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 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 getMoietys(self):
"""
Extracts the unique moieties in the molecule.
:return list-Moiety: Unique Moiety in molecule
"""
names = list(
set([m_s.moiety.name for m_s in self.moiety_stoichiometrys]))
names.sort()
return [Moiety(n) for n in names]
def _getMoietys(self):
"""
Sees if there is a valid moiety structure.
If not, the molecule is a single moiety.
"""
moietys = []
for molecule in self.molecules:
try:
new_moietys = ([
m_s.moiety for m_s in molecule.moiety_stoichiometrys
])
except ValueError:
new_moietys = [Moiety(molecule.name)]
moietys.extend(new_moietys)
return util.uniqueify(moietys)
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)))
import os
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:
def testStoichiometry(self):
moiety_stoichiometry = MoietyStoichiometry(Moiety(MOIETY_NAME1), NUM1)
self.assertEqual(moiety_stoichiometry.moiety.name, MOIETY_NAME1)
self.assertEqual(moiety_stoichiometry.stoichiometry, NUM1)
def testConstructor(self):
if IGNORE_TEST:
return
self.assertEqual(Moiety(MOIETY_NAME1).name, MOIETY_NAME1)