def setUp(self):
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE_GAMES_PP1)
self.reaction = self.simple.getReaction(PGA_CONS)
self.pga = self.reaction.reactants[0]
self.pga_ss = SOMStoichiometry(som=SOM([self.pga.molecule]),
stoichiometry=self.pga.stoichiometry)
self.rubp = self.reaction.products[0]
self.rubp_ss = SOMStoichiometry(som=SOM([self.rubp.molecule]),
stoichiometry=self.rubp.stoichiometry)
self.som_reaction = SOMReaction(reactants=[self.pga_ss],
products=[self.rubp_ss],
label=self.reaction.label)
def setUp(self):
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE3)
self.molecules = self.simple.molecules
self.soms = []
for mole in self.molecules:
self.soms.append(SOM({mole}))
def setUp(self):
self.simple = SimpleSBML()
self.simple.initialize(cn.TEST_FILE_GAMES_PP1)
self.reaction = self.simple.getReaction(PGA_CONS)
self.rubp = self.reaction.products[0]
self.rubl_ss = SOMStoichiometry(som=SOM([self.rubp.molecule]),
stoichiometry=self.rubp.stoichiometry)
def initializeSOMs(self, molecules):
"""
Create a list of one-molecule SOMs
:param list-Molecule molecules:
:return list-SOM soms:
"""
soms = []
for molecule in molecules:
if molecule.name == cn.EMPTYSET:
continue
else:
soms.append(SOM({molecule}))
return soms
def initializeSOMs(self, simple):
"""
Create a list of one-molecule SOMs
:param SimpleSBML simple:
:return list-SOM:
"""
soms = []
if type(simple) == SimpleSBML:
for molecule in simple.molecules:
if molecule.name == cn.EMPTYSET:
continue
else:
soms.append(SOM({molecule}))
return soms