Bindings for protocols::genetic_algorithm namespace

Classes
		builtins.object Entity EntityElement EntityElementCreator EntityElementsEqual EntityRandomizer DiscreteRandomizer PositionSpecificRandomizer Mutate1Randomizer FitnessFunction GeneticAlgorithmBase GeneticAlgorithm Vec1Hash rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t(builtins.object) EntityElementFactory   class DiscreteRandomizer(EntityRandomizer)     /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: DiscreteRandomizer EntityRandomizer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_choice(...) from builtins.PyCapsule add_choice(self : rosetta.protocols.genetic_algorithm.DiscreteRandomizer, choice : rosetta.protocols.genetic_algorithm.EntityElement) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.DiscreteRandomizer,  : rosetta.protocols.genetic_algorithm.DiscreteRandomizer) -> rosetta.protocols.genetic_algorithm.DiscreteRandomizer choices(...) from builtins.PyCapsule choices(rosetta.protocols.genetic_algorithm.DiscreteRandomizer) -> rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t library_size(...) from builtins.PyCapsule library_size(rosetta.protocols.genetic_algorithm.DiscreteRandomizer) -> int mutate(...) from builtins.PyCapsule mutate(self : rosetta.protocols.genetic_algorithm.DiscreteRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_choices(...) from builtins.PyCapsule set_choices(self : rosetta.protocols.genetic_algorithm.DiscreteRandomizer, choices : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> NoneType Methods inherited from EntityRandomizer: crossover(...) from builtins.PyCapsule crossover(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1 : rosetta.protocols.genetic_algorithm.Entity, entity2 : rosetta.protocols.genetic_algorithm.Entity) -> NoneType entity_length(...) from builtins.PyCapsule entity_length(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> int entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity mutation_rate(...) from builtins.PyCapsule mutation_rate(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> float random_entity(...) from builtins.PyCapsule random_entity(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_mutation_rate(...) from builtins.PyCapsule set_mutation_rate(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, rate : float) -> NoneType   class Entity(builtins.object)     Entity: a vector of EntityElements used to describe the state for a system under optimization.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.genetic_algorithm.Entity, other : rosetta.protocols.genetic_algorithm.Entity) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.genetic_algorithm.Entity) -> NoneType   3. __init__(self : handle, line : str) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.genetic_algorithm.Entity) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.Entity,  : rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity clone(...) from builtins.PyCapsule clone(rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity fitness(...) from builtins.PyCapsule fitness(rosetta.protocols.genetic_algorithm.Entity) -> float fitness_valid(...) from builtins.PyCapsule fitness_valid(rosetta.protocols.genetic_algorithm.Entity) -> bool set_entity_element(...) from builtins.PyCapsule set_entity_element(self : rosetta.protocols.genetic_algorithm.Entity, index : int, element : rosetta.protocols.genetic_algorithm.EntityElement) -> NoneType set_fitness(...) from builtins.PyCapsule set_fitness(self : rosetta.protocols.genetic_algorithm.Entity, val : float) -> NoneType set_traits(...) from builtins.PyCapsule set_traits(self : rosetta.protocols.genetic_algorithm.Entity, traits : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> NoneType set_traits_size(...) from builtins.PyCapsule set_traits_size(self : rosetta.protocols.genetic_algorithm.Entity, size : int) -> NoneType to_string(...) from builtins.PyCapsule to_string(rosetta.protocols.genetic_algorithm.Entity) -> str traits(...) from builtins.PyCapsule traits(rosetta.protocols.genetic_algorithm.Entity) -> rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t traits_string(...) from builtins.PyCapsule traits_string(rosetta.protocols.genetic_algorithm.Entity) -> str   class EntityElement(builtins.object)     Entity element     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.genetic_algorithm.EntityElement, rhs : rosetta.protocols.genetic_algorithm.EntityElement) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.genetic_algorithm.EntityElement) -> NoneType   2. __init__(self : rosetta.protocols.genetic_algorithm.EntityElement, index : int) -> NoneType   3. __init__(self : rosetta.protocols.genetic_algorithm.EntityElement, word : str) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.EntityElement, rhs : rosetta.protocols.genetic_algorithm.EntityElement) -> rosetta.protocols.genetic_algorithm.EntityElement clone(...) from builtins.PyCapsule clone(rosetta.protocols.genetic_algorithm.EntityElement) -> rosetta.protocols.genetic_algorithm.EntityElement fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.genetic_algorithm.EntityElement) -> rosetta.protocols.genetic_algorithm.EntityElement hash(...) from builtins.PyCapsule hash(rosetta.protocols.genetic_algorithm.EntityElement) -> int index(...) from builtins.PyCapsule index(*args, **kwargs) Overloaded function.   1. index(rosetta.protocols.genetic_algorithm.EntityElement) -> int   2. index(self : rosetta.protocols.genetic_algorithm.EntityElement, index : int) -> NoneType name(...) from builtins.PyCapsule name(rosetta.protocols.genetic_algorithm.EntityElement) -> str to_string(...) from builtins.PyCapsule to_string(rosetta.protocols.genetic_algorithm.EntityElement) -> str   class EntityElementCreator(builtins.object)     Entity element creator     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.genetic_algorithm.EntityElementCreator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.EntityElementCreator,  : rosetta.protocols.genetic_algorithm.EntityElementCreator) -> rosetta.protocols.genetic_algorithm.EntityElementCreator new_entity(...) from builtins.PyCapsule new_entity(self : rosetta.protocols.genetic_algorithm.EntityElementCreator, word : str) -> rosetta.protocols.genetic_algorithm.EntityElement widget_name(...) from builtins.PyCapsule widget_name(rosetta.protocols.genetic_algorithm.EntityElementCreator) -> str   class EntityElementFactory(rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t)     The %EntityElementFactory is responsible for instantiating entity elements from strings.     Method resolution order: EntityElementFactory rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. element_from_string(...) from builtins.PyCapsule element_from_string(self : rosetta.protocols.genetic_algorithm.EntityElementFactory,  : str) -> rosetta.protocols.genetic_algorithm.EntityElement factory_name(...) from builtins.PyCapsule factory_name(rosetta.protocols.genetic_algorithm.EntityElementFactory) -> str Methods inherited from rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t: assign(...) from builtins.PyCapsule assign(self : rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t,  : rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t) -> rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t, creator : protocols::genetic_algorithm::EntityElementCreator) -> NoneType   class EntityElementsEqual(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.genetic_algorithm.EntityElementsEqual, elems1 : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t, elems2 : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.genetic_algorithm.EntityElementsEqual) -> NoneType   2. __init__(self : rosetta.protocols.genetic_algorithm.EntityElementsEqual,  : rosetta.protocols.genetic_algorithm.EntityElementsEqual) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.EntityElementsEqual,  : rosetta.protocols.genetic_algorithm.EntityElementsEqual) -> rosetta.protocols.genetic_algorithm.EntityElementsEqual   class EntityRandomizer(builtins.object)     /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.EntityRandomizer,  : rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.EntityRandomizer crossover(...) from builtins.PyCapsule crossover(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1 : rosetta.protocols.genetic_algorithm.Entity, entity2 : rosetta.protocols.genetic_algorithm.Entity) -> NoneType entity_length(...) from builtins.PyCapsule entity_length(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> int entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity library_size(...) from builtins.PyCapsule library_size(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> int mutate(...) from builtins.PyCapsule mutate(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType mutation_rate(...) from builtins.PyCapsule mutation_rate(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> float random_entity(...) from builtins.PyCapsule random_entity(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_mutation_rate(...) from builtins.PyCapsule set_mutation_rate(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, rate : float) -> NoneType   class FitnessFunction(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.genetic_algorithm.FitnessFunction) -> NoneType   2. __init__(rosetta.protocols.genetic_algorithm.FitnessFunction, rosetta.protocols.genetic_algorithm.FitnessFunction) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.FitnessFunction,  : rosetta.protocols.genetic_algorithm.FitnessFunction) -> rosetta.protocols.genetic_algorithm.FitnessFunction evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.genetic_algorithm.FitnessFunction, entity : rosetta.protocols.genetic_algorithm.Entity) -> float   class GeneticAlgorithm(GeneticAlgorithmBase)       Method resolution order: GeneticAlgorithm GeneticAlgorithmBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.genetic_algorithm.GeneticAlgorithm) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithm,  : rosetta.protocols.genetic_algorithm.GeneticAlgorithm) -> rosetta.protocols.genetic_algorithm.GeneticAlgorithm evaluate_fitnesses(...) from builtins.PyCapsule evaluate_fitnesses(rosetta.protocols.genetic_algorithm.GeneticAlgorithm) -> NoneType set_func(...) from builtins.PyCapsule set_func(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithm, f : rosetta.protocols.genetic_algorithm.FitnessFunction) -> NoneType Data descriptors defined here: fitness_function_ Methods inherited from GeneticAlgorithmBase: add_entity(...) from builtins.PyCapsule add_entity(*args, **kwargs) Overloaded function.   1. add_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> rosetta.protocols.genetic_algorithm.Entity   2. add_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity add_parent_entity(...) from builtins.PyCapsule add_parent_entity(*args, **kwargs) Overloaded function.   1. add_parent_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> rosetta.protocols.genetic_algorithm.Entity   2. add_parent_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity add_parents_from_current_generation(...) from builtins.PyCapsule add_parents_from_current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType best_fitness_from_current_generation(...) from builtins.PyCapsule best_fitness_from_current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> float clear_parents(...) from builtins.PyCapsule clear_parents(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType complete(...) from builtins.PyCapsule complete(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool curr_gen_entity(...) from builtins.PyCapsule curr_gen_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, index : int) -> rosetta.protocols.genetic_algorithm.Entity   retreive a particular entity for the current generation current_generation(...) from builtins.PyCapsule current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int current_generation_begin(...) from builtins.PyCapsule current_generation_begin(*args, **kwargs) Overloaded function.   1. current_generation_begin(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> > > >   2. current_generation_begin(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity> const*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > > current_generation_complete(...) from builtins.PyCapsule current_generation_complete(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool current_generation_end(...) from builtins.PyCapsule current_generation_end(*args, **kwargs) Overloaded function.   1. current_generation_end(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> > > >   2. current_generation_end(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity> const*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > > entities_checkpoint_filename(...) from builtins.PyCapsule entities_checkpoint_filename(*args, **kwargs) Overloaded function.   1. entities_checkpoint_filename(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str   2. entities_checkpoint_filename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix : str) -> str entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.protocols.genetic_algorithm.Entity evolve_next_generation(...) from builtins.PyCapsule evolve_next_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType fill_by_crossover(...) from builtins.PyCapsule fill_by_crossover(*args, **kwargs) Overloaded function.   1. fill_by_crossover(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_by_crossover(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_by_mutation(...) from builtins.PyCapsule fill_by_mutation(*args, **kwargs) Overloaded function.   1. fill_by_mutation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_by_mutation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_with_perturbations_of_existing_entities(...) from builtins.PyCapsule fill_with_perturbations_of_existing_entities(*args, **kwargs) Overloaded function.   1. fill_with_perturbations_of_existing_entities(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_with_perturbations_of_existing_entities(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_with_random_entities(...) from builtins.PyCapsule fill_with_random_entities(*args, **kwargs) Overloaded function.   1. fill_with_random_entities(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_with_random_entities(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fraction_by_recombination(...) from builtins.PyCapsule fraction_by_recombination(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> float generations(...) from builtins.PyCapsule generations(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t generations_checkpoint_filename(...) from builtins.PyCapsule generations_checkpoint_filename(*args, **kwargs) Overloaded function.   1. generations_checkpoint_filename(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str   2. generations_checkpoint_filename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix : str) -> str max_generations(...) from builtins.PyCapsule max_generations(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int max_population_size(...) from builtins.PyCapsule max_population_size(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int new_entity(...) from builtins.PyCapsule new_entity(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.protocols.genetic_algorithm.Entity number_to_propagate(...) from builtins.PyCapsule number_to_propagate(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int population(...) from builtins.PyCapsule population(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, gen_num : int) -> 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 propagate_best_from_previous_generation(...) from builtins.PyCapsule propagate_best_from_previous_generation(*args, **kwargs) Overloaded function.   1. propagate_best_from_previous_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. propagate_best_from_previous_generation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType   3. propagate_best_from_previous_generation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int, unique : bool) -> NoneType read_checkpoint(...) from builtins.PyCapsule read_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool read_entities_checkpoint(...) from builtins.PyCapsule read_entities_checkpoint(*args, **kwargs) Overloaded function.   1. read_entities_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   for checkpointing fitness cache   2. read_entities_checkpoint(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, overwrite : bool) -> bool   for checkpointing fitness cache read_generations_checkpoint(...) from builtins.PyCapsule read_generations_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool rename_checkpoint_files(...) from builtins.PyCapsule rename_checkpoint_files(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   allows the prevention of accidental reuse of checkpoint files set_checkpoint_gzip(...) from builtins.PyCapsule set_checkpoint_gzip(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b : bool) -> NoneType set_checkpoint_prefix(...) from builtins.PyCapsule set_checkpoint_prefix(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, p : str) -> NoneType set_checkpoint_rename(...) from builtins.PyCapsule set_checkpoint_rename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b : bool) -> NoneType set_checkpoint_write_interval(...) from builtins.PyCapsule set_checkpoint_write_interval(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, i : int) -> NoneType set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_frac_by_recomb(...) from builtins.PyCapsule set_frac_by_recomb(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, f : float) -> NoneType set_max_generations(...) from builtins.PyCapsule set_max_generations(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_max_pop_size(...) from builtins.PyCapsule set_max_pop_size(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_num_to_propagate(...) from builtins.PyCapsule set_num_to_propagate(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_rand(...) from builtins.PyCapsule set_rand(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, r : rosetta.protocols.genetic_algorithm.EntityRandomizer) -> NoneType tournament_select(...) from builtins.PyCapsule tournament_select(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, pvec : rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t) -> rosetta.protocols.genetic_algorithm.Entity write_entities_checkpoint(...) from builtins.PyCapsule write_entities_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   for checkpointing fitness cache write_generations_checkpoint(...) from builtins.PyCapsule write_generations_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   class GeneticAlgorithmBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_entity(...) from builtins.PyCapsule add_entity(*args, **kwargs) Overloaded function.   1. add_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> rosetta.protocols.genetic_algorithm.Entity   2. add_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity add_parent_entity(...) from builtins.PyCapsule add_parent_entity(*args, **kwargs) Overloaded function.   1. add_parent_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, traits : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> rosetta.protocols.genetic_algorithm.Entity   2. add_parent_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> rosetta.protocols.genetic_algorithm.Entity add_parents_from_current_generation(...) from builtins.PyCapsule add_parents_from_current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase,  : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase best_fitness_from_current_generation(...) from builtins.PyCapsule best_fitness_from_current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> float clear_parents(...) from builtins.PyCapsule clear_parents(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType complete(...) from builtins.PyCapsule complete(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool curr_gen_entity(...) from builtins.PyCapsule curr_gen_entity(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, index : int) -> rosetta.protocols.genetic_algorithm.Entity   retreive a particular entity for the current generation current_generation(...) from builtins.PyCapsule current_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int current_generation_begin(...) from builtins.PyCapsule current_generation_begin(*args, **kwargs) Overloaded function.   1. current_generation_begin(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> > > >   2. current_generation_begin(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity> const*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > > current_generation_complete(...) from builtins.PyCapsule current_generation_complete(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool current_generation_end(...) from builtins.PyCapsule current_generation_end(*args, **kwargs) Overloaded function.   1. current_generation_end(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> > > >   2. current_generation_end(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::genetic_algorithm::Entity> const*, std::vector<std::shared_ptr<protocols::genetic_algorithm::Entity>, std::allocator<std::shared_ptr<protocols::genetic_algorithm::Entity> > > > entities_checkpoint_filename(...) from builtins.PyCapsule entities_checkpoint_filename(*args, **kwargs) Overloaded function.   1. entities_checkpoint_filename(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str   2. entities_checkpoint_filename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix : str) -> str entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.protocols.genetic_algorithm.Entity evolve_next_generation(...) from builtins.PyCapsule evolve_next_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType fill_by_crossover(...) from builtins.PyCapsule fill_by_crossover(*args, **kwargs) Overloaded function.   1. fill_by_crossover(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_by_crossover(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_by_mutation(...) from builtins.PyCapsule fill_by_mutation(*args, **kwargs) Overloaded function.   1. fill_by_mutation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_by_mutation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_with_perturbations_of_existing_entities(...) from builtins.PyCapsule fill_with_perturbations_of_existing_entities(*args, **kwargs) Overloaded function.   1. fill_with_perturbations_of_existing_entities(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_with_perturbations_of_existing_entities(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fill_with_random_entities(...) from builtins.PyCapsule fill_with_random_entities(*args, **kwargs) Overloaded function.   1. fill_with_random_entities(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. fill_with_random_entities(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType fraction_by_recombination(...) from builtins.PyCapsule fraction_by_recombination(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> float generations(...) from builtins.PyCapsule generations(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t generations_checkpoint_filename(...) from builtins.PyCapsule generations_checkpoint_filename(*args, **kwargs) Overloaded function.   1. generations_checkpoint_filename(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> str   2. generations_checkpoint_filename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, suffix : str) -> str max_generations(...) from builtins.PyCapsule max_generations(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int max_population_size(...) from builtins.PyCapsule max_population_size(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int new_entity(...) from builtins.PyCapsule new_entity(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> rosetta.protocols.genetic_algorithm.Entity number_to_propagate(...) from builtins.PyCapsule number_to_propagate(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> int population(...) from builtins.PyCapsule population(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, gen_num : int) -> 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 propagate_best_from_previous_generation(...) from builtins.PyCapsule propagate_best_from_previous_generation(*args, **kwargs) Overloaded function.   1. propagate_best_from_previous_generation(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   2. propagate_best_from_previous_generation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int) -> NoneType   3. propagate_best_from_previous_generation(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, size : int, unique : bool) -> NoneType read_checkpoint(...) from builtins.PyCapsule read_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool read_entities_checkpoint(...) from builtins.PyCapsule read_entities_checkpoint(*args, **kwargs) Overloaded function.   1. read_entities_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   for checkpointing fitness cache   2. read_entities_checkpoint(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, overwrite : bool) -> bool   for checkpointing fitness cache read_generations_checkpoint(...) from builtins.PyCapsule read_generations_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool rename_checkpoint_files(...) from builtins.PyCapsule rename_checkpoint_files(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> NoneType   allows the prevention of accidental reuse of checkpoint files set_checkpoint_gzip(...) from builtins.PyCapsule set_checkpoint_gzip(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b : bool) -> NoneType set_checkpoint_prefix(...) from builtins.PyCapsule set_checkpoint_prefix(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, p : str) -> NoneType set_checkpoint_rename(...) from builtins.PyCapsule set_checkpoint_rename(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, b : bool) -> NoneType set_checkpoint_write_interval(...) from builtins.PyCapsule set_checkpoint_write_interval(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, i : int) -> NoneType set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_frac_by_recomb(...) from builtins.PyCapsule set_frac_by_recomb(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, f : float) -> NoneType set_max_generations(...) from builtins.PyCapsule set_max_generations(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_max_pop_size(...) from builtins.PyCapsule set_max_pop_size(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_num_to_propagate(...) from builtins.PyCapsule set_num_to_propagate(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, s : int) -> NoneType set_rand(...) from builtins.PyCapsule set_rand(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, r : rosetta.protocols.genetic_algorithm.EntityRandomizer) -> NoneType tournament_select(...) from builtins.PyCapsule tournament_select(self : rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase, pvec : rosetta.utility.vector1_std_shared_ptr_const_protocols_genetic_algorithm_Entity_t) -> rosetta.protocols.genetic_algorithm.Entity write_entities_checkpoint(...) from builtins.PyCapsule write_entities_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   for checkpointing fitness cache write_generations_checkpoint(...) from builtins.PyCapsule write_generations_checkpoint(rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase) -> bool   class Mutate1Randomizer(PositionSpecificRandomizer)       Method resolution order: Mutate1Randomizer PositionSpecificRandomizer EntityRandomizer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.Mutate1Randomizer,  : rosetta.protocols.genetic_algorithm.Mutate1Randomizer) -> rosetta.protocols.genetic_algorithm.Mutate1Randomizer mutate(...) from builtins.PyCapsule mutate(self : rosetta.protocols.genetic_algorithm.Mutate1Randomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType Methods inherited from PositionSpecificRandomizer: append_choices(...) from builtins.PyCapsule append_choices(self : rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, choices : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> NoneType choices(...) from builtins.PyCapsule choices(rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) -> rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t library_size(...) from builtins.PyCapsule library_size(rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) -> int Methods inherited from EntityRandomizer: crossover(...) from builtins.PyCapsule crossover(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1 : rosetta.protocols.genetic_algorithm.Entity, entity2 : rosetta.protocols.genetic_algorithm.Entity) -> NoneType entity_length(...) from builtins.PyCapsule entity_length(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> int entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity mutation_rate(...) from builtins.PyCapsule mutation_rate(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> float random_entity(...) from builtins.PyCapsule random_entity(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_mutation_rate(...) from builtins.PyCapsule set_mutation_rate(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, rate : float) -> NoneType   class PositionSpecificRandomizer(EntityRandomizer)     /////////////////////////////////////////////////////////////////////////////////////////////////     different set of choices at each position in Entity's traits     Method resolution order: PositionSpecificRandomizer EntityRandomizer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. append_choices(...) from builtins.PyCapsule append_choices(self : rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, choices : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer,  : rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) -> rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer choices(...) from builtins.PyCapsule choices(rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) -> rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t library_size(...) from builtins.PyCapsule library_size(rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer) -> int mutate(...) from builtins.PyCapsule mutate(self : rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType Methods inherited from EntityRandomizer: crossover(...) from builtins.PyCapsule crossover(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity1 : rosetta.protocols.genetic_algorithm.Entity, entity2 : rosetta.protocols.genetic_algorithm.Entity) -> NoneType entity_length(...) from builtins.PyCapsule entity_length(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> int entity_template(...) from builtins.PyCapsule entity_template(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity mutation_rate(...) from builtins.PyCapsule mutation_rate(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> float random_entity(...) from builtins.PyCapsule random_entity(rosetta.protocols.genetic_algorithm.EntityRandomizer) -> rosetta.protocols.genetic_algorithm.Entity set_entity_template(...) from builtins.PyCapsule set_entity_template(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, entity : rosetta.protocols.genetic_algorithm.Entity) -> NoneType set_mutation_rate(...) from builtins.PyCapsule set_mutation_rate(self : rosetta.protocols.genetic_algorithm.EntityRandomizer, rate : float) -> NoneType   class Vec1Hash(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.genetic_algorithm.Vec1Hash, vec1 : rosetta.utility.vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.genetic_algorithm.Vec1Hash) -> NoneType   2. __init__(self : rosetta.protocols.genetic_algorithm.Vec1Hash,  : rosetta.protocols.genetic_algorithm.Vec1Hash) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.genetic_algorithm.Vec1Hash,  : rosetta.protocols.genetic_algorithm.Vec1Hash) -> rosetta.protocols.genetic_algorithm.Vec1Hash