示例#1
0
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)
示例#2
0
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)
示例#3
0
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)
示例#4
0
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)