Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | W A add_perturbations() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) all_targets (pydruglogics.InteractionModel property) (pydruglogics.model.InteractionModel.InteractionModel property) attractor_tool (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) attractor_type (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) attractors (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) B best_boolean_models (pydruglogics.Evolution property) (pydruglogics.model.Evolution.Evolution property) binary_boolean_equations (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) bnet_string_to_dict() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) BNetworkUtil (class in pydruglogics.utils.BNetworkUtil) boolean_equations (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) BooleanModel (class in pydruglogics) (class in pydruglogics.model.BooleanModel) BooleanModelOptimizer (class in pydruglogics.model.BooleanModelOptimizer) C calculate_attractors() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) calculate_fitness() (pydruglogics.Evolution method) (pydruglogics.model.Evolution.Evolution method) calculate_global_output() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) clone() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) compare_two_simulations() (in module pydruglogics) (in module pydruglogics.statistics.Statistics) create_equation_from_bnet() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) create_initial_population() (pydruglogics.Evolution method) (pydruglogics.model.Evolution.Evolution method) create_interaction() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) D drug_effects (pydruglogics.input.Perturbations.Perturbation property) (pydruglogics.Perturbation property) drug_names (pydruglogics.input.Perturbations.Perturbation property) (pydruglogics.Perturbation property) drug_targets (pydruglogics.input.Perturbations.Perturbation property) (pydruglogics.Perturbation property) drugs (pydruglogics.input.Perturbations.Perturbation property) (pydruglogics.Perturbation property) E Evolution (class in pydruglogics) (class in pydruglogics.model.Evolution) execute() (in module pydruglogics) (in module pydruglogics.execution.Executor) F from_binary() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) G get_activating_regulators() (pydruglogics.InteractionModel method) (pydruglogics.model.InteractionModel.InteractionModel method) get_file_extension() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) get_inhibitory_regulators() (pydruglogics.InteractionModel method) (pydruglogics.model.InteractionModel.InteractionModel method) get_interaction() (pydruglogics.InteractionModel method) (pydruglogics.model.InteractionModel.InteractionModel method) get_model_output() (pydruglogics.input.ModelOutputs.ModelOutputs method) (pydruglogics.ModelOutputs method) get_prediction_matrix() (pydruglogics.model.ModelPredictions.ModelPredictions method) (pydruglogics.ModelPredictions method) get_stable_states() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) get_target() (pydruglogics.InteractionModel method) (pydruglogics.model.InteractionModel.InteractionModel method) global_output (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) H has_attractors() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) has_global_output() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) has_stable_states() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) I InteractionModel (class in pydruglogics) (class in pydruglogics.model.InteractionModel) interactions (pydruglogics.InteractionModel property) (pydruglogics.model.InteractionModel.InteractionModel property) is_numeric_string() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) L Logger (class in pydruglogics) (class in pydruglogics.utils.Logger) M max_output (pydruglogics.input.ModelOutputs.ModelOutputs property) (pydruglogics.ModelOutputs property) min_output (pydruglogics.input.ModelOutputs.ModelOutputs property) (pydruglogics.ModelOutputs property) model_name (pydruglogics.BooleanModel property) (pydruglogics.InteractionModel property) (pydruglogics.model.BooleanModel.BooleanModel property) (pydruglogics.model.InteractionModel.InteractionModel property) model_outputs (pydruglogics.input.ModelOutputs.ModelOutputs property) (pydruglogics.ModelOutputs property) ModelOutputs (class in pydruglogics) (class in pydruglogics.input.ModelOutputs) ModelPredictions (class in pydruglogics) (class in pydruglogics.model.ModelPredictions) module pydruglogics pydruglogics.execution pydruglogics.execution.Executor pydruglogics.input pydruglogics.input.ModelOutputs pydruglogics.input.Perturbations pydruglogics.input.TrainingData pydruglogics.model pydruglogics.model.BooleanModel pydruglogics.model.BooleanModelOptimizer pydruglogics.model.Evolution pydruglogics.model.InteractionModel pydruglogics.model.ModelPredictions pydruglogics.statistics.Statistics pydruglogics.utils pydruglogics.utils.BNetworkUtil pydruglogics.utils.Logger pydruglogics.utils.PlotUtil mutation_type (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel property) N node_names (pydruglogics.input.ModelOutputs.ModelOutputs property) (pydruglogics.ModelOutputs property) O observations (pydruglogics.input.TrainingData.TrainingData property) (pydruglogics.TrainingData property) P parse_interaction() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) Perturbation (class in pydruglogics) (class in pydruglogics.input.Perturbations) perturbations (pydruglogics.input.Perturbations.Perturbation property) (pydruglogics.Perturbation property) plot_pr_curve_with_ci() (pydruglogics.PlotUtil static method) (pydruglogics.utils.PlotUtil.PlotUtil static method) plot_roc_and_pr_curve() (pydruglogics.PlotUtil static method) (pydruglogics.utils.PlotUtil.PlotUtil static method) PlotUtil (class in pydruglogics) (class in pydruglogics.utils.PlotUtil) predict() (in module pydruglogics.execution.Executor) predicted_synergy_scores (pydruglogics.model.ModelPredictions.ModelPredictions property) (pydruglogics.ModelPredictions property) print() (pydruglogics.BooleanModel method) (pydruglogics.input.ModelOutputs.ModelOutputs method) (pydruglogics.input.Perturbations.Perturbation method) (pydruglogics.input.TrainingData.TrainingData method) (pydruglogics.InteractionModel method) (pydruglogics.model.BooleanModel.BooleanModel method) (pydruglogics.model.InteractionModel.InteractionModel method) (pydruglogics.ModelOutputs method) (pydruglogics.Perturbation method) (pydruglogics.TrainingData method) pydruglogics module pydruglogics.execution module pydruglogics.execution.Executor module pydruglogics.input module pydruglogics.input.ModelOutputs module pydruglogics.input.Perturbations module pydruglogics.input.TrainingData module pydruglogics.model module pydruglogics.model.BooleanModel module pydruglogics.model.BooleanModelOptimizer module pydruglogics.model.Evolution module pydruglogics.model.InteractionModel module pydruglogics.model.ModelPredictions module pydruglogics.statistics.Statistics module pydruglogics.utils module pydruglogics.utils.BNetworkUtil module pydruglogics.utils.Logger module pydruglogics.utils.PlotUtil module R read_lines_from_file() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) remove_extension() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) reset_attractors() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) response (pydruglogics.input.TrainingData.TrainingData property) (pydruglogics.TrainingData property) responses (pydruglogics.input.TrainingData.TrainingData property) (pydruglogics.TrainingData property) run() (pydruglogics.Evolution method) (pydruglogics.model.BooleanModelOptimizer.BooleanModelOptimizer method) (pydruglogics.model.Evolution.Evolution method) run_simulations() (pydruglogics.model.ModelPredictions.ModelPredictions method) (pydruglogics.ModelPredictions method) S sampling_with_ci() (in module pydruglogics) (in module pydruglogics.statistics.Statistics) save_to_file_models() (pydruglogics.Evolution method) (pydruglogics.model.BooleanModelOptimizer.BooleanModelOptimizer method) (pydruglogics.model.Evolution.Evolution method) save_to_file_predictions() (pydruglogics.model.ModelPredictions.ModelPredictions method) (pydruglogics.ModelPredictions method) set_logger() (pydruglogics.Logger class method) (pydruglogics.utils.Logger.Logger class method) size() (pydruglogics.input.ModelOutputs.ModelOutputs method) (pydruglogics.input.TrainingData.TrainingData method) (pydruglogics.InteractionModel method) (pydruglogics.model.InteractionModel.InteractionModel method) (pydruglogics.ModelOutputs method) (pydruglogics.TrainingData method) T timed_execution() (in module pydruglogics.execution.Executor) to_binary() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) to_bnet_format() (pydruglogics.utils.BNetworkUtil.BNetworkUtil static method) train() (in module pydruglogics) (in module pydruglogics.execution.Executor) TrainingData (class in pydruglogics) (class in pydruglogics.input.TrainingData) W weight_sum (pydruglogics.input.TrainingData.TrainingData property) (pydruglogics.TrainingData property) weights (pydruglogics.input.TrainingData.TrainingData property) (pydruglogics.TrainingData property)