本文整理汇总了Python中psamm.metabolicmodel.MetabolicModel.load_model方法的典型用法代码示例。如果您正苦于以下问题:Python MetabolicModel.load_model方法的具体用法?Python MetabolicModel.load_model怎么用?Python MetabolicModel.load_model使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类psamm.metabolicmodel.MetabolicModel
的用法示例。
在下文中一共展示了MetabolicModel.load_model方法的12个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction("rxn_1", parse_reaction("=> |A|"))
self.database.set_reaction("rxn_2", parse_reaction("(0.000001) |A| =>"))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
self.solver = cplex.Solver()
示例2: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
self._database.set_reaction('rxn_3', parse_reaction('B[e] => D[e]'))
self._database.set_reaction('rxn_4', parse_reaction('C[e] => E[e]'))
self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))
self._mm = MetabolicModel.load_model(
self._database, self._database.reactions)
self._assoc = {
'rxn_1': boolean.Expression('gene_1'),
'rxn_2': boolean.Expression('gene_2 or gene_3'),
'rxn_5': boolean.Expression('gene_3 and gene_4')
}
self._obj_reaction = 'rxn_6'
try:
self._solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
self._prob = fluxanalysis.FluxBalanceProblem(self._mm, self._solver)
示例3: test_load_model_with_reaction_subset
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def test_load_model_with_reaction_subset(self):
database = DictDatabase()
database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
database.set_reaction('rxn_2', parse_reaction('|B| => |C|'))
database.set_reaction('rxn_3', parse_reaction('|C| => |D|'))
model = MetabolicModel.load_model(database, {'rxn_1'})
self.assertEqual(set(model.reactions), {'rxn_1'})
示例4: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
# TODO use mock database instead of actual database
self.database = DictDatabase()
self.database.set_reaction("rxn_1", parse_reaction("=> (2) |A|"))
self.database.set_reaction("rxn_2", parse_reaction("|A| <=> |B|"))
self.database.set_reaction("rxn_3", parse_reaction("|A| => |D[e]|"))
self.database.set_reaction("rxn_4", parse_reaction("|A| => |C|"))
self.database.set_reaction("rxn_5", parse_reaction("|C| => |D[e]|"))
self.database.set_reaction("rxn_6", parse_reaction("|D[e]| =>"))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
示例5: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) A[c]'))
self.database.set_reaction('rxn_2', parse_reaction('A[c] <=> B[c]'))
self.database.set_reaction('rxn_3', parse_reaction('A[c] => D[e]'))
self.database.set_reaction('rxn_4', parse_reaction('A[c] => C[c]'))
self.database.set_reaction('rxn_5', parse_reaction('C[c] => D[e]'))
self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
示例6: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
model = MetabolicModel.load_model(self.database, self.database.reactions)
self.model = FlipableModelView(model)
示例7: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
self.solver = cplex.Solver()
示例8: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction(
'|A| + |B| => |C|'))
self.database.set_reaction('rxn_2', parse_reaction(
'|C| + |Z| => |A| + |B|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
self.solver = cplex.Solver()
示例9: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
self.database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
示例10: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_2',
parse_reaction('(0.000001) |A| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
示例11: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
self.database.set_reaction('rxn_7', parse_reaction('|E| => |F|'))
self.database.set_reaction('rxn_8', parse_reaction('|F| => |E|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver(integer=True)
except generic.RequirementsError:
self.skipTest('Unable to find an MILP solver for tests')
示例12: setUp
# 需要导入模块: from psamm.metabolicmodel import MetabolicModel [as 别名]
# 或者: from psamm.metabolicmodel.MetabolicModel import load_model [as 别名]
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
self.database.set_reaction('rxn_2', parse_reaction('|B| => |G|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |G|'))
self.database.set_reaction('rxn_4', parse_reaction('|B| => |H|'))
self.database.set_reaction('rxn_5', parse_reaction('|B| => |C| + |F|'))
self.database.set_reaction('rxn_6', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_7', parse_reaction('|E| <=> |D|'))
self.database.set_reaction('rxn_9', parse_reaction('|I| => |J|'))
self.database.set_reaction('rxn_10', parse_reaction('|J| => |K|'))
self.database.set_reaction('rxn_A', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_G', parse_reaction('|G| =>'))
self.database.set_reaction('rxn_E', parse_reaction('|E| =>'))
self.database.set_reaction(
'rxn_bio', parse_reaction('|D| + (2.5) |F| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')