def main():
estimators = LoadAllEstimators()
args, _ = MakeOpts(estimators).parse_args(sys.argv)
# Make sure we have all the data.
db = SqliteDatabase("../res/gibbs.sqlite")
G = GroupContribution(db=db, html_writer=NullHtmlWriter(), transformed=args.transformed)
G.init()
print "Exporting KEGG compounds to %s" % args.compounds_out_filename
csv_writer = csv.writer(open(args.compounds_out_filename, "w"))
csv_writer.writerow(["KEGG ID", "nH", "CHARGE", "nMg", "dG0_f"])
for cid in sorted(G.get_all_cids()):
try:
for nH, z, nMg, dG0 in G.cid2PseudoisomerMap(cid).ToMatrix():
csv_writer.writerow(["C%05d" % cid, nH, z, nMg, "%.1f" % dG0])
except MissingCompoundFormationEnergy as e:
csv_writer.writerow(["C%05d" % cid, None, None, None, str(e)])
print "Exporting KEGG reactions to %s" % args.reactions_out_filename
csv_writer = csv.writer(open(args.reactions_out_filename, "w"))
csv_writer.writerow(
["KEGG ID", "dG'0_r (pH=%.1f, I=%.2f, pMg=%.1f, T=%.1f)" % (args.ph, args.i_s, args.pmg, args.temp)]
)
for rid in sorted(G.kegg.get_all_rids()):
reaction = G.kegg.rid2reaction(rid)
try:
reaction.Balance(balance_water=True)
dG0_r = reaction.PredictReactionEnergy(G, pH=args.ph, pMg=args.pmg, I=args.i_s, T=args.temp)
csv_writer.writerow(["R%05d" % rid, "%.1f" % dG0_r])
except (
KeggParseException,
MissingCompoundFormationEnergy,
KeggReactionNotBalancedException,
MissingReactionEnergy,
KeyError,
OpenBabelError,
) as e:
csv_writer.writerow(["R%05d" % rid, str(e)])
def main():
estimators = LoadAllEstimators()
args, _ = MakeOpts(estimators).parse_args(sys.argv)
# Make sure we have all the data.
db = SqliteDatabase('../res/gibbs.sqlite')
G = GroupContribution(db=db, html_writer=NullHtmlWriter(),
transformed=args.transformed)
G.init()
print 'Exporting KEGG compounds to %s' % args.compounds_out_filename
csv_writer = csv.writer(open(args.compounds_out_filename, 'w'))
csv_writer.writerow(["KEGG ID", "nH", "CHARGE", "nMg", "dG0_f"])
for cid in sorted(G.get_all_cids()):
try:
for nH, z, nMg, dG0 in G.cid2PseudoisomerMap(cid).ToMatrix():
csv_writer.writerow(["C%05d" % cid, nH, z, nMg, "%.1f" % dG0])
except MissingCompoundFormationEnergy as e:
csv_writer.writerow(["C%05d" % cid, None, None, None, str(e)])
print 'Exporting KEGG reactions to %s' % args.reactions_out_filename
csv_writer = csv.writer(open(args.reactions_out_filename, 'w'))
csv_writer.writerow(["KEGG ID", "dG'0_r (pH=%.1f, I=%.2f, pMg=%.1f, T=%.1f)" %
(args.ph, args.i_s, args.pmg, args.temp)])
for rid in sorted(G.kegg.get_all_rids()):
reaction = G.kegg.rid2reaction(rid)
try:
reaction.Balance(balance_water=True)
dG0_r = reaction.PredictReactionEnergy(G, pH=args.ph,
pMg=args.pmg, I=args.i_s, T=args.temp)
csv_writer.writerow(["R%05d" % rid, "%.1f" % dG0_r])
except (KeggParseException,
MissingCompoundFormationEnergy,
KeggReactionNotBalancedException,
MissingReactionEnergy,
KeyError,
OpenBabelError) as e:
csv_writer.writerow(["R%05d" % rid, str(e)])
