msmodel

get_reaction_constraints_from_direction()

A function that converts direction symbols (“>” or “<”) to lower and upper bound, where any other value is returned as reversible bounds:

lower_bound, upper_bound = get_reaction_constraints_from_direction(direction)

  • direction str: The name of the metabolite that is will be returned by the function.

returns lower_bound & upper_bound float: The lower and upper bounds of a reaction are deduced from the parameterized direction string.

get_direction_from_constraints()

A function that deduces a direction symbol (“>”, “<”, or “=”) from the lower and upper reaction bounds:

rxn_direction = get_direction_from_constraints(lower_bound, upper_bound)

  • lower_bound & upper_bound float: The flux boundaries that are used to deduce the representative reaction direction symbol.

returns rxn_direction float: The representative direction symbol for the reaction that is described by the lower and upper flux bounds.

get_gpr_string()

A function that constructs a GRP string from the parameterized iterable collection of GRPs:

gpr_string = get_gpr_string(gpr)

  • gpr list: The collection of GPRs that will be assembled into a string via the function.

returns gpr_string str: An assembled string of all GPRs that are provided in the parameterized list.

split_compartment_from_index()

A function that splits an index from its associated compartment:

compartment, index = split_compartment_from_index(cmp_str)

  • cmp_str str: The compartment string that will be parsed.

returns compartment & index str: The compartment and index of the parameterized compartment string, respectively.

get_cmp_token()

A function that filters a list of compartments to determine the compartment of greatest interest:

compartment_index = get_cmp_token(compartments)

  • compartments list: The collection of compartments that will be parsed.

returns compartment_index str: The compartment of greatest interest among the parameterized collection of compartments.

get_set()

A function that filters a list of compartments to determine the compartment of greatest interest:

dnf_set = get_set(expression_string)

  • expression_string str: The expression string that will be parsed.

returns dnf_set set: The set collection of all dnf objects from the parameterized expression string.

MSModel()

This class is a representation of ModelSEED models:

from modelseedpy.core import MSModel
msmodel = MSModel(id_or_model=None, genome=None, template=None)

  • id_or_model str || cobra.core.model.Model: Either the ID of a model or the actual CobraKBase model object that will be represented through this class. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

  • genome genome object: The representative object of the genome.

  • template modelseedpy.core.mstemplate.MSTemplate: The template of the represented model.

template() & genome()

returns template modelseedpy.core.mstemplate.MSTemplate & genome object : The template and genome that are associated with the model that is passed to the class instance.