Python ConcreteModel.EpitopeConsConst方法代码示例

# 需要导入模块: from pyomo.environ import ConcreteModel [as 别名]
# 或者: from pyomo.environ.ConcreteModel import EpitopeConsConst [as 别名]

#.........这里部分代码省略.........
        res_df = results.xs(results.index.values[0][1], level="Method")
        res_df = res_df[res_df.apply(lambda x: any(x[a] > self.__thresh.get(a.name, -float("inf"))
                                                   for a in res_df.columns), axis=1)]

        for tup in res_df.itertuples():
            p = tup[0]
            seq = str(p)
            peps[seq] = p
            for a, s in itr.izip(res_df.columns, tup[1:]):
                if method in ["smm", "smmpmbec", "arb", "comblibsidney"]:
                    try:
                        thr = min(1., max(0.0, 1.0 - math.log(self.__thresh.get(a.name),
                                                      50000))) if a.name in self.__thresh else -float("inf")
                    except:
                        thr = 0

                    if s >= thr:
                        alleles_I.setdefault(a.name, set()).add(seq)
                    imm[seq, a.name] = min(1., max(0.0, 1.0 - math.log(s, 50000)))
                else:
                    if s > self.__thresh.get(a.name, -float("inf")):
                        alleles_I.setdefault(a.name, set()).add(seq)
                    imm[seq, a.name] = s

            prots = set(pr for pr in p.get_all_proteins())
            cons[seq] = len(prots)
            for prot in prots:
                variations.append(prot.gene_id)
                epi_var.setdefault(prot.gene_id, set()).add(seq)
        self.__peptideSet = peps

        #calculate conservation
        variations = set(variations)
        total = len(variations)
        for e, v in cons.iteritems():
            try:
                cons[e] = v / total
            except ZeroDivisionError:
                cons[e] = 1
        model = ConcreteModel()

        #set definition
        model.Q = Set(initialize=variations)

        model.E = Set(initialize=set(peps.keys()))

        model.A = Set(initialize=alleles_I.keys())
        model.E_var = Set(model.Q, initialize=lambda mode, v: epi_var[v])
        model.A_I = Set(model.A, initialize=lambda model, a: alleles_I[a])


        #parameter definition
        model.k = Param(initialize=self.__k, within=PositiveIntegers, mutable=True)
        model.p = Param(model.A, initialize=lambda model, a: probs[a])

        model.c = Param(model.E, initialize=lambda model, e: cons[e],mutable=True)

        #threshold parameters
        model.i = Param(model.E, model.A, initialize=lambda model, e, a: imm[e, a])
        model.t_allele = Param(initialize=0, within=NonNegativeIntegers, mutable=True)
        model.t_var = Param(initialize=0, within=NonNegativeIntegers, mutable=True)
        model.t_c = Param(initialize=0.0, within=NonNegativeReals, mutable=True)

        # Variable Definition
        model.x = Var(model.E, within=Binary)
        model.y = Var(model.A, within=Binary)
        model.z = Var(model.Q, within=Binary)

        # Objective definition
        model.Obj = Objective(
            rule=lambda model: sum(model.x[e] * sum(model.p[a] * model.i[e, a] for a in model.A) for e in model.E),
            sense=maximize)


        #Obligatory Constraint (number of selected epitopes)
        model.NofSelectedEpitopesCov = Constraint(rule=lambda model: sum(model.x[e] for e in model.E) <= model.k)

        #optional constraints (in basic model they are disabled)
        model.IsAlleleCovConst = Constraint(model.A,
                                            rule=lambda model, a: sum(model.x[e] for e in model.A_I[a]) >= model.y[a])
        model.MinAlleleCovConst = Constraint(rule=lambda model: sum(model.y[a] for a in model.A) >= model.t_allele)

        model.IsAntigenCovConst = Constraint(model.Q,
                                             rule=lambda model, q: sum(model.x[e] for e in model.E_var[q]) >= model.z[q])
        model.MinAntigenCovConst = Constraint(rule=lambda model: sum(model.z[q] for q in model.Q) >= model.t_var)
        model.EpitopeConsConst = Constraint(model.E,
                                            rule=lambda model, e: (1 - model.c[e]) * model.x[e] <= 1 - model.t_c)

        #generate instance
        self.instance = model
        if self.__verbosity > 0:
            print "MODEL INSTANCE"
            self.instance.pprint()

        #constraints
        self.instance.IsAlleleCovConst.deactivate()
        self.instance.MinAlleleCovConst.deactivate()
        self.instance.IsAntigenCovConst.deactivate()
        self.instance.MinAntigenCovConst.deactivate()
        self.instance.EpitopeConsConst.deactivate()

# 需要导入模块: from pyomo.environ import ConcreteModel [as 别名]
# 或者: from pyomo.environ.ConcreteModel import EpitopeConsConst [as 别名]

#.........这里部分代码省略.........
                result = []
                for s1,s2 in itr.combinations(model.E,2):
                    if s1 != s2:
                        if s1 in s2 or s2 in s1:
                            result.append((s1,s2))
                        m = [[0] * (1 + len(s2)) for i in xrange(1 + len(s1))]
                        longest, x_longest = 0, 0
                        for x in xrange(1, 1 + len(s1)):
                            for y in xrange(1, 1 + len(s2)):
                                if s1[x - 1] == s2[y - 1]:
                                    m[x][y] = m[x - 1][y - 1] + 1
                                    if m[x][y] > longest:
                                        longest = m[x][y]
                                        x_longest = x
                                else:
                                    m[x][y] = 0
                        if len(s1[x_longest - longest: x_longest]) >= overlap:
                            result.append((s1,s2))
                return set(result)
            model.O = Set(dimen=2, initialize=longest_common_substring)

        # parameter definition
        model.k = Param(initialize=self.__k, within=PositiveIntegers, mutable=True)
        model.k_taa = Param(initialize=self.__k_taa, within=NonNegativeIntegers, mutable=True)
        model.p = Param(model.A, initialize=lambda model, a: max(0, math.log(probs[a]+0.001,2)))
        model.c = Param(model.E, initialize=lambda model, e: cons[e],mutable=True)
        model.sigma = Param (model. E, model.A, initialize=lambda model, e, a: uncertainty.get((e,a), 0))
        model.i = Param(model.E, model.A, initialize=lambda model, e, a: imm[e, a])
        model.t_allele = Param(initialize=0, within=NonNegativeIntegers, mutable=True)
        model.t_var = Param(initialize=0, within=NonNegativeIntegers, mutable=True)
        model.t_c = Param(initialize=0.0, within=NonNegativeReals, mutable=True)
        model.abd = Param(model.Q, initialize=lambda model, g: max(0, math.log(expression.get(g, 2)+0.001, 2)))
        model.eps1 = Param(initialize=1e6, mutable=True)
        model.eps2 = Param(initialize=1e6, mutable=True)

        # variable Definition
        model.x = Var(model.E, within=Binary)
        model.y = Var(model.A, within=Binary)
        model.z = Var(model.Q, within=Binary)

        # objective definition
        model.Obj1 = Objective(
            rule=lambda model: -sum(model.x[e] * sum(model.abd[g] for g in model.G[e])
                             * sum(model.p[a] * model.i[e, a] for a in model.A) for e in model.E),
            sense=minimize)
        model.Obj2 = Objective(
            rule=lambda model: sum(model.x[e]*sum(model.sigma[e,a] for a in model.A) for e in model.E),
            sense=minimize)

        # constraints
        # obligatory Constraint (number of selected epitopes)
        model.NofSelectedEpitopesCov1 = Constraint(rule=lambda model: sum(model.x[e] for e in model.E) >= model.k)
        model.NofSelectedEpitopesCov2 = Constraint(rule=lambda model: sum(model.x[e] for e in model.E) <= model.k)
        model.NofSelectedTAACov = Constraint(rule=lambda model: sum(model.x[e] for e in model.TAA) <= model.k_taa)

        # optional constraints (in basic model they are disabled)
        model.IsAlleleCovConst = Constraint(model.A,
                                            rule=lambda model, a: sum(model.x[e] for e in model.A_I[a]) >= model.y[a])

        model.MinAlleleCovConst = Constraint(rule=lambda model: sum(model.y[a] for a in model.A) >= model.t_allele)

        model.IsAntigenCovConst = Constraint(model.Q,
                                             rule=lambda model, q: sum(model.x[e] for e in model.E_var[q]) >= model.z[q])
        model.MinAntigenCovConst = Constraint(rule=lambda model: sum(model.z[q] for q in model.Q) >= model.t_var)

        model.EpitopeConsConst = Constraint(model.E,
                                            rule=lambda model, e: (1 - model.c[e]) * model.x[e] <= 1 - model.t_c)

        if overlap > 0:
            model.OverlappingConstraint = Constraint(model.O, rule=lambda model, e1, e2: model.x[e1]+model.x[e2] <= 1)

        # constraints for Pareto optimization
        model.ImmConst = Constraint(rule=lambda model: sum(model.x[e] * sum(model.abd[g] for g in model.G[e])
                                                       * sum(model.p[a] * model.i[e, a]
                                                       for a in model.A) for e in model.E) <= model.eps1)
        model.UncertaintyConst = Constraint(rule=lambda model:sum(model.x[e]*sum(model.sigma[e,a]
                                                                                 for a in model.A)
                                                                  for e in model.E) <= model.eps2)
        self.__objectives = [model.Obj1, model.Obj2]
        self.__constraints = [model.UncertaintyConst, model.ImmConst]
        self.__epsilons = [model.eps2, model.eps1]

        # include constraint
        model.IncludeEpitopeConstraint = Constraint(model.Include, rule=lambda model, e: model.x[e] >= 1)

        # generate instance
        self.instance = model
        if self.__verbosity > 0:
            print "MODEL INSTANCE"
            self.instance.pprint()

        # constraints
        self.instance.Obj2.deactivate()
        self.instance.ImmConst.deactivate()
        self.instance.UncertaintyConst.deactivate()
        self.instance.IsAlleleCovConst.deactivate()
        self.instance.MinAlleleCovConst.deactivate()
        self.instance.IsAntigenCovConst.deactivate()
        self.instance.MinAntigenCovConst.deactivate()
        self.instance.EpitopeConsConst.deactivate()