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 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 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 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)