def test_all_modules():
from pygibbs.groups import GroupContribution
gc = GroupContribution(sqlite_name="gibbs.sqlite", html_name="dG0_test")
gc.init()
c_range = (1e-6, 1e-2)
c_mid = 1e-3
pH = 8
I = 0.1
T = 300
map_cid = {201:2, 454:8} # CIDs that should be mapped to other CIDs because they are unspecific (like NTP => ATP)
cids_with_missing_dG_f = set()
f = open("../res/feasibility.csv", "w")
csv_output = csv.writer(f)
csv_output.writerow(("MID", "module name", "pH", "I", "T", "pCr", "MTDF"))
for mid in sorted(gc.kegg().mid2rid_map.keys()):
module_name = gc.kegg().mid2name_map[mid]
try:
S, _rids, _fluxes, cids = gc.kegg().get_module(mid)
except KeggMissingModuleException as e:
sys.stderr.write("WARNING: " + str(e) + "\n")
continue
_Nr, Nc = S.shape
for pH in [5, 6, 7, 8, 9]:
for I in [0.0, 0.1, 0.2, 0.3, 0.4]:
dG0_f = pylab.zeros((Nc, 1))
bounds = []
for c in range(Nc):
cid = map_cid.get(cids[c], cids[c])
try:
pmap = gc.cid2PseudoisomerMap(cid)
dG0_f[c] = gc.pmap_to_dG0(pmap, pH, I, T)
except MissingCompoundFormationEnergy as e:
if (cid not in cids_with_missing_dG_f):
sys.stderr.write("Setting the dG0_f of C%05d to NaN because: %s\n"\
% (cid, str(e)))
cids_with_missing_dG_f.add(cid)
dG0_f[c] = pylab.nan
bounds = [gc.kegg().cid2bounds.get(cid, (None, None)) for cid in cids]
try:
_dG_f, _concentrations, pCr = find_pCr(S, dG0_f, c_mid=c_mid, ratio=3.0, bounds=bounds)
except LinProgNoSolutionException:
sys.stderr.write("M%05d: Pathway is theoretically infeasible\n" % mid)
pCr = None
try:
_dG_f, _concentrations, MTDF = find_mtdf(S, dG0_f, c_range=c_range, bounds=bounds)
except LinProgNoSolutionException:
sys.stderr.write("M%05d: Pathway is theoretically infeasible\n" % mid)
MTDF = None
csv_output.writerow([mid, module_name, pH, I, T, pCr, MTDF])
f.close()
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)])
def test_all_modules():
from pygibbs.groups import GroupContribution
gc = GroupContribution(sqlite_name="gibbs.sqlite", html_name="dG0_test")
gc.init()
c_range = (1e-6, 1e-2)
c_mid = 1e-3
pH = 8
I = 0.1
T = 300
map_cid = {
201: 2,
454: 8
} # CIDs that should be mapped to other CIDs because they are unspecific (like NTP => ATP)
cids_with_missing_dG_f = set()
f = open("../res/feasibility.csv", "w")
csv_output = csv.writer(f)
csv_output.writerow(("MID", "module name", "pH", "I", "T", "pCr", "MTDF"))
for mid in sorted(gc.kegg().mid2rid_map.keys()):
module_name = gc.kegg().mid2name_map[mid]
try:
S, _rids, _fluxes, cids = gc.kegg().get_module(mid)
except KeggMissingModuleException as e:
sys.stderr.write("WARNING: " + str(e) + "\n")
continue
_Nr, Nc = S.shape
for pH in [5, 6, 7, 8, 9]:
for I in [0.0, 0.1, 0.2, 0.3, 0.4]:
dG0_f = pylab.zeros((Nc, 1))
bounds = []
for c in range(Nc):
cid = map_cid.get(cids[c], cids[c])
try:
pmap = gc.cid2PseudoisomerMap(cid)
dG0_f[c] = gc.pmap_to_dG0(pmap, pH, I, T)
except MissingCompoundFormationEnergy as e:
if (cid not in cids_with_missing_dG_f):
sys.stderr.write("Setting the dG0_f of C%05d to NaN because: %s\n"\
% (cid, str(e)))
cids_with_missing_dG_f.add(cid)
dG0_f[c] = pylab.nan
bounds = [
gc.kegg().cid2bounds.get(cid, (None, None)) for cid in cids
]
try:
_dG_f, _concentrations, pCr = find_pCr(S,
dG0_f,
c_mid=c_mid,
ratio=3.0,
bounds=bounds)
except LinProgNoSolutionException:
sys.stderr.write(
"M%05d: Pathway is theoretically infeasible\n" % mid)
pCr = None
try:
_dG_f, _concentrations, MTDF = find_mtdf(S,
dG0_f,
c_range=c_range,
bounds=bounds)
except LinProgNoSolutionException:
sys.stderr.write(
"M%05d: Pathway is theoretically infeasible\n" % mid)
MTDF = None
csv_output.writerow([mid, module_name, pH, I, T, pCr, MTDF])
f.close()