def equationStringFromReaction(
reaction: libsbml.Reaction,
sep_reversible: str = "⇆",
sep_irreversible: str = "➞",
modifiers: bool = False,
) -> str:
"""Create equation for reaction.
:param reaction: SBML reaction instance for which equation is to be generated
:param sep_reversible: escape sequence for reversible equation (<=>) separator
:param sep_irreversible: escape sequence for irreversible equation (=>) separator
:param modifiers: boolean flag to use modifiers
:return equation string generated for the reaction
"""
left = _halfEquation(reaction.getListOfReactants())
right = _halfEquation(reaction.getListOfProducts())
if reaction.getReversible():
# '<=>'
sep = sep_reversible
else:
# '=>'
sep = sep_irreversible
if modifiers:
mods = _modifierEquation(reaction.getListOfModifiers())
if mods is None:
return " ".join([left, sep, right])
else:
return " ".join([left, sep, right, mods])
return " ".join([left, sep, right])
def __init__(self, reaction: libsbml.Reaction):
super().__init__(reaction)
# references, not actual species
self.reactants = list(reaction.getListOfReactants())
self.products = list(reaction.getListOfProducts())
# inhibitors / activators
self.modifiers = list(reaction.getListOfModifiers())
self.reversible: bool = reaction.getReversible()
self.kl = reaction.getKineticLaw()
self.unit = libsbml.UnitDefinition.printUnits(
self.kl.getDerivedUnitDefinition())
self.regex = re.compile(
"(" + "|".join([p.id
for p in self.kl.getListOfParameters()]) + ")",
re.VERBOSE,
)
self.text_formula = self.regex.sub(f"{self.id}_\\1", self.kl.formula)
self.formula = compile(self.text_formula, "<string>", "eval")