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_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 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_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 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_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 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_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_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)