def main():
pH, pMg, I, T = (7.0, 3, 0.1, 298.15)
db = SqliteDatabase('../res/gibbs.sqlite')
kegg = Kegg.getInstance()
alberty = PsuedoisomerTableThermodynamics(
'../data/thermodynamics/alberty_pseudoisomers.csv')
cids = alberty.get_all_cids()
dG0_f = pylab.zeros((len(cids), 1))
for i, cid in enumerate(cids):
dG0_f[i, 0] = alberty.cid2dG0_tag(cid, pH=pH, pMg=pMg, I=I, T=T)
S = pylab.zeros((0, len(cids)))
rids = []
ec_numbers = []
for rid in kegg.get_all_rids():
sparse = kegg.rid2sparse_reaction(rid)
if not set(cids).issuperset(sparse.keys()):
continue
rids.append(rid)
ec_numbers.append(kegg.rid2ec_list(rid))
S_row = pylab.zeros((1, len(cids)))
for cid, coeff in sparse.iteritems():
S_row[0, cids.index(cid)] = coeff
S = pylab.vstack([S, S_row])
dG0_r = pylab.dot(S, dG0_f)
util._mkdir('../res/arren')
s_writer = csv.writer(open('../res/arren/stoichiomety.csv', 'w'))
r_writer = csv.writer(open('../res/arren/reactions.csv', 'w'))
e_writer = csv.writer(open('../res/arren/ec_numbers.csv', 'w'))
r_writer.writerow(['rid', 'dG0_r'])
e_writer.writerow(['rid', 'ec0', 'ec1', 'ec2', 'ec3'])
for i in xrange(S.shape[0]):
s_writer.writerow(["%d" % x for x in S[i, :]])
for ec in ec_numbers[i].split(';'):
e_writer.writerow(['%d' % rids[i]] + ec.split('.'))
r_writer.writerow(["%d" % rids[i], '%.1f' % dG0_r[i, 0]])
c_writer = csv.writer(open('../res/arren/compounds.csv', 'w'))
c_writer.writerow(['cid', 'dG0_f'])
for j in xrange(len(cids)):
c_writer.writerow(['%d' % cids[j], '%.1f' % dG0_f[j, 0]])
def main():
pH, pMg, I, T = (7.0, 3, 0.1, 298.15)
db = SqliteDatabase('../res/gibbs.sqlite')
kegg = Kegg.getInstance()
alberty = PsuedoisomerTableThermodynamics('../data/thermodynamics/alberty_pseudoisomers.csv')
cids = alberty.get_all_cids()
dG0_f = pylab.zeros((len(cids), 1))
for i, cid in enumerate(cids):
dG0_f[i, 0] = alberty.cid2dG0_tag(cid, pH=pH, pMg=pMg, I=I, T=T)
S = pylab.zeros((0, len(cids)))
rids = []
ec_numbers = []
for rid in kegg.get_all_rids():
sparse = kegg.rid2sparse_reaction(rid)
if not set(cids).issuperset(sparse.keys()):
continue
rids.append(rid)
ec_numbers.append(kegg.rid2ec_list(rid))
S_row = pylab.zeros((1, len(cids)))
for cid, coeff in sparse.iteritems():
S_row[0, cids.index(cid)] = coeff
S = pylab.vstack([S, S_row])
dG0_r = pylab.dot(S, dG0_f)
util._mkdir('../res/arren')
s_writer = csv.writer(open('../res/arren/stoichiomety.csv', 'w'))
r_writer = csv.writer(open('../res/arren/reactions.csv', 'w'))
e_writer = csv.writer(open('../res/arren/ec_numbers.csv', 'w'))
r_writer.writerow(['rid', 'dG0_r'])
e_writer.writerow(['rid', 'ec0', 'ec1', 'ec2', 'ec3'])
for i in xrange(S.shape[0]):
s_writer.writerow(["%d" % x for x in S[i,:]])
for ec in ec_numbers[i].split(';'):
e_writer.writerow(['%d' % rids[i]] + ec.split('.'))
r_writer.writerow(["%d" % rids[i], '%.1f' % dG0_r[i,0]])
c_writer = csv.writer(open('../res/arren/compounds.csv', 'w'))
c_writer.writerow(['cid', 'dG0_f'])
for j in xrange(len(cids)):
c_writer.writerow(['%d' % cids[j], '%.1f' % dG0_f[j, 0]])
