def __init__(
self,
id: Union[str, Metabolite] = None,
concentration: float = None,
molecular_weight: float = 0.0,
name: str = "",
):
"""Initialize with id."""
self.concentration = concentration
self.mw = molecular_weight
self._flux = None
self.lower_bound = 0
self._reaction = set()
self._ub = config.upper_bound
self.compartment = "c"
self.__metabolites = {}
self._annotation = {}
if isinstance(id, Metabolite):
self.from_metabolite(id)
else:
Object.__init__(self, id, name)
self.formula = ""
self.charge = 0.0
self.kcats = Kcats(self)
self._reaction.add(self)
def from_metabolite(self, met: Metabolite):
"""Initialize `Protein` from `Metabolite`; i.e., when reading from SBML."""
if not UNIPROT_PATTERN.match(met.id):
LOGGER.warning(f"Metabolite {met.id} does not use Uniprot ID.")
Object.__init__(self, met.id, met.name)
self.compartment = met.compartment
self._reaction = met._reaction
self.charge = met.charge
self.formula = ""
self._annotation = met._annotation