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 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_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 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_5ala_3_hop(self):
""" Correct input for HOP with one basis """
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_3_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
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 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 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 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_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule)
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_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_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_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_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_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_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 setUp(self):
self.molecule = fileToMol("tests/1UAO.pdb")
self.fragmentation = Fragmentation(self.molecule)
self.standardwriter = Standard(self.fragmentation)
def setUp(self):
directories = {'share':''}
self.molecule = fileToMol("tests/1UAO.pdb")
self.fragmentation = Fragmentation(self.molecule)
self.standardwriter = Standard(self.fragmentation, directories)
def setUp(self):
directories = {'share': ''}
self.molecule = fileToMol("tests/1UAO.pdb")
self.fragmentation = Fragmentation(self.molecule)
self.standardwriter = Standard(self.fragmentation, directories)
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 setUp(self):
self.molecule = fileToMol("tests/watercluster4.xyz")
self.fragmentation = Fragmentation(self.molecule)
self.fixtures = 'tests/gamess-fmo-fixtures'
