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))
def main():
kegg = Kegg.getInstance()
options, args = MakeOpts().parse_args(sys.argv)
print ('Parameters: T=%f K, pMg=%.2g, I=%.2gM' %
(options.T, options.pMg, options.I))
print "reaction:", args[-1]
estimators = LoadAllEstimators()
plt.rcParams['legend.fontsize'] = 8
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.size'] = 12
plt.rcParams['lines.linewidth'] = 2
colormap = {}
colormap['markers'] = (64.0/255, 111.0/255, 29.0/255, 3.0)
#colormap['hatzi_gc'] = (54.0/255, 182.0/255, 202.0/255, 1.0)
colormap['UGC'] = (202.0/255, 101.0/255, 54.0/255, 1.0)
#colormap['alberty'] = (202.0/255, 54.0/255, 101.0/255, 1.0)
colormap['PGC'] = (101.0/255, 202.0/255, 54.0/255, 1.0)
fig = plt.figure(figsize=(6,6), dpi=90)
fig.hold(True)
if options.rid is None:
reaction = GetSparseReactionInput(args[-1], kegg)
else:
reaction = kegg.rid2reaction(options.rid)
reaction.Balance()
print 'Reaction: %s' % reaction.FullReactionString()
nist = Nist()
nist_rows = nist.SelectRowsFromNist(reaction, check_reverse=True)
pH_min = 7.0 - options.pH/2.0
pH_max = 7.0 + options.pH/2.0
if nist_rows:
dG0_list = []
pH_list = []
for row_data in nist_rows:
pH_list.append(row_data.pH)
if row_data.reaction == reaction:
dG0_list.append(row_data.dG0_r)
else:
dG0_list.append(-row_data.dG0_r)
plt.plot(pH_list, dG0_list, marker='.', linestyle='none',
label='measured data', markeredgecolor='none',
markerfacecolor=colormap['markers'], markersize=5)
pH_max = max(pH_list + [pH_max])
pH_min = min(pH_list + [pH_min])
pH_range = np.arange(pH_min-0.1, pH_max+0.1, 0.02)
for key, thermo in estimators.iteritems():
if key not in colormap:
continue
print key, 'dG0 at pH=7: %.2f' % reaction.PredictReactionEnergy(thermo,
pH=7.0, pMg=options.pMg, I=options.I, T=options.T)
dG0 = []
for pH in pH_range:
dG0.append(reaction.PredictReactionEnergy(thermo,
pH=pH, pMg=options.pMg, I=options.I, T=options.T))
plt.plot(pH_range, dG0, marker='None', linestyle='solid', color=colormap[key],
figure=fig, label=thermo.name)
plt.xlabel('pH')
plt.ylabel(r'$\Delta_r G^\circ$ [kJ/mol]')
plt.title(kegg.reaction2string(reaction), fontsize=8)
plt.legend(loc='lower left')
if not options.output:
plt.tight_layout()
plt.show()
else:
fig.savefig(options.output, format='svg')