def python_main():
logger = logging.getLogger('')
logger.setLevel(logging.INFO)
from python.component_contribution import ComponentContribution
from python.kegg_model import KeggModel
from python.thermodynamic_constants import default_RT
cc = ComponentContribution.init()
reaction_strings = open(REACTION_FNAME, 'r').readlines()
model = KeggModel.from_formulas(reaction_strings)
model.add_thermo(cc)
dG0_prime, dG0_std = model.get_transformed_dG0(7.0, 0.2, 298.15)
cid2c_range = {cid : (1e-6, 1e-2) for cid in model.cids}
cid2c_range['C00001'] = (1.0, 1.0) # water must be always set to 1 (equivalent to 55M)
ln_conc = np.log(np.matrix([cid2c_range[cid] for cid in model.cids]))
ln_conc_min = ln_conc[:, 0]
ln_conc_max = ln_conc[:, 1]
S_minus, S_plus = model.get_unidirectional_S()
dG_prime_min = dG0_prime + default_RT * (S_minus.T * ln_conc_max + S_plus.T * ln_conc_min)
dG_prime_max = dG0_prime + default_RT * (S_minus.T * ln_conc_min + S_plus.T * ln_conc_max)
for i, r in enumerate(reaction_strings):
print '-'*50
print r.strip()
print "dG'0 = %8.1f +- %5.1f" % (dG0_prime[i, 0], dG0_std[i, i] * 1.96)
print "dG' range = %8.1f - %8.1f" % (dG_prime_min[i, 0], dG_prime_max[i, 0])
if dG_prime_min[i, 0] < 0 and dG_prime_max[i, 0] > 0:
print "REVERSIBLE!"
else:
print "IRREVERSIBLE!"
def python_main():
logger = logging.getLogger('')
logger.setLevel(logging.INFO)
from python.component_contribution import ComponentContribution
from python.kegg_model import KeggModel
cc = ComponentContribution.init()
reaction_strings = open(REACTION_FNAME, 'r').readlines()
model = KeggModel.from_formulas(reaction_strings)
model.add_thermo(cc)
dG0_prime, dG0_std = model.get_transformed_dG0(7.0, 0.2, 298.15)
print "For a linear problem, define two vector variables 'x' and 'y', each of length Nr (i.e. " + \
"the same length as the list of reactions). Then add these following " + \
"constraints: \n" + \
"-1 <= y <= 1\n" + \
"x = dG0_prime + 3 * dG0_std * y\n" + \
"Then use 'x' as the value of the standard Gibbs energy for all reactions."
print "The results are writteng to: " + OUTPUT_FNAME
savemat(OUTPUT_FNAME, {
'dG0_prime': dG0_prime,
'dG0_std': dG0_std
},
oned_as='row')
def python_main():
logger = logging.getLogger("")
logger.setLevel(logging.INFO)
from python.component_contribution import ComponentContribution
from python.kegg_model import KeggModel
cc = ComponentContribution.init()
reaction_strings = open(REACTION_FNAME, "r").readlines()
model = KeggModel.from_formulas(reaction_strings)
model.add_thermo(cc)
dG0_prime, dG0_std = model.get_transformed_dG0(7.0, 0.2, 298.15)
print "For a linear problem, define two vector variables 'x' and 'y', each of length Nr (i.e. " + "the same length as the list of reactions). Then add these following " + "constraints: \n" + "-1 <= y <= 1\n" + "x = dG0_prime + 3 * dG0_std * y\n" + "Then use 'x' as the value of the standard Gibbs energy for all reactions."
print "The results are writteng to: " + OUTPUT_FNAME
savemat(OUTPUT_FNAME, {"dG0_prime": dG0_prime, "dG0_std": dG0_std}, oned_as="row")
def python_main():
logger = logging.getLogger('')
logger.setLevel(logging.INFO)
from python.component_contribution import ComponentContribution
from python.kegg_model import KeggModel
from python.thermodynamic_constants import default_RT
cc = ComponentContribution.init()
reaction_strings = open(REACTION_FNAME, 'r').readlines()
model = KeggModel.from_formulas(reaction_strings)
model.add_thermo(cc)
dG0_prime, dG0_std = model.get_transformed_dG0(7.0, 0.2, 298.15)
cid2c_range = {cid: (1e-6, 1e-2) for cid in model.cids}
cid2c_range['C00001'] = (
1.0, 1.0) # water must be always set to 1 (equivalent to 55M)
ln_conc = np.log(np.matrix([cid2c_range[cid] for cid in model.cids]))
ln_conc_min = ln_conc[:, 0]
ln_conc_max = ln_conc[:, 1]
S_minus, S_plus = model.get_unidirectional_S()
dG_prime_min = dG0_prime + default_RT * (S_minus.T * ln_conc_max +
S_plus.T * ln_conc_min)
dG_prime_max = dG0_prime + default_RT * (S_minus.T * ln_conc_min +
S_plus.T * ln_conc_max)
for i, r in enumerate(reaction_strings):
print '-' * 50
print r.strip()
print "dG'0 = %8.1f +- %5.1f" % (dG0_prime[i, 0],
dG0_std[i, i] * 1.96)
print "dG' range = %8.1f - %8.1f" % (dG_prime_min[i, 0],
dG_prime_max[i, 0])
if dG_prime_min[i, 0] < 0 and dG_prime_max[i, 0] > 0:
print "REVERSIBLE!"
else:
print "IRREVERSIBLE!"
if not os.path.exists(REPORT_CACHE_FNAME):
fp = open(REPORT_CACHE_FNAME, 'w')
cc = ComponentContribution()
cc.train()
csv_out = csv.writer(fp)
csv_out.writerow(['cid', 'dG0_f'])
for compound_id in cc.ccache.get_all_compound_ids():
dG0_f = cc.get_major_ms_dG0_f(compound_id)
csv_out.writerow([compound_id, '%8.2f' % dG0_f])
cid2dG0[compound_id] = dG0_f
else:
for row in csv.DictReader(open(REPORT_CACHE_FNAME, 'r')):
cid2dG0[row['cid']] = float(row['dG0_f'])
REACTION_FNAME = 'tests/report_gc_reactions.txt'
reaction_strings = open(REACTION_FNAME, 'r').readlines()
model = KeggModel.from_formulas(reaction_strings)
# compare the dG0_r of the model to the one we get if multiplying
# the model stoichiometric matrix by the formation energies
model_dG0_f = np.matrix([cid2dG0[cid] for cid in model.cids]).T
model_dG0_r = model.S.T * model_dG0_f
cc2 = ComponentContribution()
model.add_thermo(cc2)
plt.plot(model.dG0, model_dG0_r, '.')
plt.show()
#dG0_prime, dG0_std = model.get_transformed_dG0(pH=7.5, I=0.2, T=298.15)
cid2dG0 = {}
if not os.path.exists(REPORT_CACHE_FNAME):
fp = open(REPORT_CACHE_FNAME, 'w')
cc = ComponentContribution()
cc.train()
csv_out = csv.writer(fp)
csv_out.writerow(['cid', 'dG0_f'])
for compound_id in cc.ccache.get_all_compound_ids():
dG0_f = cc.get_major_ms_dG0_f(compound_id)
csv_out.writerow([compound_id, '%8.2f' % dG0_f])
cid2dG0[compound_id] = dG0_f
else:
for row in csv.DictReader(open(REPORT_CACHE_FNAME, 'r')):
cid2dG0[row['cid']] = float(row['dG0_f'])
REACTION_FNAME = 'tests/report_gc_reactions.txt'
reaction_strings = open(REACTION_FNAME, 'r').readlines()
model = KeggModel.from_formulas(reaction_strings)
# compare the dG0_r of the model to the one we get if multiplying
# the model stoichiometric matrix by the formation energies
model_dG0_f = np.matrix([cid2dG0[cid] for cid in model.cids]).T
model_dG0_r = model.S.T * model_dG0_f
cc2 = ComponentContribution()
model.add_thermo(cc2)
plt.plot(model.dG0, model_dG0_r, '.')
plt.show()
#dG0_prime, dG0_std = model.get_transformed_dG0(pH=7.5, I=0.2, T=298.15)