def test_one_left_to_right_reaction_set_positive_ub(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
model.add_reactions([d1])
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, 0)
d1.upper_bound = .1
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, .1)
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
def test_weird_left_to_right_reaction_issue(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
# print d1.reaction, d1.lower_bound, d1.upper_bound
model.add_reactions([d1])
self.assertFalse(d1.reversibility)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
with TimeMachine() as tm:
d1.knock_out(time_machine=tm)
self.assertEqual(d1.lower_bound, 0)
self.assertEqual(d1._lower_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
def test_one_left_to_right_reaction_set_positive_ub(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
model.add_reactions([d1])
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, 0)
d1.upper_bound = .1
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, .1)
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
def test_weird_left_to_right_reaction_issue(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
# print d1.reaction, d1.lower_bound, d1.upper_bound
model.add_reactions([d1])
self.assertFalse(d1.reversibility)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
with TimeMachine() as tm:
d1.knock_out(time_machine=tm)
self.assertEqual(d1.lower_bound, 0)
self.assertEqual(d1._lower_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
def construct_universal_model(list_of_db_prefixes):
# Select which reactions to include in universal reaction database
reaction_selection = reac_prop[[
any([source.startswith(db_prefix) for db_prefix in list_of_db_prefixes]) and re.match('.*biomass.*', source,
re.I) is None for source
in reac_prop.Source]]
reactions = list()
for index, row in reaction_selection.iterrows():
try:
stoichiometry = parse_reaction(row.Equation, rev_arrow='=')
except ValueError:
continue
else:
for met, coeff in stoichiometry.items():
met.name = chem_prop.loc[met.id]['name']
try:
met.formula = Formula(chem_prop.loc[met.id].formula)
except:
logger.debug('Cannot parse formula %s. Skipping formula' % chem_prop.loc[met.id].formula)
continue
# if met.formula.weight is None:
# logger.debug('Cannot calculate weight for formula %s. Skipping reaction %s' % (met.formula, row.Equation))
# # print('Cannot calculate weight for formula %s. Skipping reaction %s' % (met.formula, row.Equation))
# continue
try:
met.charge = int(chem_prop.loc[met.id].charge)
except (ValueError, TypeError):
logger.debug('Cannot parse charge %s. Skipping charge' % chem_prop.loc[met.id].charge)
pass
rest = chem_prop.loc[met.id].to_dict()
met.annotation = dict((key, rest[key]) for key in rest if key in ('mass', 'InChI', 'source'))
mets = [met.id for met in stoichiometry.keys()]
if len(mets) != len(set(mets)):
continue
reaction = Reaction(index)
reaction.add_metabolites(stoichiometry)
try:
if len(reaction.check_mass_balance()) != 0:
continue
except AttributeError as e:
logger.debug(str(e))
continue
if row.Balance:
reaction.lower_bound = -1 * reaction.upper_bound
reaction.name = row['Source']
row = row.fillna("")
rest = row.to_dict()
reaction.annotation = dict((key, rest[key]) for key in rest if key in ('EC', 'Description'))
reactions.append(reaction)
model = Model('metanetx_universal_model_' + '_'.join(list_of_db_prefixes), solver_interface=optlang.interface)
model.add_reactions(reactions)
# Add sinks for all metabolites
for metabolite in model.metabolites:
model.add_demand(metabolite)
return model
def construct_universal_model(list_of_db_prefixes):
# Select which reactions to include in universal reaction database
reaction_selection = reac_prop[[
any([source.startswith(db_prefix) for db_prefix in list_of_db_prefixes]) and re.match('.*biomass.*', source,
re.I) is None for source
in reac_prop.Source]]
reactions = list()
for index, row in reaction_selection.iterrows():
try:
stoichiometry = parse_reaction(row.Equation, rev_arrow='=')
except ValueError:
continue
else:
for met, coeff in stoichiometry.iteritems():
met.name = chem_prop.loc[met.id]['name']
try:
met.formula = Formula(chem_prop.loc[met.id].formula)
except:
logger.debug('Cannot parse formula %s. Skipping formula' % chem_prop.loc[met.id].formula)
continue
# if met.formula.weight is None:
# logger.debug('Cannot calculate weight for formula %s. Skipping reaction %s' % (met.formula, row.Equation))
# # print('Cannot calculate weight for formula %s. Skipping reaction %s' % (met.formula, row.Equation))
# continue
try:
met.charge = int(chem_prop.loc[met.id].charge)
except (ValueError, TypeError):
logger.debug('Cannot parse charge %s. Skipping charge' % chem_prop.loc[met.id].charge)
pass
rest = chem_prop.loc[met.id].to_dict()
met.annotation = dict((key, rest[key]) for key in rest if key in ('mass', 'InChI', 'source'))
mets = [met.id for met in stoichiometry.keys()]
if len(mets) != len(set(mets)):
continue
reaction = Reaction(index)
reaction.add_metabolites(stoichiometry)
if reaction.check_mass_balance() != []:
continue
if row.Balance:
reaction.lower_bound = -1 * reaction.upper_bound
reaction.name = row['Source']
rest = row.to_dict()
reaction.annotation = dict((key, rest[key]) for key in rest if key in ('EC', 'Description'))
reactions.append(reaction)
model = Model('metanetx_universal_model_' + '_'.join(list_of_db_prefixes), solver_interface=optlang.interface)
model.add_reactions(reactions)
# Add sinks for all metabolites
for metabolite in model.metabolites:
model.add_demand(metabolite)
return model