Index

_

__copy__() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) __format__() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) __molecules (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem attribute) __repr__() (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) (uo.algorithm.algorithm.Algorithm method) (uo.problem.problem.Problem method), [1]

__str__() (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) (uo.algorithm.algorithm.Algorithm method) (uo.problem.problem.Problem method), [1]

A

add_to_catalogue() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) additional_statistics_control (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic property) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) Algorithm (class in uo.algorithm.algorithm)

argument() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] atom_switch_mutation() (in module opt.single_objective.comb.drug_discovery_problem.solver)

B

best_solution (uo.algorithm.algorithm.Algorithm property)

C

cache (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics property) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics property), [1] cache_hit_count (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics property) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics property), [1] cache_request_count (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics property) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics property), [1] calc_fitness() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) calculate_average_qed() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) calculate_quality() (uo.solution.solution.Solution method), [1] calculate_quality_directly() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] ClickableGroupBox (class in opt.single_objective.comb.drug_discovery_problem.molecule_boxes) copy() (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem method), [1] (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem method), [1] (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method), [1] (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem method) (uo.algorithm.algorithm.Algorithm method), [1] (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer method) (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) (uo.algorithm.metaheuristic.metaheuristic_void.MetaheuristicVoid method) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizer method) (uo.algorithm.metaheuristic.population_based_metaheuristic.PopulationBasedMetaheuristic method) (uo.algorithm.metaheuristic.single_solution_metaheuristic.SingleSolutionMetaheuristic method) (uo.algorithm.metaheuristic.single_solution_metaheuristic_void.SingleSolutionMetaheuristicVoid method) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer method) (uo.algorithm.output_control.OutputControl method) (uo.problem.problem.Problem method), [1], [2], [3] (uo.solution.solution.Solution method), [1]

copy_from() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] create_molecule_box() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) crossover() (in module opt.single_objective.comb.drug_discovery_problem.solver) current_population (uo.algorithm.metaheuristic.population_based_metaheuristic.PopulationBasedMetaheuristic property) current_solution (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer property) (uo.algorithm.metaheuristic.single_solution_metaheuristic.SingleSolutionMetaheuristic property)

D

deletion_mutation() (in module opt.single_objective.comb.drug_discovery_problem.solver) determine_fields_val() (uo.algorithm.algorithm.Algorithm method) (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) dimension (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem attribute) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem property) (opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem.MinOnesCountProblem property) dimension() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem method) DistanceCalculationCacheControlStatistics (class in uo.solution.distance_calculation_cache_control_statistics) domain_from (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution property)

domain_high (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblemElements attribute) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem property) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblemElements attribute) domain_low (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblemElements attribute) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem property) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblemElements attribute) domain_to (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution property) DrugDiscoveryProblem (class in opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem)

E

elapsed_seconds() (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) ensure_dir() (in module uo.utils.files) enterEvent() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.ClickableGroupBox method) evaluate() (uo.solution.solution.Solution method), [1] evaluation (uo.algorithm.algorithm.Algorithm property) evaluation_best_found (uo.algorithm.algorithm.Algorithm property)

evaluation_cache_cs (uo.solution.solution.Solution property), [1] EvaluationCacheControlStatistics (class in uo.solution.evaluation_cache_control_statistics), [1] expression (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblemElements attribute) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem property) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblemElements attribute)

F

fields (uo.algorithm.output_control.OutputControl property) fields_definitions (uo.algorithm.output_control.OutputControl property) fields_headings (uo.algorithm.output_control.OutputControl property) finish_control (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic property) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) Fitness (class in opt.single_objective.comb.drug_discovery_problem.fitness) fitness_value (uo.solution.quality_of_solution.QualityOfSolution property) (uo.solution.solution.Solution property), [1] fitness_values (uo.solution.quality_of_solution.QualityOfSolution property) (uo.solution.solution.Solution property), [1] from_construction_tuple() (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer class method) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizer class method) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizer class method) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer class method)

from_dimension() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem class method) (opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem.MinOnesCountProblem class method) from_graph_and_source_terminal_pairs() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem class method) from_input_file() (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem class method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem class method) (opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem.MinOnesCountProblem class method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem class method) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem class method) from_input_files() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem class method) FunctionOneVariableMaxProblemBitArraySolution (class in opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution) FunctionOneVariableMaxProblemIntSolution (class in opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution)

G

GAParameters (class in opt.single_objective.comb.drug_discovery_problem.ga_parameters) genetic_algorithm() (in module opt.single_objective.comb.drug_discovery_problem.solver) get_best() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) get_description() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) get_form() (opt.single_objective.comb.drug_discovery_problem.insert_molecule.NewMoleculeForm method) get_GA_parameters_widget() (opt.single_objective.comb.drug_discovery_problem.ga_parameters.GAParameters method) get_input_description_text() (opt.single_objective.comb.drug_discovery_problem.insert_molecule.NewMoleculeForm method) get_input_smiles_text() (opt.single_objective.comb.drug_discovery_problem.insert_molecule.NewMoleculeForm method) get_precedent_scroll_area() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) get_qed() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method)

get_random_individual() (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem method), [1] get_second_scroll_area() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) get_selection_widget() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) get_sliders_widget() (opt.single_objective.comb.drug_discovery_problem.hyper_parameters.HyperParameters method) get_smiles() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) get_weights() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) graph (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem attribute) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem property) graph() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) group_switch_mutation() (in module opt.single_objective.comb.drug_discovery_problem.solver)

H

HyperParameters (class in opt.single_objective.comb.drug_discovery_problem.hyper_parameters)

I

increment_cache_hit_count() (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics method) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics method), [1] increment_cache_request_count() (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics method) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics method), [1] Individual (class in opt.single_objective.comb.drug_discovery_problem.individual) init() (uo.algorithm.algorithm.Algorithm method) (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer method) (uo.algorithm.metaheuristic.metaheuristic_void.MetaheuristicVoid method) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizer method) (uo.algorithm.metaheuristic.population_based_metaheuristic_void.PopulationBasedMetaheuristicVoid method) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizer method) (uo.algorithm.metaheuristic.single_solution_metaheuristic_void.SingleSolutionMetaheuristicVoid method) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer method) init_from() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] init_random() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1]

insertion_mutation() (in module opt.single_objective.comb.drug_discovery_problem.solver) is_better() (uo.solution.solution.Solution method), [1] is_feasible (uo.solution.quality_of_solution.QualityOfSolution property) (uo.solution.solution.Solution property), [1] is_feasible_sol() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) is_minimization (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem attribute) (uo.problem.problem.Problem attribute), [1] (uo.problem.problem.Problem property), [1] is_minimization() (uo.problem.problem.Problem method), [1] is_multi_objective (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem attribute) (uo.problem.problem.Problem attribute), [1] (uo.problem.problem.Problem property), [1] is_multi_objective() (uo.problem.problem.Problem method), [1] is_valid_smiles() (in module opt.single_objective.comb.drug_discovery_problem.solver) (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) iteration (uo.algorithm.algorithm.Algorithm property) iteration_best_found (uo.algorithm.algorithm.Algorithm property)

K

k_max (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer property) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute)

k_min (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer property) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute)

L

leaveEvent() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.ClickableGroupBox method) load_boxes() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method)

load_new_generation() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) load_selected_boxes() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method)

M

main() (in module opt.single_objective.glob.max_function_one_variable_problem.solver) main_loop() (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) main_loop_iteration() (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) (uo.algorithm.metaheuristic.metaheuristic_void.MetaheuristicVoid method) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizer method) (uo.algorithm.metaheuristic.population_based_metaheuristic_void.PopulationBasedMetaheuristicVoid method) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizer method) (uo.algorithm.metaheuristic.single_solution_metaheuristic_void.SingleSolutionMetaheuristicVoid method) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer method) max_cache_size (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics property) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics property), [1] MaxFunctionOneVariableMaxProblem (class in opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem) MaxFunctionOneVariableMaxProblemElements (class in opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem) MaxOnesCountProblem (class in opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem) MaxOnesCountProblemBitArraySolution (class in opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution) MaxOnesCountProblemIntSolution (class in opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution) Metaheuristic (class in uo.algorithm.metaheuristic.metaheuristic) MetaheuristicVoid (class in uo.algorithm.metaheuristic.metaheuristic_void) MinFunctionOneVariableProblem (class in opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem) MinFunctionOneVariableProblemElements (class in opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem) MinMultiCutProblem (class in opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem) MinMultiCutProblemBitArraySolution (class in opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution) MinOnesCountProblem (class in opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem) module opt opt.multi_objective opt.single_objective opt.single_objective.comb opt.single_objective.comb.drug_discovery_problem opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem opt.single_objective.comb.drug_discovery_problem.fitness opt.single_objective.comb.drug_discovery_problem.ga_parameters opt.single_objective.comb.drug_discovery_problem.hyper_parameters opt.single_objective.comb.drug_discovery_problem.individual opt.single_objective.comb.drug_discovery_problem.insert_molecule opt.single_objective.comb.drug_discovery_problem.molecule_boxes opt.single_objective.comb.drug_discovery_problem.mutation_info opt.single_objective.comb.drug_discovery_problem.solver opt.single_objective.comb.max_ones_count_problem opt.single_objective.comb.max_ones_count_problem.command_line opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution opt.single_objective.comb.min_multi_cut_problem opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution opt.single_objective.comb.min_ones_count_problem opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem opt.single_objective.comb.min_set_cover_problem opt.single_objective.comb.traveling_salesperson_problem opt.single_objective.constraint opt.single_objective.glob opt.single_objective.glob.max_function_one_variable_problem opt.single_objective.glob.max_function_one_variable_problem.command_line opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution opt.single_objective.glob.max_function_one_variable_problem.solver opt.single_objective.glob.min_function_one_variable_problem opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem opt.tests opt.tests.single_objective opt.tests.single_objective.comb opt.tests.single_objective.comb.drug_discovery_problem opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem opt.tests.single_objective.comb.drug_discovery_problem.test_fitness opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters opt.tests.single_objective.comb.drug_discovery_problem.test_main opt.tests.single_objective.comb.drug_discovery_problem.test_solver uo uo.algorithm uo.algorithm.algorithm uo.algorithm.exact uo.algorithm.exact.total_enumeration uo.algorithm.exact.total_enumeration.te_optimizer uo.algorithm.metaheuristic uo.algorithm.metaheuristic.electro_magnetism_like_metaheuristic uo.algorithm.metaheuristic.genetic_algorithm uo.algorithm.metaheuristic.metaheuristic uo.algorithm.metaheuristic.metaheuristic_void uo.algorithm.metaheuristic.monte_carlo uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer uo.algorithm.metaheuristic.population_based_metaheuristic uo.algorithm.metaheuristic.population_based_metaheuristic_void uo.algorithm.metaheuristic.simulated_annealing, [1] uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer uo.algorithm.metaheuristic.single_solution_metaheuristic uo.algorithm.metaheuristic.single_solution_metaheuristic_void uo.algorithm.metaheuristic.variable_neighborhood_search uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer uo.algorithm.output_control uo.problem, [1] uo.problem.problem, [1] uo.solution, [1] uo.solution.distance_calculation_cache_control_statistics uo.solution.evaluation_cache_control_statistics, [1] uo.solution.quality_of_solution uo.solution.solution, [1] uo.tests uo.utils uo.utils.files uo.utils.logger

molecule (opt.single_objective.comb.drug_discovery_problem.fitness.Fitness attribute) MoleculeBoxes (class in opt.single_objective.comb.drug_discovery_problem.molecule_boxes) molecules (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem property) moments (uo.algorithm.output_control.OutputControl property) MonteCarloOptimizer (class in uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer) MonteCarloOptimizerConstructionParameters (class in uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer) mousePressEvent() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.ClickableGroupBox method) mutation() (in module opt.single_objective.comb.drug_discovery_problem.solver) MutationInfo (class in opt.single_objective.comb.drug_discovery_problem.mutation_info)

N

name (opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem.DrugDiscoveryProblem attribute) (uo.algorithm.algorithm.Algorithm attribute) (uo.problem.problem.Problem attribute), [1] (uo.problem.problem.Problem property), [1] name() (uo.problem.problem.Problem method), [1] native_representation() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1]

NewMoleculeForm (class in opt.single_objective.comb.drug_discovery_problem.insert_molecule) number_of_intervals (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution property) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution property) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem property)

O

objective_value (uo.solution.quality_of_solution.QualityOfSolution property) (uo.solution.solution.Solution property), [1] objective_values (uo.solution.quality_of_solution.QualityOfSolution property) (uo.solution.solution.Solution property), [1] obtain_feasible_representation() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] on_final_button_clicked() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) on_generate_button_clicked() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) on_launch_button_clicked() (opt.single_objective.comb.drug_discovery_problem.ga_parameters.GAParameters method) on_reset_button_clicked() (opt.single_objective.comb.drug_discovery_problem.hyper_parameters.HyperParameters method) on_restart_button_clicked() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) on_roulette_changed() (opt.single_objective.comb.drug_discovery_problem.ga_parameters.GAParameters method) on_save_button_clicked() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) on_select_all_button_clicked() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) opt module opt.multi_objective module opt.single_objective module opt.single_objective.comb module opt.single_objective.comb.drug_discovery_problem module opt.single_objective.comb.drug_discovery_problem.drug_discovery_problem module opt.single_objective.comb.drug_discovery_problem.fitness module opt.single_objective.comb.drug_discovery_problem.ga_parameters module opt.single_objective.comb.drug_discovery_problem.hyper_parameters module opt.single_objective.comb.drug_discovery_problem.individual module opt.single_objective.comb.drug_discovery_problem.insert_molecule module opt.single_objective.comb.drug_discovery_problem.molecule_boxes module opt.single_objective.comb.drug_discovery_problem.mutation_info module opt.single_objective.comb.drug_discovery_problem.solver module opt.single_objective.comb.max_ones_count_problem module opt.single_objective.comb.max_ones_count_problem.command_line module opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem module opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution module opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution module opt.single_objective.comb.min_multi_cut_problem module opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem module

opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution module opt.single_objective.comb.min_ones_count_problem module opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem module opt.single_objective.comb.min_set_cover_problem module opt.single_objective.comb.traveling_salesperson_problem module opt.single_objective.constraint module opt.single_objective.glob module opt.single_objective.glob.max_function_one_variable_problem module opt.single_objective.glob.max_function_one_variable_problem.command_line module opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem module opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution module opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution module opt.single_objective.glob.max_function_one_variable_problem.solver module opt.single_objective.glob.min_function_one_variable_problem module opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem module opt.tests module opt.tests.single_objective module opt.tests.single_objective.comb module opt.tests.single_objective.comb.drug_discovery_problem module opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem module opt.tests.single_objective.comb.drug_discovery_problem.test_fitness module opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters module opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters module opt.tests.single_objective.comb.drug_discovery_problem.test_main module opt.tests.single_objective.comb.drug_discovery_problem.test_solver module optimize() (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer method) (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) output_control (uo.algorithm.algorithm.Algorithm attribute) (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) output_file (uo.algorithm.output_control.OutputControl property) OutputControl (class in uo.algorithm.output_control)

P

parse_arguments() (in module opt.single_objective.comb.max_ones_count_problem.command_line) (in module opt.single_objective.glob.max_function_one_variable_problem.command_line) PopulationBasedMetaheuristic (class in uo.algorithm.metaheuristic.population_based_metaheuristic) PopulationBasedMetaheuristicVoid (class in uo.algorithm.metaheuristic.population_based_metaheuristic_void) Problem (class in uo.problem.problem), [1]

problem (uo.algorithm.algorithm.Algorithm attribute) (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute)

Q

qed() (opt.single_objective.comb.drug_discovery_problem.fitness.Fitness method)

quality (uo.solution.solution.Solution property), [1] QualityOfSolution (class in uo.solution.quality_of_solution)

R

random() (in module opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution) (in module opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution) (in module opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution) (in module opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution) (in module opt.single_objective.glob.max_function_one_variable_problem.solver) (in module uo.algorithm.exact.total_enumeration.te_optimizer) (in module uo.algorithm.metaheuristic.metaheuristic) (in module uo.algorithm.metaheuristic.metaheuristic_void) (in module uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer) (in module uo.algorithm.metaheuristic.population_based_metaheuristic) (in module uo.algorithm.metaheuristic.population_based_metaheuristic_void) (in module uo.algorithm.metaheuristic.single_solution_metaheuristic) (in module uo.algorithm.metaheuristic.single_solution_metaheuristic_void) (in module uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer) (in module uo.solution.solution), [1] random_seed (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic property) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) (uo.solution.solution.Solution property), [1]

remove_boxes() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) remove_new_generation_boxes() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) remove_selected_boxes() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) representation (uo.solution.solution.Solution property), [1] representation_distance() (uo.solution.solution.Solution method), [1] representation_distance_cache_cs (uo.solution.solution.Solution property), [1] representation_distance_directly() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (uo.solution.solution.Solution method), [1] roulette_wheel_selection() (in module opt.single_objective.comb.drug_discovery_problem.solver)

S

sa_neighborhood (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) sa_temperature (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) SaOptimizer (class in uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer) SaOptimizerConstructionParameters (class in uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer) selection() (in module opt.single_objective.comb.drug_discovery_problem.solver) set_description() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) set_smiles() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) set_weights() (opt.single_objective.comb.drug_discovery_problem.individual.Individual method) setUp() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) (opt.tests.single_objective.comb.drug_discovery_problem.test_fitness.TestFitness method) (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters method) (opt.tests.single_objective.comb.drug_discovery_problem.test_main.TestApplicationInitialization method) (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) setUpClass() (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters class method) (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters class method) should_finish() (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) SingleSolutionMetaheuristic (class in uo.algorithm.metaheuristic.single_solution_metaheuristic) SingleSolutionMetaheuristicVoid (class in uo.algorithm.metaheuristic.single_solution_metaheuristic_void) Solution (class in uo.solution.solution), [1] solution_template (uo.algorithm.algorithm.Algorithm attribute) (uo.algorithm.algorithm.Algorithm property) (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizerConstructionParameters attribute) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) source_terminal_pairs (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem attribute) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem property)

source_terminal_pairs() (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) string_rep() (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem.MaxOnesCountProblem method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_bit_array_solution.MaxOnesCountProblemBitArraySolution method) (opt.single_objective.comb.max_ones_count_problem.max_ones_count_problem_int_solution.MaxOnesCountProblemIntSolution method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem.MinMultiCutProblem method) (opt.single_objective.comb.min_multi_cut_problem.min_multi_cut_problem_bit_array_solution.MinMultiCutProblemBitArraySolution method) (opt.single_objective.comb.min_ones_count_problem.min_ones_count_problem.MinOnesCountProblem method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem.MaxFunctionOneVariableMaxProblem method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_bit_array_solution.FunctionOneVariableMaxProblemBitArraySolution method) (opt.single_objective.glob.max_function_one_variable_problem.max_function_one_variable_problem_int_solution.FunctionOneVariableMaxProblemIntSolution method) (opt.single_objective.glob.min_function_one_variable_problem.min_function_one_variable_problem.MinFunctionOneVariableProblem method) (uo.algorithm.algorithm.Algorithm method) (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizer method) (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) (uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer.MonteCarloOptimizer method) (uo.algorithm.metaheuristic.population_based_metaheuristic.PopulationBasedMetaheuristic method) (uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer.SaOptimizer method) (uo.algorithm.metaheuristic.single_solution_metaheuristic.SingleSolutionMetaheuristic method) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer method) (uo.algorithm.output_control.OutputControl method) (uo.problem.problem.Problem method), [1] (uo.solution.distance_calculation_cache_control_statistics.DistanceCalculationCacheControlStatistics method) (uo.solution.evaluation_cache_control_statistics.EvaluationCacheControlStatistics method), [1] (uo.solution.solution.Solution method), [1] string_representation() (uo.solution.solution.Solution method), [1] suppress_rdkit_warnings() (in module opt.single_objective.comb.drug_discovery_problem.solver)

T

tanimoto() (opt.single_objective.comb.drug_discovery_problem.molecule_boxes.MoleculeBoxes method) te_operations_support (uo.algorithm.exact.total_enumeration.te_optimizer.TeOptimizerConstructionParameters attribute) tearDown() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) (opt.tests.single_objective.comb.drug_discovery_problem.test_main.TestApplicationInitialization method) tearDownClass() (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters class method) (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters class method) TeOptimizer (class in uo.algorithm.exact.total_enumeration.te_optimizer) TeOptimizerConstructionParameters (class in uo.algorithm.exact.total_enumeration.te_optimizer) test_atom_switch_mutation() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_components_initialized() (opt.tests.single_objective.comb.drug_discovery_problem.test_main.TestApplicationInitialization method) test_copy_method() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_crossover_fail_reuse_parents() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_crossover_success() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_custom_weights() (opt.tests.single_objective.comb.drug_discovery_problem.test_fitness.TestFitness method) test_deletion_mutation_fail() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_deletion_mutation_success() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_from_construction_tuple() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_from_input_file_empty() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_from_input_file_success() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_genetic_algorithm_runs() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_get_random_individual() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_get_random_individual_empty() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_get_sliders_widget_returns_qwidget() (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters method) test_group_switch_mutation() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_init_default() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_init_method_initializes_solutions() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_initial_slider_values() (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters method) test_initial_values() (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters method) test_initialization_with_valid_parameters() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_insertion_mutation_fallback_to_deletion() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_insertion_mutation_success() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method)

test_invalid_molecule_raises() (opt.tests.single_objective.comb.drug_discovery_problem.test_fitness.TestFitness method) test_invalid_parameter_types_in_constructor() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_is_valid_smiles_invalid() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_is_valid_smiles_valid() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_launch_button_click_updates_ui_state() (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters method) test_layout_structure() (opt.tests.single_objective.comb.drug_discovery_problem.test_main.TestApplicationInitialization method) test_load_from_file() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_main_loop_iteration_no_improvement() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_molecules_setter_and_getter_valid() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_molecules_setter_invalid_element() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_molecules_setter_invalid_type() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_mutation_no_effect_when_probability_zero() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_problem_not_properly_defined() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_qed_returns_float() (opt.tests.single_objective.comb.drug_discovery_problem.test_fitness.TestFitness method) test_qed_value_in_range() (opt.tests.single_objective.comb.drug_discovery_problem.test_fitness.TestFitness method) test_random_seed_affects_randomness() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_reset_button_resets_all_sliders() (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters method) test_selection_roulette() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_selection_tournament() (opt.tests.single_objective.comb.drug_discovery_problem.test_solver.TestGeneticAlgorithm method) test_set_parameters() (opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters.TestGAParameters method) test_str_repr_format() (opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem.TestDrugDiscoveryProblem method) test_string_representation() (uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer.TestMonteCarloOptimizer method) test_submit_button_behavior() (opt.tests.single_objective.comb.drug_discovery_problem.test_main.TestApplicationInitialization method) test_update_param_label_changes_label_and_triggers_updates() (opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters.TestHyperParameters method) TestApplicationInitialization (class in opt.tests.single_objective.comb.drug_discovery_problem.test_main) TestDrugDiscoveryProblem (class in opt.tests.single_objective.comb.drug_discovery_problem.test_drug_discovery_problem) TestFitness (class in opt.tests.single_objective.comb.drug_discovery_problem.test_fitness) TestGAParameters (class in opt.tests.single_objective.comb.drug_discovery_problem.test_ga_parameters) TestGeneticAlgorithm (class in opt.tests.single_objective.comb.drug_discovery_problem.test_solver) TestHyperParameters (class in opt.tests.single_objective.comb.drug_discovery_problem.test_hyper_parameters) TestMonteCarloOptimizer (class in uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer) tournament_selection() (in module opt.single_objective.comb.drug_discovery_problem.solver)

U

uo module uo.algorithm module uo.algorithm.algorithm module uo.algorithm.exact module uo.algorithm.exact.total_enumeration module uo.algorithm.exact.total_enumeration.te_optimizer module uo.algorithm.metaheuristic module uo.algorithm.metaheuristic.electro_magnetism_like_metaheuristic module uo.algorithm.metaheuristic.genetic_algorithm module uo.algorithm.metaheuristic.metaheuristic module uo.algorithm.metaheuristic.metaheuristic_void module uo.algorithm.metaheuristic.monte_carlo module uo.algorithm.metaheuristic.monte_carlo.monte_carlo_optimizer module uo.algorithm.metaheuristic.monte_carlo.test_monte_carlo_optimizer module uo.algorithm.metaheuristic.population_based_metaheuristic module uo.algorithm.metaheuristic.population_based_metaheuristic_void module uo.algorithm.metaheuristic.simulated_annealing module, [1] uo.algorithm.metaheuristic.simulated_annealing.sa_optimizer module

uo.algorithm.metaheuristic.single_solution_metaheuristic module uo.algorithm.metaheuristic.single_solution_metaheuristic_void module uo.algorithm.metaheuristic.variable_neighborhood_search module uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer module uo.algorithm.output_control module uo.problem module, [1] uo.problem.problem module, [1] uo.solution module, [1] uo.solution.distance_calculation_cache_control_statistics module uo.solution.evaluation_cache_control_statistics module, [1] uo.solution.quality_of_solution module uo.solution.solution module, [1] uo.tests module uo.utils module uo.utils.files module uo.utils.logger module update_additional_statistics_if_required() (uo.algorithm.metaheuristic.metaheuristic.Metaheuristic method) update_param_label() (opt.single_objective.comb.drug_discovery_problem.hyper_parameters.HyperParameters method)

V

vns_ls_support (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer property) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute) vns_shaking_support (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizer property) (uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer.VnsOptimizerConstructionParameters attribute)

VnsOptimizer (class in uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer) VnsOptimizerConstructionParameters (class in uo.algorithm.metaheuristic.variable_neighborhood_search.vns_optimizer)

W

weights (opt.single_objective.comb.drug_discovery_problem.fitness.Fitness attribute) write_after_algorithm (uo.algorithm.output_control.OutputControl property) write_after_evaluation (uo.algorithm.output_control.OutputControl property) write_after_iteration (uo.algorithm.output_control.OutputControl property)

write_after_step_in_iteration (uo.algorithm.output_control.OutputControl property) write_before_algorithm (uo.algorithm.output_control.OutputControl property) write_before_evaluation (uo.algorithm.output_control.OutputControl property) write_before_iteration (uo.algorithm.output_control.OutputControl property) write_before_step_in_iteration (uo.algorithm.output_control.OutputControl property)