pydruglogics.model.BooleanModel module

class pydruglogics.model.BooleanModel.BooleanModel(model=None, file=None, attractor_tool='mpbn', attractor_type='stable_states', mutation_type='topology', model_name='', cloned_equations=None, cloned_binary_equations=None)

Bases: object

Initializes the BooleanModel instance. :param model: An InteractionModel instance. :param file: The path to the file containing Boolean Equations in ‘.bnet’ format. :param attractor_tool: The tool to be used for attractor calculation. Possible values: ‘mpbn’, ‘pyboolnet’. :param attractor_type: The type of the attractor calculation. Possible values: ‘stable_states’, ‘trapspaces’. :param mutation_type: The type of mutation to be performed. Possible values: ‘topology’, ‘binary’, ‘balanced’. :param model_name: Name for the model. :param cloned_equations: Boolean Equations representing the model’s interactions. (only for cloning) :param cloned_binary_equations: A list representing the Mutate Boolean Model in binary representation. (only for cloning)

add_perturbations(perturbations)

Adds perturbations to the Boolean Model. :param perturbations: A list of Perturbations. :return: None

property attractor_tool: str

property attractor_type: str

property attractors: object

property binary_boolean_equations

property boolean_equations

calculate_attractors(attractor_tool, attractor_type) → None

Calculate attractors based on the chosen attractor_tool and attractor_type. :param attractor_tool: Tool for attractor calculation. Possible values: ‘mpbn’, ‘pyboolnet’. :param attractor_type: Type of attractor. Possible values: ‘stable_states’, ‘trapspaces’. :return: None

calculate_global_output(model_outputs, normalized=True)

Calculates the (normalized) global output of the model. :param model_outputs: An instance containing node weights defined in the ModelOutputs class. :param normalized: Whether to normalize the global output. :return: float

clone()

from_binary(binary_representation, mutation_type: str)

Updates the Boolean Equations from a binary representation based on the mutation type. :param binary_representation: The binary representation of the Boolean Equations as a list. :param mutation_type: The type of mutation can be: ‘topology’, ‘balanced’, ‘mixed’. :return: Updated Boolean Equations as a list.

get_stable_states() → object

property global_output

has_attractors() → bool

has_global_output() → bool

has_stable_states() → bool

property model_name: str

property mutation_type: str

print()

reset_attractors() → None

to_binary(mutation_type: str)

Converts the Boolean Equations to a binary representation. The representation is based on the mutation type. :param mutation_type: The type of mutation can be: ‘topology’, ‘balanced’, ‘mixed’ :return: The binary representation of the Boolean Equations as a list.