def __init__(self, species, parameters, propensities, stoichiometry_matrix):
r"""
Creates a `Model` object that stores the model of reactions we want to analyse
:param species: variables of the model, as `sympy.Symbol`s, i.e. species
:param parameters: parameters of the model, as `sympy` symbols
:param propensities: a matrix of propensities for each of the reaction in the model.
:param stoichiometry_matrix: stoichiometry matrix for the model
"""
self.__parameters = to_list_of_symbols(parameters)
self.__species = to_list_of_symbols(species)
self.__propensities = to_sympy_column_matrix(to_sympy_matrix(propensities))
self.__stoichiometry_matrix = to_sympy_matrix(stoichiometry_matrix)
self.validate()
def __init__(self, species, parameters, propensities,
stoichiometry_matrix):
r"""
Creates a `Model` object that stores the model of reactions we want to analyse
:param species: variables of the model, as `sympy.Symbol`s, i.e. species
:param parameters: parameters of the model, as `sympy` symbols
:param propensities: a matrix of propensities for each of the reaction in the model.
:param stoichiometry_matrix: stoichiometry matrix for the model
"""
self.__parameters = to_list_of_symbols(parameters)
self.__species = to_list_of_symbols(species)
self.__propensities = to_sympy_column_matrix(
to_sympy_matrix(propensities))
self.__stoichiometry_matrix = to_sympy_matrix(stoichiometry_matrix)
self.validate()
def __init__(self, method, left_hand_side_descriptors, right_hand_side, parameters):
"""
:param method: a string describing the method used to generate the problem.
Currently, 'MEA' and 'LNA' are supported"
:param left_hand_side_descriptors: the left hand side of equations as a list of
:class:`~means.core.descriptors.Descriptor` objects (such as :class:`~means.core.descriptors.Moment`)
:param right_hand_side: the right hand side of equations
:param parameters: the parameters of the model
"""
self.__left_hand_side_descriptors = left_hand_side_descriptors
self.__left_hand_side = to_sympy_column_matrix(to_sympy_matrix(
[plhs.symbol for plhs in left_hand_side_descriptors])
)
self.__right_hand_side = to_sympy_column_matrix(right_hand_side)
self.__parameters = to_list_of_symbols(parameters)
self.__method = method
def variables(self):
return to_list_of_symbols(self.__left_hand_side)