def FromFiles():
feist = Feist()
reaction_file = '../data/metabolic_models/iAF1260_reactions.csv'
# Read compounds ids 2 Kegg cid's mapping file into a dict
counters = {
'kegg_error': 0,
'translocation': 0,
'exchange': 0,
'sink': 0,
'unbalanced': 0,
'okay': 0
}
for row in csv.DictReader(open(reaction_file, 'r')):
#if 'Transport' in row['subSystem']:
# counters['translocation'] += 1
# continue
if row['abbreviation'][0:3] == 'EX_':
counters['exchange'] += 1
continue
if row['abbreviation'][0:3] == 'DM_':
counters['sink'] += 1
continue
sparse = Feist.parse_equation(row['equation'])
kegg_sparse = {}
for biggID, coeff in sparse.iteritems():
keggID = feist.bigg2kegg[biggID]
kegg_sparse[keggID] = kegg_sparse.get(keggID, 0) + coeff
if 0 in kegg_sparse:
logging.debug('Some compounds are missing KEGG IDs in %s: %s' %
(row['abbreviation'], row['equation']))
counters['kegg_error'] += 1
continue
for keggID in [k for k, v in kegg_sparse.iteritems() if v == 0]:
del kegg_sparse[keggID]
directionality = row["directionality without uncertainty (pH 7.2)"]
#directionaliry = row['reconstruction directionality']
if directionality == 'reversible':
direction = '<=>'
elif directionality == 'forward only':
direction = '=>'
elif directionality == 'reverse only':
direction = '<='
else:
raise ValueError('unknown directionality tag: ' +
directionality)
reaction = Reaction(row['abbreviation'],
kegg_sparse,
direction=direction)
if row['delta G (pH 7)'] == 'Not calculated':
dG0 = np.nan
else:
dG0 = float(row['delta G (pH 7)']) * J_per_cal
try:
reaction.Balance(balance_water=True,
exception_if_unknown=False)
counters['okay'] += 1
except KeggReactionNotBalancedException as e:
logging.debug(str(e) + ' - ' + str(reaction))
counters['unbalanced'] += 1
continue
feist.reactions.append(reaction)
feist.dG0s.append(dG0)
logging.debug(" ; ".join(
["%s : %d" % (key, val) for (key, val) in counters.iteritems()]))
return feist
#H.ToDatabase(db, 'hatzi_gc')
#H.I = 0.25
#H.T = 300;
#sparse_reaction = {13:-1, 1:-1, 9:2}
#sparse_reaction = {36:-1, 3981:1}
#sparse_reaction = {6:-1, 143:-1, 234:1, 5:1}
#sparse_reaction = {1:-1, 499:-1, 603:1, 86:1}
#sparse_reaction = {1:-1, 6:-1, 311:-1, 288:1, 5:1, 80:2, 26:1}
#sparse_reaction = {408:-1, 6:-1, 4092:1, 5:1}
#sparse_reaction = {588:-1, 1:-1, 114:1, 9:1}
#sparse_reaction = {1:-1, 3:-1, 149:-1, 288:1, 4:1, 80:2, 22:1}
react = Reaction("reaction", {408: -1, 6: -1, 4092: 1, 5: 1})
#sys.stdout.write("The dG0_r of PPi + H20 <=> 2 Pi: \n\n")
react.Balance()
print react.FullReactionString()
sys.stdout.write("%5s | %5s | %6s | %6s\n" % ("pH", "I", "T", "dG0_r"))
for pH in np.arange(5, 10.01, 0.25):
H_withpka.pH = pH
sys.stdout.write("%5.2f | %5.2f | %6.1f | %6.2f\n" %
(H_withpka.pH, H_withpka.I, H_withpka.T,
react.PredictReactionEnergy(H_withpka)))
for cid in react.get_cids():
print '-' * 50
print "C%05d - %s:" % (cid, H_withpka.kegg.cid2name(cid))
print H_withpka.kegg.cid2inchi(cid)
print "Pseudoisomers:\n", H_withpka.cid2PseudoisomerMap(cid)
print "dG0'_f = %.1f kJ/mol" % H_withpka.cid2PseudoisomerMap(