def test_qmmm_advanced_2(self):
""" 2 qm fragments in qm/mm interface with bond breaking """
filename = "temp.inp"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataPE)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
ref_fragments = copy.deepcopy(fragmentation.getFragments()[:])
self.assertEqual(len(ref_fragments), 5)
qmmm = QMMM(fragmentation, [2, 3])
qmfrag, qmcharge = qmmm.pop_qm_fragment()
new_fragments = copy.deepcopy(fragmentation.getFragments()[:])
self.assertEqual(len(new_fragments), 5)
self.assertEqual(len(qmfrag),
len(ref_fragments[1]) + len(ref_fragments[2]) +
2) # two atoms added to QM region from two fragments
self.assertEqual(len(new_fragments[0]),
len(ref_fragments[0]) +
1) # one atom added to MM region for one fragment
self.assertEqual(len(new_fragments[3]),
len(ref_fragments[3]) +
1) # one atom added to MM region for one fragment
def test_2form8wat_2(self):
filename = "temp.inp"
otherfile = self.fixtures + "/2form8wat_2.fixture"
molecule = fileToMol("tests/2form8wat.pdb")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
fragmentation.setFMOEFPWatersFromLayer(1)
directories = {'share': ''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("3.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
ignoring = False
for i in range(len(fixture)):
if "EFRAG" in generated[i] or "EFRAG" in fixture[i]:
ignoring = True
if ignoring:
if "END" in generated[i] or "END" in fixture[i]:
ignoring = False
if not ignoring:
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
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 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)
def test_2form8wat_2(self):
filename = "temp.inp"
otherfile = self.fixtures + "/2form8wat_2.fixture"
molecule = fileToMol("tests/2form8wat.pdb")
fragmentation = Fragmentation(molecule)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
fragmentation.setFMOEFPWatersFromLayer(1)
directories = {'share':''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("3.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
ignoring = False
for i in range(len(fixture)):
if "EFRAG" in generated[i] or "EFRAG" in fixture[i]:
ignoring = True
if ignoring:
if "END" in generated[i] or "END" in fixture[i]:
ignoring = False
if not ignoring:
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
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)
def test_qmmm_simple_2(self):
""" 2 qm fragments in qm/mm interface without bond breaking """
filename = "temp.inp"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataPE)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
ref_fragments = fragmentation.getFragments()
self.assertEqual(len(ref_fragments), 4)
qmmm = QMMM(fragmentation, [1, 3]) # extracts fragments 1 and 3
qmfrag, qmcharge = qmmm.pop_qm_fragment()
new_fragments = fragmentation.getFragments()
self.assertEqual(qmfrag, [1, 2, 3, 7, 8, 9])
self.assertEqual(len(new_fragments), 4)
self.assertEqual(new_fragments[0], [-1, -1, -1])
self.assertEqual(new_fragments[2], [-1, -1, -1])
def test_5ala_1_hop(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_1_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.setFMOHOPFragmentation()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': 'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_2_afo(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_2_afo.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.setQMBasis('3-21G:6-31G(d)')
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': 'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_qmmm_simple_1(self):
""" 1 qm fragment in qm/mm interface without bond breaking """
filename = "temp.inp"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataPE)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
ref_fragments = fragmentation.getFragments()
self.assertEqual(len(ref_fragments), 4)
qmmm = QMMM(fragmentation,
[1]) # extracts first fragment (for user this is #1)
qmfrag, qmcharge = qmmm.pop_qm_fragment()
new_fragments = fragmentation.getFragments()
self.assertEqual(qmfrag, [1, 2, 3]) # extracts first fragment
self.assertEqual(len(new_fragments),
4) # must leave all fragments intact
self.assertEqual(new_fragments[0],
[-1, -1, -1]) # -1 signals "DO NOT USE"
def test_qmmm_advanced_1(self):
""" 1 qm fragment in qm/mm interface with bond breaking """
filename = "temp.inp"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataPE)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
ref_fragments = copy.deepcopy(fragmentation.getFragments()[:])
self.assertEqual(len(ref_fragments), 5)
qmmm = QMMM(fragmentation,
[1]) # extracts first fragment (for user this is #1)
qmfrag, qmcharge = qmmm.pop_qm_fragment()
new_fragments = fragmentation.getFragments()[:]
self.assertEqual(len(new_fragments), 5)
self.assertEqual(len(qmfrag),
len(ref_fragments[0]) +
1) # one atom added to QM region
self.assertEqual(len(new_fragments[1]),
len(ref_fragments[1]) +
1) # one atom added to MM region
def test_5ala_1_hop(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_1_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setFMOHOPFragmentation()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
directories = {'share': ''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_2_afo(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_2_afo.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setQMBasis('3-21G:6-31G(d)')
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_5(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_5.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': ''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setActiveAtomsDistance(1.0)
gamessfmo.setBufferMaxDistance(1.0)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_5(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_5.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setActiveAtomsDistance(1.0)
gamessfmo.setBufferMaxDistance(1.0)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_3_hop(self):
""" Regression test to make sure if only one basis
set is specified we get the correct input file
FMO with HOP
"""
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_3_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setFMOHOPFragmentation()
fragmentation.setQMBasis('3-21G')
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def setUp(self):
directories = {'share': ''}
self.molecule = fileToMol("tests/1UAO.pdb")
self.fragmentation = Fragmentation(self.molecule)
self.standardwriter = Standard(self.fragmentation, directories)
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)
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)
def setUp(self):
self.molecule = fileToMol("tests/watercluster4.xyz")
self.fragmentation = Fragmentation(self.molecule)
self.fixtures = 'tests/gamess-fmo-fixtures'
def test_qmmm_advanced_3(self):
""" 1 qm fragment + cov bound in qm/mm interface with bond breaking """
filename = "temp.inp"
m1 = fileToMol("tests/5ala.xyz")
frag1 = Fragmentation(m1, defaults=FragItDataPE)
frag1.beginFragmentation()
frag1.doFragmentation()
frag1.finishFragmentation()
qm1 = QMMM(frag1, [2, 3, 4])
qmf1, qmq1 = qm1.pop_qm_fragment()
m2 = fileToMol("tests/5ala.xyz")
frag2 = Fragmentation(m2, defaults=FragItDataPE)
frag2.values['qmmm']['includecovalent'] = True
frag2.beginFragmentation()
frag2.doFragmentation()
frag2.finishFragmentation()
qm2 = QMMM(frag2, [3])
qmf2, qmq2 = qm2.pop_qm_fragment()
# must produce identical results
self.assertEqual(len(qmf1), len(qmf2))
self.assertEqual(frag1.getFragments(), frag2.getFragments())
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)
class TestGamessFMOOutputModule(unittest.TestCase):
def setUp(self):
self.molecule = fileToMol("tests/watercluster4.xyz")
self.fragmentation = Fragmentation(self.molecule)
self.fixtures = 'tests/gamess-fmo-fixtures'
def delete_file(self,filename):
try:
f = open(filename)
except IOError:
return
finally:
f.close()
os.remove(filename)
def test_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
gamessfmo = GamessFMO(self.fragmentation)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_2(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_2.fixture"
self.fragmentation.beginFragmentation()
self.fragmentation.doFragmentation()
self.fragmentation.finishFragmentation()
gamessfmo = GamessFMO(self.fragmentation)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_3(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_3.fixture"
self.fragmentation.beginFragmentation()
self.fragmentation.doFragmentation()
self.fragmentation.finishFragmentation()
gamessfmo = GamessFMO(self.fragmentation)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_4(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_4.fixture"
self.fragmentation.beginFragmentation()
self.fragmentation.doFragmentation()
self.fragmentation.finishFragmentation()
gamessfmo = GamessFMO(self.fragmentation)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_5(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_5.fixture"
self.fragmentation.beginFragmentation()
self.fragmentation.doFragmentation()
self.fragmentation.finishFragmentation()
gamessfmo = GamessFMO(self.fragmentation)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setActiveAtomsDistance(1.0)
gamessfmo.setBufferMaxDistance(1.0)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
