fill_by_crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_by_crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_crossover(unsigned long) –> void

fill_by_mutation(*args, **kwargs)

Overloaded function.

  1. fill_by_mutation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_by_mutation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_mutation(unsigned long) –> void

fill_with_perturbations_of_existing_entities(*args, **kwargs)

Overloaded function.

  1. fill_with_perturbations_of_existing_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_with_perturbations_of_existing_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_perturbations_of_existing_entities(unsigned long) –> void

fill_with_random_entities(*args, **kwargs)

Overloaded function.

  1. fill_with_random_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_with_random_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_random_entities(unsigned long) –> void

property fitness_function_
fraction_by_recombination(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) float

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fraction_by_recombination() const –> double

generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::generations() const –> const class utility::vector1<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > >, class std::allocator<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > > > &

generations_checkpoint_filename(*args, **kwargs)

Overloaded function.

  1. generations_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str

  2. generations_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix: str) -> str

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::generations_checkpoint_filename(std::string) const –> std::string

max_generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::max_generations() const –> unsigned long

max_population_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::max_population_size() const –> unsigned long

new_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::new_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

number_to_propagate(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::number_to_propagate() const –> unsigned long

population(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, gen_num: int) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t

true const (read-only) access to entity population: new vector of const pointers

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::population(unsigned long) const –> class utility::vector1<class std::shared_ptr<const class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<const class protocols::genetic_algorithm::Entity> > >

print_cache(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_cache(std::ostream &) const –> void

print_generation_statistics(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, os: pyrosetta.rosetta.std.ostream, gen_num: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_generation_statistics(std::ostream &, unsigned long) const –> void

print_population(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_population(std::ostream &) const –> void

propagate_best_from_previous_generation(*args, **kwargs)

Overloaded function.

  1. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

  3. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int, unique: bool) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::propagate_best_from_previous_generation(unsigned long, bool) –> void

read_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_checkpoint() –> bool

read_entities_checkpoint(*args, **kwargs)

Overloaded function.

  1. read_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool

  2. read_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, overwrite: bool) -> bool

for checkpointing fitness cache

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint(bool) –> bool

read_generations_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint() –> bool

rename_checkpoint_files(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

allows the prevention of accidental reuse of checkpoint files

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::rename_checkpoint_files() const –> void

set_checkpoint_gzip(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b: bool) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_gzip(bool) –> void

set_checkpoint_prefix(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, p: str) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_prefix(const std::string &) –> void

set_checkpoint_rename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b: bool) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_rename(bool) –> void

set_checkpoint_write_interval(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, i: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_write_interval(unsigned long) –> void

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_frac_by_recomb(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, f: float) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_frac_by_recomb(double) –> void

set_func(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm, f: pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction) None

C++: protocols::genetic_algorithm::GeneticAlgorithm::set_func(class std::shared_ptr<class protocols::genetic_algorithm::FitnessFunction>) –> void

set_max_generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_generations(unsigned long) –> void

set_max_pop_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_pop_size(unsigned long) –> void

set_num_to_propagate(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_num_to_propagate(unsigned long) –> void

set_rand(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, r: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_rand(class std::shared_ptr<class protocols::genetic_algorithm::EntityRandomizer>) –> void

tournament_select(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, pvec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::tournament_select(const class utility::vector1<class std::shared_ptr<const class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<const class protocols::genetic_algorithm::Entity> > > &) const –> const class protocols::genetic_algorithm::Entity &

write_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

for checkpointing fitness cache

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint() const –> bool

write_generations_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint() const –> bool

class pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase

Bases: pybind11_builtins.pybind11_object

add_entity(*args, **kwargs)

Overloaded function.

  1. add_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

  1. add_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity(class std::shared_ptr<class protocols::genetic_algorithm::Entity>) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

add_parent_entity(*args, **kwargs)

Overloaded function.

  1. add_parent_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

  1. add_parent_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) -> pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity(class std::shared_ptr<class protocols::genetic_algorithm::Entity>) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

add_parents_from_current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::add_parents_from_current_generation() –> void

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, : pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::operator=(const class protocols::genetic_algorithm::GeneticAlgorithmBase &) –> class protocols::genetic_algorithm::GeneticAlgorithmBase &

best_fitness_from_current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) float

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::best_fitness_from_current_generation() const –> double

clear_parents(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::clear_parents() –> void

complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::complete() –> bool

curr_gen_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, index: int) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

retreive a particular entity for the current generation

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::curr_gen_entity(unsigned long) –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

current_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation() const –> unsigned long

current_generation_begin(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity>*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > >

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> *, class std::vector<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > >

current_generation_complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_complete() –> bool

current_generation_end(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity>*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > >

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> *, class std::vector<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > >

entities_checkpoint_filename(*args, **kwargs)

Overloaded function.

  1. entities_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str

  2. entities_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix: str) -> str

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::entities_checkpoint_filename(std::string) const –> std::string

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

evolve_next_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::evolve_next_generation() –> void

fill_by_crossover(*args, **kwargs)

Overloaded function.

  1. fill_by_crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_by_crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_crossover(unsigned long) –> void

fill_by_mutation(*args, **kwargs)

Overloaded function.

  1. fill_by_mutation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_by_mutation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_mutation(unsigned long) –> void

fill_with_perturbations_of_existing_entities(*args, **kwargs)

Overloaded function.

  1. fill_with_perturbations_of_existing_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_with_perturbations_of_existing_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_perturbations_of_existing_entities(unsigned long) –> void

fill_with_random_entities(*args, **kwargs)

Overloaded function.

  1. fill_with_random_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. fill_with_random_entities(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_random_entities(unsigned long) –> void

fraction_by_recombination(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) float

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::fraction_by_recombination() const –> double

generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::generations() const –> const class utility::vector1<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > >, class std::allocator<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::Entity> > > > > &

generations_checkpoint_filename(*args, **kwargs)

Overloaded function.

  1. generations_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str

  2. generations_checkpoint_filename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix: str) -> str

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::generations_checkpoint_filename(std::string) const –> std::string

max_generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::max_generations() const –> unsigned long

max_population_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::max_population_size() const –> unsigned long

new_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::new_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

number_to_propagate(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) int

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::number_to_propagate() const –> unsigned long

population(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, gen_num: int) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t

true const (read-only) access to entity population: new vector of const pointers

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::population(unsigned long) const –> class utility::vector1<class std::shared_ptr<const class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<const class protocols::genetic_algorithm::Entity> > >

print_cache(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_cache(std::ostream &) const –> void

print_generation_statistics(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, os: pyrosetta.rosetta.std.ostream, gen_num: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_generation_statistics(std::ostream &, unsigned long) const –> void

print_population(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::print_population(std::ostream &) const –> void

propagate_best_from_previous_generation(*args, **kwargs)

Overloaded function.

  1. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> None

  2. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int) -> None

  3. propagate_best_from_previous_generation(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size: int, unique: bool) -> None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::propagate_best_from_previous_generation(unsigned long, bool) –> void

read_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_checkpoint() –> bool

read_entities_checkpoint(*args, **kwargs)

Overloaded function.

  1. read_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool

  2. read_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, overwrite: bool) -> bool

for checkpointing fitness cache

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint(bool) –> bool

read_generations_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint() –> bool

rename_checkpoint_files(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) None

allows the prevention of accidental reuse of checkpoint files

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::rename_checkpoint_files() const –> void

set_checkpoint_gzip(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b: bool) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_gzip(bool) –> void

set_checkpoint_prefix(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, p: str) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_prefix(const std::string &) –> void

set_checkpoint_rename(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b: bool) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_rename(bool) –> void

set_checkpoint_write_interval(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, i: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_write_interval(unsigned long) –> void

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_frac_by_recomb(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, f: float) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_frac_by_recomb(double) –> void

set_max_generations(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_generations(unsigned long) –> void

set_max_pop_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_pop_size(unsigned long) –> void

set_num_to_propagate(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s: int) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_num_to_propagate(unsigned long) –> void

set_rand(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, r: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) None

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::set_rand(class std::shared_ptr<class protocols::genetic_algorithm::EntityRandomizer>) –> void

tournament_select(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, pvec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::tournament_select(const class utility::vector1<class std::shared_ptr<const class protocols::genetic_algorithm::Entity>, class std::allocator<class std::shared_ptr<const class protocols::genetic_algorithm::Entity> > > &) const –> const class protocols::genetic_algorithm::Entity &

write_entities_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

for checkpointing fitness cache

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint() const –> bool

write_generations_checkpoint(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) bool

C++: protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint() const –> bool

class pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer

Bases: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer

append_choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, choices: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) None

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::append_choices(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer, : pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer

C++: protocols::genetic_algorithm::Mutate1Randomizer::operator=(const class protocols::genetic_algorithm::Mutate1Randomizer &) –> class protocols::genetic_algorithm::Mutate1Randomizer &

choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::choices() const –> const class utility::vector1<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > >, class std::allocator<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > > > &

crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, entity2: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::crossover(class protocols::genetic_algorithm::Entity &, class protocols::genetic_algorithm::Entity &) –> void

entity_length(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) int

C++: protocols::genetic_algorithm::EntityRandomizer::entity_length() const –> unsigned long

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

library_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) int

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::library_size() const –> unsigned long

mutate(self: pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::Mutate1Randomizer::mutate(class protocols::genetic_algorithm::Entity &) –> void

mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) float

C++: protocols::genetic_algorithm::EntityRandomizer::mutation_rate() const –> double

random_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::random_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, rate: float) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_mutation_rate(double) –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer

Bases: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer

different set of choices at each position in Entity’s traits

append_choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, choices: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) None

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::append_choices(const class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, : pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::operator=(const class protocols::genetic_algorithm::PositionSpecificRandomizer &) –> class protocols::genetic_algorithm::PositionSpecificRandomizer &

choices(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::choices() const –> const class utility::vector1<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > >, class std::allocator<class utility::vector1<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement>, class std::allocator<class std::shared_ptr<class protocols::genetic_algorithm::EntityElement> > > > > &

crossover(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, entity2: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::crossover(class protocols::genetic_algorithm::Entity &, class protocols::genetic_algorithm::Entity &) –> void

entity_length(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) int

C++: protocols::genetic_algorithm::EntityRandomizer::entity_length() const –> unsigned long

entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::entity_template() const –> class std::shared_ptr<const class protocols::genetic_algorithm::Entity>

library_size(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) int

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::library_size() const –> unsigned long

mutate(self: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::PositionSpecificRandomizer::mutate(class protocols::genetic_algorithm::Entity &) –> void

mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) float

C++: protocols::genetic_algorithm::EntityRandomizer::mutation_rate() const –> double

random_entity(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer) pyrosetta.rosetta.protocols.genetic_algorithm.Entity

C++: protocols::genetic_algorithm::EntityRandomizer::random_entity() –> class std::shared_ptr<class protocols::genetic_algorithm::Entity>

set_entity_template(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_entity_template(class std::shared_ptr<const class protocols::genetic_algorithm::Entity>) –> void

set_mutation_rate(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer, rate: float) None

C++: protocols::genetic_algorithm::EntityRandomizer::set_mutation_rate(double) –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash, : pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash) pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash

C++: protocols::genetic_algorithm::Vec1Hash::operator=(const struct protocols::genetic_algorithm::Vec1Hash &) –> struct protocols::genetic_algorithm::Vec1Hash &