def combine(fname, text_out):
modules = {}
for row in csv.DictReader(open(fname, 'r')):
options = modules.setdefault(row['Module'], {})
enzymes = options.setdefault(row['Option'], [])
reaction = Reaction.FromFormula(row['Formula'])
reaction.Balance(balance_water=False, exception_if_unknown=False)
enzymes.append((row['Enzyme'], row['Formula'], float(row['Flux'])))
l_mod = []
for module, options in sorted(modules.iteritems()):
l_opt = []
for option, enzymes in sorted(options.iteritems()):
l_opt.append(("%s%s" % (module, option), enzymes))
l_mod.append(l_opt)
for combination in itertools.product(*l_mod):
entry = '_'.join([mod for mod, enzymes in combination])
text_out.write('ENTRY %s\n' % entry)
text_out.write('THERMO merged\n')
firstrow = True
for mod, enzymes in combination:
for enzyme, formula, flux in enzymes:
if firstrow:
text_out.write('REACTION %-6s %s (x%g)\n' %
(enzyme, formula, flux))
firstrow = False
else:
text_out.write(' %-6s %s (x%g)\n' %
(enzyme, formula, flux))
text_out.write('///\n')
def GetForamtionEnergies(self, thermo):
self.db.CreateTable(self.GIBBS_ENERGY_TABLE_NAME, "equation TEXT, dG0 REAL, dGc REAL", drop_if_exists=True)
self.db.CreateIndex('gibbs_equation_idx', self.GIBBS_ENERGY_TABLE_NAME, 'equation', unique=True, drop_if_exists=True)
all_equations = set()
for row in self.db.Execute("SELECT distinct(equation) FROM %s" %
(self.EQUATION_TABLE_NAME)):
all_equations.add(str(row[0]))
from pygibbs.kegg import Kegg
kegg = Kegg.getInstance()
all_kegg_cids = set(kegg.get_all_cids())
for equation in all_equations:
try:
rxn = Reaction.FromFormula(equation)
if not rxn.get_cids().issubset(all_kegg_cids):
raise KeggNonCompoundException
rxn.Balance(balance_water=True, exception_if_unknown=True)
dG0 = thermo.GetTransfromedKeggReactionEnergies([rxn], conc=1)[0, 0]
dGc = thermo.GetTransfromedKeggReactionEnergies([rxn], conc=1e-3)[0, 0]
self.db.Insert(self.GIBBS_ENERGY_TABLE_NAME, [equation, dG0, dGc])
except (KeggParseException, KeggNonCompoundException, KeggReactionNotBalancedException):
self.db.Insert(self.GIBBS_ENERGY_TABLE_NAME, [equation, None, None])
self.db.Commit()
def GetC1Thermodynamics(
html_writer,
reaction_fname='../data/thermodynamics/c1_reaction_thermodynamics.csv'
):
html_writer.write("<h1>C1 thermodynamics</h1>\n")
dict_list = []
db_public = SqliteDatabase('../data/public_data.sqlite')
alberty = PsuedoisomerTableThermodynamics.FromDatabase(\
db_public, 'alberty_pseudoisomers', name='alberty')
alberty.AddPseudoisomer(101, nH=23, z=0, nMg=0, dG0=0)
reacthermo = ReactionThermodynamics(alberty, 'C1')
reacthermo.pH = 7
reacthermo.I = 0.1
reacthermo.T = 298.15
reacthermo.pMg = 14
c1_reactions = []
for row in csv.DictReader(open(reaction_fname, 'r')):
r = Reaction.FromFormula(row['formula'])
r.Balance(balance_water=False)
r.SetNames(row['enzyme'])
dG0_r_prime = float(row['dG0_r_prime'])
pH, I, pMg, T = [float(row[k]) for k in ['pH', 'I', 'pMg', 'T']]
reacthermo.AddReaction(r, dG0_r_prime, pH=pH, I=I, pMg=pMg, T=T)
c1_reactions.append(r)
row['formula'] = r.to_hypertext(show_cids=False)
dict_list.append(row)
html_writer.write_table(
dict_list, headers=['acronym', 'enzyme', 'formula', 'dG0_r_prime'])
reacthermo._Recalculate()
return reacthermo
def runBeta2Alpha(thermo, reactionList):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/Beta2Alpha.html'),
thermo=thermo,
max_solutions=None,
max_reactions=15,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
add_redox_reactions(pl)
for r in reactionList:
pl.add_reaction(Reaction.FromFormula(r, "Auto generate #%s" % hash(r)))
r = Reaction.FromFormula("C00099 => C01401")
pl.find_path("Beta2Alpha", r)
def example_formate(thermo, product_cid=22, co2_conc=1e-5):
co2_hydration = Reaction.FromFormula("C00011 + C00001 => C00288")
co2_hydration_dG0_prime = float(thermo.GetTransfromedKeggReactionEnergies([co2_hydration]))
carbonate_conc = co2_conc * np.exp(-co2_hydration_dG0_prime / (R*default_T))
thermo.bounds[11] = (co2_conc, co2_conc)
thermo.bounds[288] = (carbonate_conc, carbonate_conc)
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=20,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl, free_ATP_hydrolysis=True)
add_redox_reactions(pl, NAD_only=False)
pl.delete_reaction(134) # formate:NADP+ oxidoreductase
pl.delete_reaction(519) # Formate:NAD+ oxidoreductase
pl.delete_reaction(24) # Rubisco
pl.delete_reaction(581) # L-serine:NAD+ oxidoreductase (deaminating)
pl.delete_reaction(220) # L-serine ammonia-lyase
pl.delete_reaction(13) # glyoxylate carboxy-lyase (dimerizing; tartronate-semialdehyde-forming)
pl.delete_reaction(585) # L-Serine:pyruvate aminotransferase
pl.delete_reaction(1440) # D-Xylulose-5-phosphate:formaldehyde glycolaldehydetransferase
pl.delete_reaction(5338) # 3-hexulose-6-phosphate synthase
pl.add_reaction(Reaction.FromFormula("C06265 => C00011", name="CO2 uptake"))
pl.add_reaction(Reaction.FromFormula("C06265 => C00288", name="carbonate uptake"))
pl.add_reaction(Reaction.FromFormula("C06265 => C00058", name="formate uptake"))
r = Reaction.FromFormula("5 C06265 + C00058 => C%05d" % product_cid) # at least one formate to product
#r.Balance()
kegg = Kegg.getInstance()
pl.find_path("formate to %s" % kegg.cid2name(product_cid), r)
def runPathologic(thermo, reactionList):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/mog_finder.html'),
thermo=thermo,
max_solutions=None,
max_reactions=15,
maximal_dG=-3.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
add_redox_reactions(pl)
for r in reactionList:
pl.add_reaction(Reaction.FromFormula(r, "Auto generate #%s" % hash(r)))
pl.delete_reaction(134)
pl.delete_reaction(344)
pl.delete_reaction(575)
pl.delete_reaction(212)
#pl.add_reaction(Reaction.FromFormula('C00149 + C00006 <=> C00036 + C00005 + C00080',
# 'malate + NADP+ = oxaloacetate + NADPH',343))
#pl.add_reaction(Reaction.FromFormula('C00222 + C00010 + C00006 <=> C00083 + C00005',
# 'malonate-semialdehyde + CoA + NADP+ = malonyl-CoA + NADPH',740))
r = Reaction.FromFormula("2 C00288 => C00048")
pl.find_path("MOG_finder", r)
def example_reductive(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=15,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
add_redox_reactions(pl)
r = Reaction.FromFormula("3 C00011 => C00022")
#r.Balance()
pl.find_path("reductive", r)
def example_oxidative(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=10,
maximal_dG=0,
thermodynamic_method=OptimizationMethods.MAX_TOTAL,
update_file=None)
add_cofactor_reactions(pl)
add_redox_reactions(pl, NAD_only=False)
r = Reaction.FromFormula("C00022 => 3 C00011")
#r.Balance()
pl.find_path("oxidative", r)
def example_lower_glycolysis(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=8,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
add_redox_reactions(pl)
#r = Reaction.FromFormula("C00003 + C00118 + C00001 => C00022 + C00004 + C00009")
r = Reaction.FromFormula("C00118 => C00022")
#r.Balance()
pl.find_path("GAP => PYR", r)
def example_rpi_bypass(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=10,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
#add_redox_reactions(pl)
pl.delete_reaction(1056) # ribose-phosphate isomerase
pl.delete_reaction(1081) # ribose isomerase
r = Reaction.FromFormula("C00117 => C01182")
#r.Balance()
pl.find_path("rpi_bypass", r)
def example_three_acetate(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=20,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl)
#add_redox_reactions(pl)
pl.delete_reaction(761) # F6P + Pi = E4P + acetyl-P
pl.delete_reaction(1621) # X5P + Pi = GA3P + acetyl-P
r = Reaction.FromFormula("C00031 => 3 C00033")
#r.Balance()
pl.find_path("three_acetate", r)
def example_glycolysis(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=15,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
add_cofactor_reactions(pl, free_ATP_hydrolysis=False)
ban_toxic_compounds(pl)
#add_carbon_counts(pl)
#r = Reaction.FromFormula("C00031 => 6 C06265")
r = Reaction.FromFormula("C00031 + 3 C00008 => 2 C00186 + 3 C00002")
#r.Balance()
pl.find_path("GLC => 2 LAC, 3 ATP, No methylglyoxal", r)
def example_glucose_to_ethanol_and_formate(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=15,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
#add_cofactor_reactions(pl)
#add_XTP_reactions(pl, '=>')
#add_redox_reactions(pl)
#pl.delete_reaction(761) # F6P + Pi = E4P + acetyl-P
#pl.delete_reaction(1621) # X5P + Pi = GA3P + acetyl-P
r = Reaction.FromFormula("2 C00031 + 3 C00001 => 6 C00058 + 3 C00469")
r.Balance()
pl.find_path("glucose_to_ethanol_and_formate", r)
def example_more_than_two_pyruvate(thermo):
pl = Pathologic(db=SqliteDatabase('../res/gibbs.sqlite', 'r'),
public_db=SqliteDatabase('../data/public_data.sqlite'),
html_writer=HtmlWriter('../res/pathologic.html'),
thermo=thermo,
max_solutions=None,
max_reactions=20,
maximal_dG=0.0,
thermodynamic_method=OptimizationMethods.GLOBAL,
update_file=None)
#add_cofactor_reactions(pl)
#add_XTP_reactions(pl, '=>')
#add_redox_reactions(pl)
#pl.delete_reaction(761) # F6P + Pi = E4P + acetyl-P
#pl.delete_reaction(1621) # X5P + Pi = GA3P + acetyl-P
r = Reaction.FromFormula("3 C00031 + 3 C00011 + C00003 => 7 C00022 + 3 C00001 + C00004")
r.Balance()
pl.find_path("more_than_two_pyr", r)
def FromCsv(csv_fname, formation_thermo):
data = []
for row in csv.DictReader(open(csv_fname, 'r')):
r = Reaction.FromFormula(row['formula'])
r.Balance(balance_water=False)
r.SetNames(row['enzyme'])
dG0_r_prime = float(row['dG0_r_prime'])
pH = float(row['pH'])
I = float(row['I'])
pMg = float(row.get('pMg', '10'))
T = float(row['T'])
data.append((r, dG0_r_prime, pH, I, pMg, T))
reacthermo = ReactionThermodynamics(formation_thermo)
reacthermo.SetConditions(pH=pH, I=I, pMg=pMg, T=T)
for r, dG0, pH, I, pMg, T in data:
reacthermo.AddReaction(r, dG0, pH=pH, I=I, pMg=pMg, T=T)
reacthermo._Recalculate()
return reacthermo
def GetStoichiometries(self):
self.db.CreateTable(self.STOICHIOMETRY_TABLE_NAME, "equation TEXT, compound TEXT, coefficient REAL", drop_if_exists=True)
self.db.CreateIndex('stoichiometry_equation_idx', self.STOICHIOMETRY_TABLE_NAME, 'equation', unique=False, drop_if_exists=True)
self.db.CreateIndex('stoichiometry_compound_idx', self.STOICHIOMETRY_TABLE_NAME, 'compound', unique=False, drop_if_exists=True)
all_kegg_reactions = []
all_equations = []
for row in self.db.Execute("SELECT distinct(equation) FROM %s" %
(self.EQUATION_TABLE_NAME)):
try:
r = Reaction.FromFormula(str(row[0]))
all_equations.append(str(row[0]))
all_kegg_reactions.append(r)
except (KeggParseException, KeggNonCompoundException):
pass
for i, equation in enumerate(all_equations):
for compound, coefficient in all_kegg_reactions[i].iteritems():
self.db.Insert(self.STOICHIOMETRY_TABLE_NAME,
[equation, "cpd:C%05d" % compound, coefficient])
self.db.Commit()
def add_carbon_counts(pl):
"""Add reactions counting carbons in various
plausible fermentation products.
"""
reactions = [
#Reaction.FromFormula("C00246 => 4 C06265", name="Butyrate makeup"),
#Reaction.FromFormula("C02632 => 4 C06265", name="Isobutyrate makeup"),
Reaction.FromFormula("C00042 => 4 C06265", name="Succinate makeup"),
#Reaction.FromFormula("C00022 => 3 C06265", name="Pyruvate makeup"),
#Reaction.FromFormula("C00163 => 3 C06265", name="Propionate makeup"),
#Reaction.FromFormula("C01013 => 3 C06265", name="3-hydroxypropionate makeup"),
Reaction.FromFormula("C00186 => 3 C06265", name="Lactate makeup"),
Reaction.FromFormula("C00033 => 2 C06265", name="Acetate makeup"),
Reaction.FromFormula("C00469 => 2 C06265", name="Ethanol makeup"),
Reaction.FromFormula("C00058 => 1 C06265", name="Formate makeup"),
Reaction.FromFormula("C00011 => 1 C06265", name="CO2 makeup"),
]
for rxn in reactions:
pl.add_reaction(rxn)
"""
row['formula'] = r.to_hypertext(show_cids=False)
dict_list.append(row)
html_writer.write_table(
dict_list, headers=['acronym', 'enzyme', 'formula', 'dG0_r_prime'])
reacthermo._Recalculate()
return reacthermo
if __name__ == "__main__":
html_writer = HtmlWriter('../res/c1_thermodynamics.html')
reacthermo = GetC1Thermodynamics(html_writer)
html_writer.close()
formulas = [
"C02051 + C00004 => C02972 + C00003",
"C00143 + C00037 + C00001 => C00101 + C00065",
"C00288 + 2 C00138 + C00862 => 2 C00001 + 2 C00139 + C01001",
"C00101 + C00003 => C00415 + C00004"
]
reactions = []
for f in formulas:
r = Reaction.FromFormula(f)
r.Balance()
reactions.append(r)
print reacthermo.GetTransfromedKeggReactionEnergies(reactions)
def add_redox_reactions(pl, NAD_only=False):
# all electron transfer reactions
pl.add_cofactor_reaction(Reaction.FromFormula("C00003 <=> C00004", name='NAD redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00006 <=> C00005", name='NADP redox'))
if not NAD_only:
pl.add_cofactor_reaction(Reaction.FromFormula("C00016 <=> C01352", name='FAD redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00138 <=> C00139", name='ferredoxin redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00030 <=> C00028", name='acceptor/donor redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00125 <=> C00126", name='ferricytochrome c redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00996 <=> C00999", name='ferricytochrome b5 redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C01070 <=> C01071", name='ferricytochrome c-553 redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C05906 <=> C01617", name='leucocyanidin redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00343 <=> C00342", name='thioredoxin disulfide redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C03648 <=> C00974", name='cis-3,4-Leucopelargonidin redox'))
pl.add_cofactor_reaction(Reaction.FromFormula("C05684 <=> C01528", name='selenide redox'))
else:
pl.ban_compound(16) # FAD(ox)
pl.ban_compound(1352) # FAD(red)
pl.ban_compound(138) # ferredoxin (ox)
pl.ban_compound(139) # ferredoxin (red)
pl.ban_compound(30) # acceptor
pl.ban_compound(28) # donor
pl.ban_compound(125) # ferricytochrome c (ox)
pl.ban_compound(126) # ferricytochrome c (red)
pl.ban_compound(996) # ferricytochrome b5 (ox)
pl.ban_compound(999) # ferricytochrome b5 (red)
pl.ban_compound(1070) # ferricytochrome c-553 (ox)
pl.ban_compound(1071) # ferricytochrome c-553 (red)
pl.ban_compound(5906) # leucocyanidin (ox)
pl.ban_compound(1617) # leucocyanidin (red)
pl.ban_compound(343) # thioredoxin disulfide (ox)
pl.ban_compound(342) # thioredoxin disulfide (red)
pl.ban_compound(3648) # cis-3,4-Leucopelargonidin (ox)
pl.ban_compound(974) # cis-3,4-Leucopelargonidin (red)
pl.ban_compound(5684) # selenide (ox)
pl.ban_compound(1528) # selenide (red)
def add_XTP_reactions(pl, direction='<=>'):
"""
Adds phosphorylated nucleotide reactions, which ignore thermodynamics
and phosphate balance constraints.
The direction arguments can be set to allow them only in one direction.
For example, a useful scenario would be to force a pathway
not to consume ATP without constraining it for zero ATP production.
"""
pl.add_cofactor_reaction(Reaction.FromFormula("C00002 %s C00008" % direction, name='ATP to ADP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00002 %s C00020" % direction, name='ATP to AMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00008 %s C00020" % direction, name='ADP to AMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00131 %s C00206" % direction, name='dATP to dADP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00131 %s C00360" % direction, name='dATP to dAMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00206 %s C00360" % direction, name='dADP to dAMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00081 %s C00104" % direction, name='ITP to IDP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00081 %s C00130" % direction, name='ITP to IMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00104 %s C00130" % direction, name='IDP to IMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00044 %s C00035" % direction, name='GTP to GDP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00044 %s C00144" % direction, name='GTP to GMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00035 %s C00144" % direction, name='GDP to GMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00063 %s C00112" % direction, name='CTP to CDP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00063 %s C00055" % direction, name='CTP to CMP'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00112 %s C00055" % direction, name='CDP to CMP'))
def add_cofactor_reactions(pl):
pl.add_cofactor_reaction(Reaction.FromFormula("C00001 <=> null", name='Free H2O'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00009 <=> null", name='Free Pi'))
pl.add_cofactor_reaction(Reaction.FromFormula("C00013 <=> null", name='Free PPi'))
ugc.init()
if args.test:
r_list = []
# r_list += [Reaction.FromFormula("C00002 + C00001 = C00008 + C00009")]
# r_list += [Reaction.FromFormula("C00036 + C00024 = C00022 + C00083")]
# r_list += [Reaction.FromFormula("C00036 + C00100 = C00022 + C00683")]
# r_list += [Reaction.FromFormula("C01013 + C00010 + C00002 = C05668 + C00020 + C00013")]
# r_list += [Reaction.FromFormula("C00091 + C00005 = C00232 + C00010 + C00006")]
# r_list += [Reaction.FromFormula("C00002 + C00493 = C00008 + C03175")]
# r_list += [Reaction.FromFormula("C00243 + C00125 = C05403 + C00126")]
# r_list += [Reaction.FromFormula("2 C00206 = C00360 + C00131")]
# r_list += [Reaction.FromFormula("C04171 + C00003 = C00196 + C00080 + C00004")]
# r_list += [Reaction.FromFormula("C00036 + C00044 = C00011 + C00035 + C00074")]
r_list += [
Reaction.FromFormula(
"C00001 + C00022 + C17569 = C00011 + C00033 + C00390")
]
kegg = Kegg.getInstance()
S, cids = kegg.reaction_list_to_S(r_list)
dG0_prime = ugc.GetTransfromedReactionEnergies(S, cids, pH=7.0, I=0.15)
ln_conc = np.matrix(np.ones((1, S.shape[0]))) * np.log(0.001)
if 1 in cids:
ln_conc[0,
cids.index(1)] = 0 # H2O should have a concentration of 1
RT = R * default_T
dGc_prime = dG0_prime + RT * ln_conc * S
for i in xrange(len(r_list)):
r_list[i].Balance()
plt.legend(['value in iAF1260', 'UGCM estimation'])
plt.savefig(FIG_FNAME + "_fig3.svg", fmt='.svg')
db = SqliteDatabase('../res/gibbs.sqlite', 'w')
ugc = UnifiedGroupContribution(db)
ugc.LoadGroups(True)
ugc.LoadObservations(True)
ugc.LoadGroupVectors(True)
ugc.LoadData(True)
ugc.init()
r_list = []
#r_list += [Reaction.FromFormula("C00036 + C00044 = C00011 + C00035 + C00074")]
#r_list += [Reaction.FromFormula("C00003 + C00037 + C00101 = C00004 + C00011 + C00014 + C00080 + C00143")] # glycine synthase
r_list += [
Reaction.FromFormula(
"C00001 + C00002 + C00064 + C04376 => C00008 + C00009 + C00025 + C04640"
)
]
#r_list += [Reaction.FromFormula("C00001 + 2 C00002 + C00064 + C00288 <=> 2 C00008 + C00009 + C00025 + C00169")]
kegg = Kegg.getInstance()
S, cids = kegg.reaction_list_to_S(r_list)
logging.getLogger('').setLevel(logging.DEBUG)
dG0_prime = ugc.GetTransfromedReactionEnergies(S,
cids,
pH=pH,
I=I,
pMg=pMg,
T=T)
def analyze(prefix, thermo):
kegg_file = ParsedKeggFile.FromKeggFile('../data/thermodynamics/%s.txt' %
prefix)
html_writer = HtmlWriter('../res/%s.html' % prefix)
co2_hydration = Reaction.FromFormula("C00011 + C00001 => C00288")
#pH_vec = np.arange(5, 9.001, 0.5)
#pH_vec = np.array([6, 7, 8])
pH_vec = np.array(
[6, 7,
8]) # this needs to be fixed so that the txt file will set the pH
#co2_conc_vec = np.array([1e-5, 1e-3])
co2_conc_vec = np.array([1e-5])
data_mat = []
override_bounds = {}
for pH in pH_vec.flat:
co2_hydration_dG0_prime = float(
thermo.GetTransfromedKeggReactionEnergies([co2_hydration], pH=pH))
for co2_conc in co2_conc_vec.flat:
carbonate_conc = co2_conc * np.exp(-co2_hydration_dG0_prime /
(R * default_T))
#print "[CO2] = %g, [carbonate] = %g, pH = %.1f, I = %.2fM" % (co2_conc, carbonate_conc, pH, I)
override_bounds[11] = (co2_conc, co2_conc)
override_bounds[288] = (carbonate_conc, carbonate_conc)
section_prefix = 'pH_%g_CO2_%g' % (pH, co2_conc * 1000)
section_title = 'pH = %g, [CO2] = %g mM' % (pH, co2_conc * 1000)
html_writer.write('<h1 id="%s_title">%s</h1>\n' %
(section_prefix, section_title))
html_writer.write_ul([
'<a href="#%s_tables">Individual result tables</a>' %
section_prefix,
'<a href="#%s_summary">Summary table</a>' % section_prefix,
'<a href="#%s_figure">Summary figure</a>' % section_prefix
])
data, labels = pareto(kegg_file,
html_writer,
thermo,
pH=pH,
section_prefix=section_prefix,
balance_water=True,
override_bounds=override_bounds)
data_mat.append(data)
data_mat = np.array(data_mat)
if data_mat.shape[0] == 1:
pareto_fig = plt.figure(figsize=(6, 6), dpi=90)
plt.plot(data_mat[0, :, 0], data_mat[0, :, 1], '.', figure=pareto_fig)
for i in xrange(data_mat.shape[1]):
if data[i, 1] < 0:
color = 'grey'
else:
color = 'black'
plt.text(data_mat[0, i, 0],
data_mat[0, i, 1],
labels[i],
ha='left',
va='bottom',
fontsize=8,
color=color,
figure=pareto_fig)
plt.title(section_title, figure=pareto_fig)
else:
pareto_fig = plt.figure(figsize=(10, 10), dpi=90)
for i in xrange(data_mat.shape[1]):
plt.plot(data_mat[:, i, 0],
data_mat[:, i, 1],
'-',
figure=pareto_fig)
plt.text(data_mat[0, i, 0],
data_mat[0, i, 1],
'%g' % pH_vec[0],
ha='center',
fontsize=6,
color='black',
figure=pareto_fig)
plt.text(data_mat[-1, i, 0],
data_mat[-1, i, 1],
'%g' % pH_vec[-1],
ha='center',
fontsize=6,
color='black',
figure=pareto_fig)
plt.legend(labels, loc='upper right')
plt.title('Pareto', figure=pareto_fig)
plt.xlabel('Optimal Energetic Efficiency [kJ/mol]', figure=pareto_fig)
plt.ylabel('Optimized Distributed Bottleneck [kJ/mol]', figure=pareto_fig)
html_writer.write('<h2 id="%s_figure">Summary figure</h1>\n' %
section_prefix)
# plot the Pareto figure showing all values (including infeasible)
html_writer.embed_matplotlib_figure(pareto_fig, name=prefix + '_0')
# set axes to hide infeasible pathways and focus on feasible ones
pareto_fig.axes[0].set_xlim(None, 0)
pareto_fig.axes[0].set_ylim(0, None)
html_writer.embed_matplotlib_figure(pareto_fig, name=prefix + '_1')
html_writer.close()