def test_reduction_potential(self):
kegg_id_to_coeff = {'C00036': -1, 'C00149': 1} # oxaloacetate = malate
reaction = Reaction(kegg_id_to_coeff)
cc = ComponentContribution(pH=7.0, ionic_strength=0.1)
E0_prime_mV, E0_uncertainty = cc.E0_prime(reaction)
self.assertAlmostEqual(E0_prime_mV, -175.2, 1)
self.assertAlmostEqual(E0_uncertainty, 5.3, 1)
try:
reaction = Reaction.parse_formula(args.reaction)
except ValueError as e:
logging.error(str(e))
sys.exit(-1)
equilibrator = ComponentContribution(pH=args.ph, ionic_strength=args.i)
n_e = reaction.check_half_reaction_balancing()
if n_e is None:
logging.error('reaction is not chemically balanced')
sys.exit(-1)
elif n_e == 0:
dG0_prime, dG0_uncertainty = equilibrator.dG0_prime(reaction)
sys.stdout.write(u'\u0394G\'\u00B0 = %.1f \u00B1 %.1f kJ/mol\n' %
(dG0_prime, dG0_uncertainty))
ln_RI = equilibrator.reversibility_index(reaction)
sys.stdout.write(u'ln(Reversibility Index) = %.1f\n' % ln_RI)
else: # treat as a half-reaction
logging.warning('This reaction isn\'t balanced, but can still be treated'
' as a half-reaction')
E0_prime_mV, E0_uncertainty = equilibrator.E0_prime(reaction)
sys.stdout.write(u'E\'\u00B0 = %.1f \u00B1 %.1f mV\n' %
(E0_prime_mV, E0_uncertainty))
sys.stdout.flush()
sys.stderr.write(r'* the range represents the 95% confidence interval'
' due to Component Contribution estimation uncertainty\n')