def main():
opt_parser = flags.MakeOpts()
options, _ = opt_parser.parse_args(sys.argv)
estimators = LoadAllEstimators()
print ('Parameters: T=%f K, pH=%.2g, pMg=%.2g, '
'I=%.2gmM, Median concentration=%.2gM' %
(default_T, options.ph, options.pmg, options.i_s, options.c_mid))
for thermo in estimators.values():
thermo.c_mid = options.c_mid
thermo.pH = options.ph
thermo.pMg = options.pmg
thermo.I = options.i_s
thermo.T = default_T
kegg = Kegg.getInstance()
while True:
cid = GetReactionIdInput()
compound = kegg.cid2compound(cid)
print 'Compound Name: %s' % compound.name
print '\tKegg ID: C%05d' % cid
print '\tFormula: %s' % compound.formula
print '\tInChI: %s' % compound.inchi
for key, thermo in estimators.iteritems():
print "\t<< %s >>" % key
try:
print thermo.cid2PseudoisomerMap(cid),
print '--> dG0\'f = %.1f kJ/mol' % compound.PredictFormationEnergy(thermo)
except Exception as e:
print '\t\tError: %s' % (str(e))
def main():
options, _ = flags.MakeOpts().parse_args(sys.argv)
kegg = Kegg.getInstance()
estimators = LoadAllEstimators()
print ('Parameters: T=%f K, pH=%.2g, pMg=%.2g, '
'I=%.2gmM, Median concentration=%.2gM' %
(default_T, options.ph, options.pmg, options.i_s, options.c_mid))
for thermo in estimators.values():
thermo.c_mid = options.c_mid
thermo.pH = options.ph
thermo.pMg = options.pmg
thermo.I = options.i_s
thermo.T = default_T
cmap = {}
if not options.ignore_cofactors:
print 'Fixing concentrations of co-factors'
cmap = reversibility.GetConcentrationMap()
else:
print 'Not fixing concentrations of co-factors'
while True:
rid = GetReactionIdInput()
reaction = kegg.rid2reaction(rid)
print 'Reaction Name: %s' % reaction.name
print '\tKegg ID: R%05d' % rid
print '\tEC: %s' % str(reaction.ec_list)
for key, thermo in estimators.iteritems():
print "\t<< %s >>" % key
try:
print '\t\tdG0\'f = %.1f kJ/mol' % reaction.PredictReactionEnergy(thermo)
rev = reversibility.CalculateReversability(reaction, thermo, concentration_map=cmap)
print '\t\tgamma = %.3g' % rev
except Exception as e:
print '\tError: %s' % (str(e))