class TestFragmentationModule(unittest.TestCase):
def setUp(self):
self.filename_pdb = "tests/1UAO.pdb"
# for testing, use OpenBabel functionality directly
self.molecule = fileToMol(self.filename_pdb)
self.fragmentation = Fragmentation(self.molecule)
def tearDown(self):
pass
def delete_file(self,filename):
try:
f = open(filename)
except IOError:
return
finally:
f.close()
os.remove(filename)
def test_FragmentationDefaultParameters(self):
frg = self.fragmentation
self.assertEqual(frg.mol != None, True)
def test_FragmentationSetActiveFragments(self):
self.fragmentation.setActiveFragments([1, 2, 3])
self.assertEqual(self.fragmentation.active_fragments, [1, 2, 3])
def test_FragmentationApplySmartProtectPatterns(self):
self.fragmentation.applySmartProtectPatterns()
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(), [1, 2, 3, 4, 10])
def test_FragmentationDetermineFormalCharges(self):
#self.fragmentation.determineFormalCharges()
self.assertAlmostEqual(sum(self.fragmentation.formalCharges), -2)
def test_FragmentationGetProtectedAtoms(self):
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(), [])
def test_FragmentationAddProtectedAtomsAfterProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.addExplicitlyProtectedAtoms([44, 55, 67])
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(), [1, 2, 3, 4, 10, 44, 55, 67])
def test_FragmentationAddBrokenBond(self):
pass
def test_FragmentationIsBondProtected(self):
bond_pair = (2, 3)
self.assertEqual(self.fragmentation.isBondProtected(bond_pair), False)
self.fragmentation.addExplicitlyProtectedAtoms([2])
self.assertEqual(self.fragmentation.isBondProtected(bond_pair), True)
def test_FragmentationRealBondBreakerNoProtect(self):
bond_atoms = (2, 3)
self.fragmentation.realBondBreaker("peptide", bond_atoms)
self.assertEqual(self.fragmentation.getExplicitlyBreakAtomPairs(), [(2, 3)])
def test_FragmentationIsValidExplicitBond(self):
self.assertRaises(ValueError, self.fragmentation.isValidExplicitBond, (1, 1))
self.assertRaises(ValueError, self.fragmentation.isValidExplicitBond, (2, 4))
def test_FragmentationBreakBondsWithNoProtect(self):
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()), 9)
def test_FragmentationBreakBondsExplcitWithNoProtect(self):
self.fragmentation.addExplicitlyBreakAtomPairs([(111, 112)])
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()), 10)
def test_FragmentationBreakBondsWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()), 8)
def test_FragmentationBreakBondsExplcitWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.addExplicitlyBreakAtomPairs([(111, 112)])
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()), 9)
def test_FragmentationDetermineFragmentsNoBreaking(self):
self.assertRaises(ValueError, self.fragmentation.determineFragments)
def test_FragmentationDetermineFragmentsWithBreaking(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.assertEqual(lenOfLists(self.fragmentation.getFragments()), [7, 21, 12, 14, 15, 14, 7, 14, 24, 10])
def test_FragmentationDetermineFragmentsWithBreakingAndGrouping(self):
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.assertEqual(lenOfLists(self.fragmentation.getFragments()), [28, 26, 29, 21, 34])
def test_FragmentationDetermineFragmentsWithBreakingAndGroupingTriple(self):
self.fragmentation.setFragmentGroupCount(3)
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.assertEqual(lenOfLists(self.fragmentation.getFragments()), [40, 43, 45, 10])
def test_FragmentationFindFragmentsCastErrors(self):
self.assertRaises(ValueError, self.fragmentation.getAtomsInSameFragment, 1, 1)
self.assertRaises(ValueError, self.fragmentation.getAtomsInSameFragment, "")
def test_FragmentationFindFragmentsNoGrouping(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.assertEqual(self.fragmentation.getAtomsInSameFragment(11, 0), [3, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
self.assertEqual(self.fragmentation.getAtomsInSameFragment(12, 0), [12, 13, 31, 32] + range(35, 43))
def test_FragmentationFindFragmentsNoGroupingWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.assertEqual(self.fragmentation.getAtomsInSameFragment(11, 0), range(1, 12)+range(14, 31))
self.assertEqual(self.fragmentation.getAtomsInSameFragment(12, 0), [12, 13, 31, 32] + range(35, 43))
def test_FragmentationFragmentChargeAfterFragment(self):
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(), [ 1, 0, -1, 0, -1, 0, 0, 0, 0, -1])
def test_FragmentationFragmentChargeAfterProtectAndFragment(self):
self.fragmentation.setProtectedAtoms()
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(), [1, -1, 0, -1, 0, 0, 0, 0, -1])
def test_FragmentationFragmentChargeAfterFragmentAndGroup(self):
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.doFragmentGrouping()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(), [1, -1, -1, 0, -1])
def test_FragmentationFragmentChargeAfterProtectFragmentAndGroup(self):
self.fragmentation.setProtectedAtoms()
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.doFragmentGrouping()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(), [0, -1, 0, 0, -1])
def test_FragmentationGetOBAtom(self):
test_atom = self.fragmentation.getOBAtom(1)
self.assertEqual(type(test_atom), type(openbabel.OBAtom()))
def test_FragmentationNameFragments(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.nameFragments()
self.assertEqual(self.fragmentation.getFragmentNames(), ['GLY', 'GLY', 'TYR', 'ASP', 'PRO', 'GLU', 'THR', 'GLY', 'THR', 'TRP'])
def test_FragmentationNameFragmentsProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.nameFragments()
self.assertEqual(self.fragmentation.getFragmentNames(), ['GLY', 'TYR', 'ASP', 'PRO', 'GLU', 'THR', 'GLY', 'THR', 'TRP'])
def test_FragmentationNameFragmentsGroupByTwo(self):
self.fragmentation.breakBonds()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.fragmentation.nameFragments()
self.assertEqual(self.fragmentation.getFragmentNames(), ['GLY', 'TYR', 'PRO', 'THR', 'THR'])
def test_writereadconfiguration_basic(self):
filename = "temp.cfg"
self.fragmentation.writeConfigurationToFile(filename)
otherfrag = Fragmentation(self.molecule)
otherfrag.readConfigurationFromFile(filename)
for key in otherfrag.values.keys():
for key2 in otherfrag.values[key].keys():
self.assertEqual(self.fragmentation.values[key][key2], otherfrag.values[key][key2])
self.delete_file(filename)
class TestFragmentationModule(unittest.TestCase):
def setUp(self):
self.filename_pdb = "tests/1UAO.pdb"
# for testing, use OpenBabel functionality directly
self.molecule = fileToMol(self.filename_pdb)
self.fragmentation = Fragmentation(self.molecule,
defaults=FragItDataFMO)
def tearDown(self):
pass
def delete_file(self, filename):
try:
f = open(filename)
except IOError:
return
finally:
f.close()
os.remove(filename)
def test_FragmentationDefaultParameters(self):
frg = self.fragmentation
self.assertEqual(frg.mol != None, True)
def test_FragmentationSetActiveFragments(self):
self.fragmentation.setActiveFragments([1, 2, 3])
self.assertEqual(self.fragmentation.active_fragments, [1, 2, 3])
def test_FragmentationApplySmartProtectPatterns(self):
self.fragmentation.applySmartProtectPatterns()
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(),
[1, 2, 3, 4, 10])
def test_FragmentationDetermineFormalCharges(self):
#self.fragmentation.determineFormalCharges()
self.assertAlmostEqual(sum(self.fragmentation.formalCharges), -2)
def test_FragmentationGetProtectedAtoms(self):
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(), [])
def test_FragmentationAddProtectedAtomsAfterProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.addExplicitlyProtectedAtoms([44, 55, 67])
self.assertEqual(self.fragmentation.getExplicitlyProtectedAtoms(),
[1, 2, 3, 4, 10, 44, 55, 67])
def test_FragmentationAddBrokenBond(self):
pass
def test_FragmentationIsBondProtected(self):
bond_pair = (2, 3)
self.assertEqual(self.fragmentation.isBondProtected(bond_pair), False)
self.fragmentation.addExplicitlyProtectedAtoms([2])
self.assertEqual(self.fragmentation.isBondProtected(bond_pair), True)
def test_FragmentationRealBondBreakerNoProtect(self):
bond_atoms = (2, 3)
self.fragmentation.addFragmentationAtomPair(bond_atoms)
self.assertEqual(self.fragmentation.getExplicitlyBreakAtomPairs(),
[(2, 3)])
def test_FragmentationIsValidExplicitBond(self):
self.assertRaises(ValueError, self.fragmentation.isValidExplicitBond,
(1, 1))
self.assertRaises(ValueError, self.fragmentation.isValidExplicitBond,
(2, 4))
def test_FragmentationBreakBondsWithNoProtect(self):
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()),
9)
def test_FragmentationBreakBondsExplcitWithNoProtect(self):
self.fragmentation.addExplicitlyBreakAtomPairs([(111, 112)])
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()),
10)
def test_FragmentationBreakBondsWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()),
8)
def test_FragmentationBreakBondsExplcitWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.addExplicitlyBreakAtomPairs([(111, 112)])
self.fragmentation.breakBonds()
self.assertEqual(len(self.fragmentation.getExplicitlyBreakAtomPairs()),
9)
def test_FragmentationDetermineFragmentsNoBreaking(self):
self.assertRaises(ValueError, self.fragmentation.determineFragments)
def test_FragmentationDetermineFragmentsWithBreaking(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
for fragment, expected_size in zip(
self.fragmentation.getFragments(),
[7, 21, 12, 14, 15, 14, 7, 14, 24, 10]):
self.assertEqual(len(fragment), expected_size)
def test_FragmentationDetermineFragmentsWithBreakingAndGrouping(self):
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.assertEqual(len(self.fragmentation.getFragments()), 5)
for fragment, expected_size in zip(self.fragmentation.getFragments(),
[28, 26, 29, 21, 34]):
self.assertEqual(len(fragment), expected_size)
def test_FragmentationDetermineFragmentsWithBreakingAndGroupingTriple(
self):
self.fragmentation.setFragmentGroupCount(3)
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.assertEqual(len(self.fragmentation.getFragments()), 4)
for fragment, expected_size in zip(self.fragmentation.getFragments(),
[40, 43, 45, 10]):
self.assertEqual(len(fragment), expected_size)
def test_FragmentationFindFragmentsCastErrors(self):
self.assertRaises(ValueError,
self.fragmentation.getAtomsInSameFragment, 1, 1)
self.assertRaises(ValueError,
self.fragmentation.getAtomsInSameFragment, "")
def test_FragmentationFindFragmentsNoGrouping(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
res1 = [12, 13, 31, 32]
res1.extend(range(35, 43))
self.assertEqual(self.fragmentation.getAtomsInSameFragment(11, 0), [
3, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30
])
self.assertEqual(self.fragmentation.getAtomsInSameFragment(12, 0),
res1)
def test_FragmentationFindFragmentsNoGroupingWithProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
res1 = list(range(1, 12))
res1.extend(list(range(14, 31)))
res2 = [12, 13, 31, 32]
res2.extend(list(range(35, 43)))
self.assertEqual(self.fragmentation.getAtomsInSameFragment(11, 0),
res1)
self.assertEqual(self.fragmentation.getAtomsInSameFragment(12, 0),
res2)
def test_FragmentationFragmentChargeAfterFragment(self):
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(),
[1, 0, -1, 0, -1, 0, 0, 0, 0, -1])
def test_FragmentationFragmentChargeAfterProtectAndFragment(self):
self.fragmentation.setProtectedAtoms()
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(),
[1, -1, 0, -1, 0, 0, 0, 0, -1])
def test_FragmentationFragmentChargeAfterFragmentAndGroup(self):
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.doFragmentGrouping()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(),
[1, -1, -1, 0, -1])
def test_FragmentationFragmentChargeAfterProtectFragmentAndGroup(self):
self.fragmentation.setProtectedAtoms()
#self.fragmentation.determineFormalCharges()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.doFragmentGrouping()
self.fragmentation.determineFragmentCharges()
self.assertEqual(self.fragmentation.getFragmentCharges(),
[0, -1, 0, 0, -1])
def test_FragmentationGetOBAtom(self):
test_atom = self.fragmentation.getOBAtom(1)
self.assertEqual(type(test_atom), type(openbabel.OBAtom()))
def test_FragmentationNameFragments(self):
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.nameFragments()
self.assertEqual(self.fragmentation.getFragmentNames(), [
'GLY', 'GLY', 'TYR', 'ASP', 'PRO', 'GLU', 'THR', 'GLY', 'THR',
'TRP'
])
def test_FragmentationNameFragmentsProtect(self):
self.fragmentation.setProtectedAtoms()
self.fragmentation.breakBonds()
self.fragmentation.determineFragments()
self.fragmentation.nameFragments()
self.assertEqual(
self.fragmentation.getFragmentNames(),
['GLY', 'TYR', 'ASP', 'PRO', 'GLU', 'THR', 'GLY', 'THR', 'TRP'])
def test_FragmentationNameFragmentsGroupByTwo(self):
self.fragmentation.breakBonds()
self.fragmentation.setFragmentGroupCount(2)
self.fragmentation.determineFragments()
self.fragmentation.doFragmentGrouping()
self.fragmentation.nameFragments()
self.assertEqual(self.fragmentation.getFragmentNames(),
['GLY', 'TYR', 'PRO', 'THR', 'THR'])
def test_writereadconfiguration_basic(self):
filename = "temp.cfg"
handle = open(filename, 'w')
self.fragmentation.writeConfigurationToFile(handle)
handle.close()
otherfrag = Fragmentation(self.molecule)
otherfrag.readConfigurationFromFile(filename)
for key in otherfrag.values.keys():
for key2 in otherfrag.values[key].keys():
self.assertEqual(self.fragmentation.values[key][key2],
otherfrag.values[key][key2])
self.delete_file(filename)