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) attractor_tool (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) attractor_type (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) attractors (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) B best_boolean_models (pydruglogics.Evolution property) binary_boolean_equations (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) boolean_equations (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) BooleanModel (class in pydruglogics) 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) (pydruglogics.statistics.Statistics method) create_initial_population() (pydruglogics.Evolution method) (pydruglogics.model.Evolution.Evolution method) D drug_effects (pydruglogics.Perturbation property) drug_names (pydruglogics.Perturbation property) drug_targets (pydruglogics.Perturbation property) drugs (pydruglogics.Perturbation property) E Evolution (class in pydruglogics) execute() (in module pydruglogics) 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() (in module pydruglogics.utils.BNetworkUtil.BNetworkUtil) 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 attribute) 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) interactions (pydruglogics.InteractionModel property) is_numeric_string() (in module pydruglogics.utils.BNetworkUtil.BNetworkUtil) L Logger (class in pydruglogics) M max_output (pydruglogics.ModelOutputs property) min_output (pydruglogics.ModelOutputs property) model_name (pydruglogics.BooleanModel property) (pydruglogics.InteractionModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) model_name() (pydruglogics.model.InteractionModel.InteractionModel method) model_outputs (pydruglogics.ModelOutputs property) ModelOutputs (class in pydruglogics) ModelPredictions (class in pydruglogics) module pydruglogics pydruglogics.execution pydruglogics.input pydruglogics.model pydruglogics.utils mutation_type (pydruglogics.BooleanModel property) (pydruglogics.model.BooleanModel.BooleanModel attribute) N node_names (pydruglogics.ModelOutputs property) O observations (pydruglogics.TrainingData property) P parse_interaction() (in module pydruglogics.utils.BNetworkUtil.BNetworkUtil) Perturbation (class in pydruglogics) perturbations (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) predict() (in module pydruglogics.execution.Executor) predicted_synergy_scores (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.input module pydruglogics.model module pydruglogics.utils module R read_lines_from_file() (in module pydruglogics.utils.BNetworkUtil.BNetworkUtil) remove_extension() (in module pydruglogics.utils.BNetworkUtil.BNetworkUtil) reset_attractors() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) response (pydruglogics.TrainingData property) responses (pydruglogics.TrainingData property) run() (pydruglogics.Evolution method) (pydruglogics.model.Evolution.Evolution method) run_simulations() (pydruglogics.model.ModelPredictions.ModelPredictions method) (pydruglogics.ModelPredictions method) S sampling_with_ci() (in module pydruglogics) (pydruglogics.statistics.Statistics method) 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() (in module pydruglogics.utils.Logger.Logger) (pydruglogics.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 to_binary() (pydruglogics.BooleanModel method) (pydruglogics.model.BooleanModel.BooleanModel method) train() (in module pydruglogics) (in module pydruglogics.execution.Executor) TrainingData (class in pydruglogics) W weight_sum (pydruglogics.TrainingData property) weights (pydruglogics.TrainingData property)