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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

class pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement¶

Bases: pybind11_builtins.pybind11_object

Entity element

assign(self: pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement, rhs: 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_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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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.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.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