genetic_algorithm¶

Bindings for protocols::genetic_algorithm namespace

class pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer¶

Bases: 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_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_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.

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

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

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_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: WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t, 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_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_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_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: GeneticAlgorithmBase

add_entity(*args, **kwargs)¶

Overloaded function.

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>

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.

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>

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_complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) → bool¶: C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_complete() –> bool

entities_checkpoint_filename(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

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

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

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

add_entity(*args, **kwargs)¶

Overloaded function.

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>

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.

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>

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_complete(self: pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) → bool¶: C++: protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_complete() –> bool

entities_checkpoint_filename(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

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

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

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