def testAppend(self):
if IGNORE_TEST:
return
moiety2 = Moiety(MOIETY_NAME2)
molecule = Molecule(MOIETY_NAME1)
new_molecule = molecule.append(moiety2)
self.assertEqual(new_molecule.name, Molecule(MOLECULE_NAME).name)
def testDifference(self):
if IGNORE_TEST:
return
df = self.comparator.difference()
self.assertLess(df.loc[MOIETY_NAME1].tolist()[0], 0)
#
comparator = MoietyComparator(self.molecules1,
self.molecules2,
implicits=[MOIETY_NAME1])
df = comparator.difference()
self.assertFalse(MOIETY_NAME1 in df.index)
#
config._config_dict[cn.CFG_PROCESS_BOUNDARY_REACTIONS] = False
molecules1 = [
MoleculeStoichiometry(Molecule(n), 0)
for n in MOLECULE_NAME_SET[:3]
]
comparator = MoietyComparator(molecules1, self.molecules2)
df = comparator.difference()
self.assertEqual(df[df.columns[0]].sum(), 0)
#
config._config_dict[cn.CFG_PROCESS_BOUNDARY_REACTIONS] = True
molecules1 = [
MoleculeStoichiometry(Molecule(n), 0)
for n in MOLECULE_NAME_SET[:3]
]
comparator = MoietyComparator(molecules1, self.molecules2)
df = comparator.difference()
self.assertNotEqual(df[df.columns[0]].sum(), 0)
def testCountMoietys(self):
if IGNORE_TEST:
return
moiety_stoich = MoietyStoichiometry(Molecule(MOIETY_NAME1), NUM1)
mole_stoich = MoleculeStoichiometry(Molecule(str(moiety_stoich)), NUM2)
df = mole_stoich.countMoietys()
self.assertEqual(df.columns.tolist(), [cn.VALUE])
expected = NUM1 * NUM2
trues = [expected == n for n in df[cn.VALUE]]
def testMoietyStoichiometrys(self):
if IGNORE_TEST:
return
config.setConfiguration(TEST_CFG_FILE)
#
molecule = Molecule("Glu6P")
self.assertEqual(molecule.moiety_stoichiometrys[0].moiety.name, "Glu")
#
molecule = Molecule("ATP")
self.assertEqual(len(molecule.moiety_stoichiometrys), 2)
def setUp(self):
self.molecules1 = [
MoleculeStoichiometry(Molecule(n), NUM1)
for n in MOLECULE_NAME_SET[:3]
]
self.molecules2 = [
MoleculeStoichiometry(Molecule(n), NUM2)
for n in MOLECULE_NAME_SET[3:]
]
self.comparator = MoietyComparator(self.molecules1, self.molecules2)
self.config_dict = copy.deepcopy(config._config_dict)
def testCountMoietys2(self):
if IGNORE_TEST:
return
m_ss = [
MoleculeStoichiometry(Molecule("A_P_P_P"), 1),
MoleculeStoichiometry(Molecule("A__P_3"), 1),
]
dfs = []
for m_s in m_ss:
dfs.append(m_s.countMoietys())
self.assertTrue(dfs[0].equals(dfs[1]))
def testGetMoietys(self):
if IGNORE_TEST:
return
m_s1 = MoietyStoichiometry(Moiety(MOIETY_NAME1), NUM1)
m_s2 = MoietyStoichiometry(MOIETY_NAME2, NUM2)
m_s3 = MoietyStoichiometry(MOIETY_NAME1, NUM2)
molecule = Molecule(str(m_s1))
molecule = molecule.append(Moiety(str(m_s2)))
moietys = molecule.getMoietys()
expected = [Moiety(MOIETY_NAME1), Moiety(MOIETY_NAME2)]
for moiety in moietys:
self.assertTrue(any([moiety.isEqual(e) for e in expected]))
def getMolecules(libsbml_reaction, func):
"""
Constructs molecules for the species returned by function.
:param Function func: gets libsbml.SpeciesReference
:return list-MoleculeStoichiometry:
"""
species = func(libsbml_reaction)
molecule_stoichiometrys = []
for spc in species:
molecule = Molecule.getMolecule(spc.getSpecies())
if molecule is None:
molecule = Molecule(spc.getSpecies())
molecule_stoichiometrys.append(
MoleculeStoichiometry(molecule, spc.getStoichiometry()))
return molecule_stoichiometrys
def testConstructor(self):
if IGNORE_TEST:
return
molecule = Molecule(MOLECULE_NAME)
m_s = MoleculeStoichiometry(molecule, NUM1)
self.assertTrue(m_s.molecule.isEqual(molecule))
self.assertEqual(m_s.stoichiometry, NUM1)
def testGetMolecules(self):
if IGNORE_TEST:
return
names = ["a", "b", "c"]
full_names = list(names)
full_names.extend(names)
m_ss = [MoleculeStoichiometry(Molecule(n), NUM1) for n in full_names]
molecules = MoleculeStoichiometry.getMolecules(m_ss)
self.assertEqual(len(molecules), len(names))
def testCountMoietysInCollection(self):
if IGNORE_TEST:
return
m_ss = [
MoleculeStoichiometry(Molecule(n), NUM1)
for n in MOLECULE_NAME_SET[:3]
]
df = MoleculeStoichiometry.countMoietysInCollection(m_ss)
indexes = df.index.tolist()
self.assertEqual(len(indexes), len(set(indexes)))
def testExtractMoietyStoichiometrys(self):
if IGNORE_TEST:
return
for expected, strings in MOLECULE_STOICHIOMETRY_STGS.items():
moietys = list(set([e[0] for e in expected]))
moietys.sort()
m_ss = [MoietyStoichiometry(m, 1) for m in moietys]
for stg in strings:
result = Molecule.getMoietyStoichiometrys(stg)
trues = [x.isEqual(y) for x, y in zip(result, m_ss)]
self.assertTrue(all(trues))
def makeMoleculeStoichiometrys(self, func_get_one, func_get_num):
"""
Creates a list of MoleculeStoichiometry
:param Function func_get_one: get one element by index
:param Function func_get_num: get number of elements
:return list-MoleculeStoichiometry:
"""
result = []
collection = [func_get_one(n) for n in range(func_get_num())]
for s_r in collection:
molecule = Molecule(s_r.species)
stoich = s_r.getStoichiometry()
result.append(MoleculeStoichiometry(molecule, stoich))
return result
def testHasMoiety(self):
if IGNORE_TEST:
return
molecule = Molecule(MOLECULE_NAME)
self.assertTrue(molecule.hasMoiety(Moiety(MOIETY_NAME1)))
self.assertTrue(molecule.hasMoiety(Moiety(MOIETY_NAME2)))
def testConstructor(self):
if IGNORE_TEST:
return
molecule = Molecule(NAME)
self.assertEqual(molecule.name, NAME)
def testExtractMoietyStoichiometrys(self):
if IGNORE_TEST:
return
moiety_stoich = MoietyStoichiometry(Molecule(MOIETY_NAME1), NUM1)
mole_stoich = MoleculeStoichiometry(Molecule(str(moiety_stoich)), NUM2)
import tesbml
import unittest
IGNORE_TEST = False
NUM1 = 2
NUM2 = 3
MOIETY_NAME1 = "first"
MOIETY_NAME2 = "second"
MOIETY_NAME3 = "third"
NAME = "name"
NO_NAME = 'not_a_name'
MOLECULE_NAME = "%s%s%s" % (MOIETY_NAME1, cn.MOIETY_DOUBLE_SEPARATOR,
MOIETY_NAME2)
MOLECULE_STOICHIOMETRY_STGS = {
((Moiety("A"), 1), (Moiety("P"), 1)):
[Molecule("A_P"), Molecule("A_1__P"),
Molecule("A__P")],
((Moiety("AA"), 1), (Moiety("PP"), 1)): [
Molecule("AA_PP"),
Molecule("AA_1__PP"),
Molecule("AA__PP"),
],
}
NAMES = [MOIETY_NAME1, MOIETY_NAME2, MOIETY_NAME3]
iterator = itertools.product([0, 1], [0, 1], [0, 1])
MOLECULE_NAME_SET = [] # A set of names from moiety combinations
for item in iterator:
name = ""
for idx, ele in enumerate(item):
if ele == 1:
if len(name) == 0:
