def testGetMoietys(self):
m_ss = []
for stgs in MOIETY_STOICHIOMETRY_STGS.values():
m_ss.extend([MoietyStoichiometry.make(s) for s in stgs])
moietys = MoietyStoichiometry.getMoietys(m_ss)
self.assertEqual(len(MOIETY_STOICHIOMETRY_STGS.keys()),
len(moietys))
def testMakeFromDct(self):
if IGNORE_TEST:
return
config.setConfiguration(TEST_CFG_FILE)
config_dct = config.getConfiguration()
dct = config_dct[cn.CFG_MOIETY_STRUCTURE]
mss1 = MoietyStoichiometry.makeFromDct(dct["ATP"])
mss2 = [MoietyStoichiometry("A", 1), MoietyStoichiometry("P", 3)]
self.assertTrue(all([m1.isEqual(m2) for m1, m2 in zip(mss1, mss2)]))
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 testMake(self):
if IGNORE_TEST:
return
for expected, strings in MOIETY_STOICHIOMETRY_STGS.items():
for stg in strings:
result = MoietyStoichiometry.make(stg)
self.assertEqual(result.moiety.name, expected[0])
self.assertEqual(result.stoichiometry, expected[1])
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 getMoietyStoichiometrys(self): """ :return list-MoietyStoichiometry: """ new_name = self._reformat() stgs = new_name.split(cn.MOIETY_DOUBLE_SEPARATOR) result = [MoietyStoichiometry.make(ms) for ms in stgs] result.sort() return result
def moiety_stoichiometrys(self):
done = False
if self._moiety_stoichiometrys is None:
config_dct = config.getConfiguration()
if cn.CFG_MOIETY_STRUCTURE in config_dct:
dct = config_dct[cn.CFG_MOIETY_STRUCTURE]
if self.name in dct.keys():
self._moiety_stoichiometrys = \
MoietyStoichiometry.makeFromDct(dct[self.name])
done = True
else:
done = True
if not done:
new_name = self._reformat()
stgs = new_name.split(cn.MOIETY_DOUBLE_SEPARATOR)
result = [MoietyStoichiometry.make(ms) for ms in stgs]
result.sort()
self._moiety_stoichiometrys = result
return self._moiety_stoichiometrys
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 testExtractMoietyStoichiometrys(self):
if IGNORE_TEST:
return
moiety_stoich = MoietyStoichiometry(Molecule(MOIETY_NAME1), NUM1)
mole_stoich = MoleculeStoichiometry(Molecule(str(moiety_stoich)), NUM2)
def testStoichiometry(self):
moiety_stoichiometry = MoietyStoichiometry(Moiety(MOIETY_NAME1), NUM1)
self.assertEqual(moiety_stoichiometry.moiety.name, MOIETY_NAME1)
self.assertEqual(moiety_stoichiometry.stoichiometry, NUM1)