def test__normalize_pseudoreaction_exchange_error_bad_coeff():
reaction = Reaction('EX_gone')
reaction.add_metabolites({Metabolite('glu__L_e'): -2})
with pytest.raises(ConflictingPseudoreaction) as excinfo:
_normalize_pseudoreaction(reaction)
assert 'with coefficient' in str(excinfo.value)
assert reaction.id == 'EX_gone'
def test__normalize_pseudoreaction_biomass_has_gpr():
reaction = Reaction('my_biomass_2')
reaction.gene_reaction_rule = 'b1779'
with pytest.raises(ConflictingPseudoreaction) as excinfo:
_normalize_pseudoreaction(reaction)
assert 'has a gene_reaction_rule' in str(excinfo.value)
assert reaction.id == 'my_biomass_2'
def test__normalize_pseudoreaction_demand():
reaction = Reaction('DM_gone')
reaction.add_metabolites({Metabolite('glu__L_c'): -1})
reaction.lower_bound = 0
reaction.upper_bound = 1000
_normalize_pseudoreaction(reaction)
assert reaction.id == 'DM_glu__L_c'
assert reaction.subsystem == 'Intracellular demand'
def test__normalize_pseudoreaction_exchange_error_has_gpr():
reaction = Reaction('EX_gone')
reaction.add_metabolites({Metabolite('glu__L_e'): -1})
reaction.gene_reaction_rule = 'b1779'
with pytest.raises(ConflictingPseudoreaction) as excinfo:
_normalize_pseudoreaction(reaction)
assert 'has a gene_reaction_rule' in str(excinfo.value)
assert reaction.id == 'EX_gone'
def test__normalize_pseudoreaction_exchange():
reaction = Reaction('EX_gone')
reaction.add_metabolites({Metabolite('glu__L_e'): -1})
reaction.lower_bound = -1000
reaction.upper_bound = 0
_normalize_pseudoreaction(reaction)
assert reaction.id == 'EX_glu__L_e'
assert reaction.subsystem == 'Extracellular exchange'
def test__normalize_pseudoreaction_sink():
reaction = Reaction('SInk_gone')
reaction.add_metabolites({Metabolite('glu__L_c'): -1})
reaction.lower_bound = -1000
reaction.upper_bound = 0
_normalize_pseudoreaction(reaction)
assert reaction.id == 'SK_glu__L_c'
assert reaction.subsystem == 'Intracellular source/sink'
def test__normalize_pseudoreaction_demand_reversed():
reaction = Reaction('DM_gone')
reaction.add_metabolites({Metabolite('glu__L_c'): 1})
reaction.lower_bound = -1000
reaction.upper_bound = 0
_normalize_pseudoreaction(reaction)
assert list(reaction.metabolites.values()) == [-1]
assert reaction.lower_bound == 0
assert reaction.upper_bound == 1000
assert reaction.id == 'DM_glu__L_c'
def test__normalize_pseudoreaction_exchange_reversed():
reaction = Reaction('EX_gone')
reaction.add_metabolites({Metabolite('glu__L_e'): 1})
reaction.lower_bound = 0
reaction.upper_bound = 1000
_normalize_pseudoreaction(reaction)
assert reaction.id == 'EX_glu__L_e'
assert reaction.lower_bound == -1000
assert reaction.upper_bound == 0
assert list(reaction.metabolites.values()) == [-1]
def test__normalize_pseudoreaction_atpm():
reaction = Reaction('notATPM')
reaction.add_metabolites({Metabolite('atp_c'): -1,
Metabolite('h2o_c'): -1,
Metabolite('pi_c'): 1,
Metabolite('h_c'): 1,
Metabolite('adp_c'): 1})
_normalize_pseudoreaction(reaction)
assert reaction.id == 'ATPM'
assert reaction.subsystem == 'Biomass and maintenance functions'
def test__normalize_pseudoreaction_sink_reversed():
reaction = Reaction('Sink_gone')
reaction.add_metabolites({Metabolite('glu__L_c'): 1})
reaction.lower_bound = 0
reaction.upper_bound = 50
_normalize_pseudoreaction(reaction)
assert list(reaction.metabolites.values()) == [-1]
assert reaction.lower_bound == -50
assert reaction.upper_bound == 0
assert reaction.id == 'SK_glu__L_c'
def test__normalize_pseudoreaction_atpm_has_gpr():
reaction = Reaction('NPT1')
reaction.add_metabolites({Metabolite('atp_c'): -1,
Metabolite('h2o_c'): -1,
Metabolite('pi_c'): 1,
Metabolite('h_c'): 1,
Metabolite('adp_c'): 1})
reaction.gene_reaction_rule = 'b1779'
_normalize_pseudoreaction(reaction)
# should not change
assert reaction.id == 'NPT1'
def test__normalize_pseudoreaction_atpm_reversed():
reaction = Reaction('notATPM')
reaction.add_metabolites({Metabolite('atp_c'): 1,
Metabolite('h2o_c'): 1,
Metabolite('pi_c'): -1,
Metabolite('h_c'): -1,
Metabolite('adp_c'): -1})
reaction.lower_bound = -50
reaction.upper_bound = 100
_normalize_pseudoreaction(reaction)
assert reaction.id == 'ATPM'
assert reaction.lower_bound == -100
assert reaction.upper_bound == 50
def test__normalize_pseudoreaction_exchange_error_bad_name():
reaction = Reaction('gone')
reaction.add_metabolites({Metabolite('glu__L_e'): -1})
_normalize_pseudoreaction(reaction)
assert reaction.id == 'EX_glu__L_e'
def test__normalize_pseudoreaction_biomass():
reaction = Reaction('my_biomass_2')
_normalize_pseudoreaction(reaction)
assert reaction.id == 'BIOMASS_my_2'
assert reaction.subsystem == 'Biomass and maintenance functions'