def main():
td = TrainingData()
cc = ComponentContribution.init()
G1 = np.matrix(cc.params['G1'])
G2 = np.matrix(cc.params['G2'])
G3 = np.matrix(cc.params['G3'])
############################################################################
#reaction = KeggReaction.parse_formula('C00002 + C00001 <=> C00008 + C00009'); fname = 'atpase';
reaction = KeggReaction.parse_formula('C00149 <=> C00122 + C00001')
fname = 'fumarase'
x, g = cc._decompose_reaction(reaction)
weights_rc = (x.T * G1).round(5)
weights_gc = (x.T * G2 + g.T * G3).round(5)
weights = weights_rc + weights_gc
orders = sorted(range(weights.shape[1]),
key=lambda j: abs(weights[0, j]),
reverse=True)
output = csv.writer(open('res/%s_analysis.csv' % fname, 'w'))
output.writerow(('Weight', 'dG\'0', 'dG0', 'reference', 'reaction'))
for j in orders:
if abs(weights[0, j]) < 1e-7:
continue
output.writerow((weights_rc[0, j], td.dG0_prime[j], td.dG0[j],
td.reference[j], td.description[j]))
def main():
td = TrainingData()
cc = ComponentContribution.init()
G1 = np.matrix(cc.params['G1'])
G2 = np.matrix(cc.params['G2'])
G3 = np.matrix(cc.params['G3'])
############################################################################
#reaction = KeggReaction.parse_formula('C00002 + C00001 <=> C00008 + C00009'); fname = 'atpase';
reaction = KeggReaction.parse_formula('C00149 <=> C00122 + C00001'); fname = 'fumarase';
x, g = cc._decompose_reaction(reaction)
weights_rc = (x.T * G1).round(5)
weights_gc = (x.T * G2 + g.T * G3).round(5)
weights = weights_rc + weights_gc
orders = sorted(range(weights.shape[1]),
key=lambda j:abs(weights[0, j]), reverse=True)
output = csv.writer(open('res/%s_analysis.csv' % fname, 'w'))
output.writerow(('Weight', 'dG\'0', 'dG0', 'reference', 'reaction'))
for j in orders:
if abs(weights[0, j]) < 1e-7:
continue
output.writerow((weights_rc[0, j], td.dG0_prime[j], td.dG0[j],
td.reference[j], td.description[j]))
@author: eladn
"""
from python.component_contribution import ComponentContribution
from python.kegg_reaction import KeggReaction
#pH = 7
I = 0.2
T = 298.15
F = 96.48 / 1000.0 # kJ/mol / mV
cc = ComponentContribution.init()
#formula = 'C00033 + C00282 <=> C00084 + C00001'
#formula = 'C00067 + C00001 <=> C00058 + C00010'
formula = 'C00003 + C00282 <=> C00004'
#############################################################################
reaction = KeggReaction.parse_formula(formula)
reaction_atom_bag = reaction._get_reaction_atom_bag()
n_e = 0
if 'e-' in reaction_atom_bag:
n_e = reaction_atom_bag['e-']
del reaction_atom_bag['e-']
if len(reaction_atom_bag) != 0:
raise Exception('Reaction is not balanced (not only with respect to e-)')
dG0_r, u_r = cc.get_dG0_r(reaction)
for pH in xrange(6, 9):
ddG0_r = reaction.get_transform_ddG0(pH=pH, I=I, T=T)
dG0_r_prime = dG0_r+ddG0_r
E0_prime = -dG0_r_prime / (n_e*F)
print 'pH = %4.1f, E\'0 = %6.0f' % (pH, E0_prime)