def __init__(self,
model_code='ecoli:iJO1366',
solver='gurobi',
min_biomass=0.55):
self.logger = get_bistream_logger(
(model_code + ':' + self.__class__.__name__).replace(':', '_'))
self.logger.setLevel(logging.INFO)
self.species = model_code.split(':')[0]
self.model_name = model_code.split(':')[-1]
if self.species.lower() == 'ecoli':
if self.model_name.lower() == 'iml1515':
self.model = load_json_model(
os.path.dirname(os.path.abspath(__file__)) +
'/data/ecoli/iML1515.json')
self.biomass_reaction = 'BIOMASS_Ec_iML1515_core_75p37M'
else:
self.model = load_json_model(
os.path.dirname(os.path.abspath(__file__)) +
'/data/ecoli/iJO1366.json')
self.biomass_reaction = 'BIOMASS_Ec_iJO1366_core_53p95M'
self.model.objective = self.biomass_reaction
self.model.reactions.get_by_id(
self.biomass_reaction).lower_bound = min_biomass
self.model.solver = solver
self._init_model()
self._print_summary()
self.reserved_bounds = {}
self.dummy_reactions = set()
def __init__(
self,
thermo_data,
model=Model(),
name=None,
growth_reaction='',
mu=None,
mu_error=0,
mu_range=None,
n_mu_bins=1,
big_M=1000,
temperature=std.TEMPERATURE_0,
min_ph=std.MIN_PH,
max_ph=std.MAX_PH,
prot_scaling=1000,
mrna_scaling=None,
):
if name is None:
name = 'ETFL_' + name if name else 'ETFL model'
LCSBModel.__init__(self, model, name)
###############
# ME part #
###############
self.logger = get_bistream_logger('ME model' + str(self.name))
self.parent = model
if model is not None:
self.sanitize_varnames()
self.init_etfl(big_M, growth_reaction, mu_range, n_mu_bins, name)
###############
# Thermo part #
###############
self.TEMPERATURE = temperature
self.thermo_data = thermo_data
self.thermo_unit = thermo_data['units']
self.reaction_cues_data = thermo_data['cues']
self.compounds_data = thermo_data['metabolites']
self.Debye_Huckel_B = get_debye_huckel_b(temperature)
self.parent = model
self.logger = get_bistream_logger('thermomodel_' + str(self.name))
# Compute internal values to adapt the the thermo_unit provided
if self.thermo_unit == "kJ/mol":
self.GAS_CONSTANT = 8.314472 / 1000 # kJ/(K mol)
self.Adjustment = 1
else:
self.GAS_CONSTANT = 1.9858775 / 1000 # Kcal/(K mol)
self.Adjustment = 4.184
self.RT = self.GAS_CONSTANT * self.TEMPERATURE
# CONSTANTS
self.MAX_pH = max_ph
self.MIN_pH = min_ph
self.logger.info('# Model initialized with units {} and temperature {} K' \
.format(self.thermo_unit, self.TEMPERATURE))
def _silence_pytfa(logger_name):
# Disables the stream logs produced by the pytfa module, keeps file logs
logger = get_bistream_logger(logger_name)
for handler in logger.handlers:
if not isinstance(handler, logging.FileHandler):
handler.setLevel(logging.ERROR)