'the following calculates dGr0 for ATP hydrolysis '
'at pH 6: calc_dGr0.py --ph 6 "C00002 + C00001 = '
'C00008 + C00009"'))
parser.add_argument('--ph', type=float, help='pH level', default=7.0)
parser.add_argument('--i',
type=float,
help='ionic strength in M',
default=0.1)
parser.add_argument('reaction', type=str, help='reaction in KEGG notation')
return parser
###############################################################################
parser = MakeParser()
args = parser.parse_args()
logging.getLogger().setLevel(logging.WARNING)
print 'pH: %.1f' % args.ph
print 'I: %.1f M' % args.i
print 'Reaction: ' + args.reaction
# parse the reaction
reaction = Reaction.parse_formula(args.reaction)
p = Preprocessing()
# use the preprocessing class to calculate the estimated dG0 and uncertainty
dG0_prime, U = p.dG0_prime(reaction, pH=args.ph, I=args.i)
print u'dGr0 = %.2f \u00B1 %.2f kJ/mol' % (dG0_prime[0, 0], U[0, 0])
description=('Estimate the Gibbs energy of a reaction. For example,'
'the following calculates dGr0 for ATP hydrolysis '
'at pH 6: calc_dGr0.py --ph 6 "C00002 + C00001 = '
'C00008 + C00009"'))
parser.add_argument('--ph', type=float, help='pH level', default=7.0)
parser.add_argument('--i', type=float,
help='ionic strength in M',
default=0.1)
parser.add_argument('reaction', type=str, help='reaction in KEGG notation')
return parser
###############################################################################
parser = MakeParser()
args = parser.parse_args()
logging.getLogger().setLevel(logging.WARNING)
print 'pH: %.1f' % args.ph
print 'I: %.1f M' % args.i
print 'Reaction: ' + args.reaction
# parse the reaction
reaction = Reaction.parse_formula(args.reaction)
p = Preprocessing()
# use the preprocessing class to calculate the estimated dG0 and uncertainty
dG0_prime, U = p.dG0_prime(reaction, pH=args.ph, I=args.i)
print u'dGr0 = %.2f \u00B1 %.2f kJ/mol' % (dG0_prime[0, 0], U[0, 0])
